How Al-Qaeda Works: The Jihadist Group’s Evolving Organizational Design


Daveed Gartenstein-Ross and Nathaniel Barr

Hudson Institute

The years following the 9/11 attacks and preceding the Arab Spring marked a period of tumult for al-Qaeda. The jihadist organization lost a number of key commanders after the United States invaded Afghanistan, including several involved in planning operations outside the region. Though al-Qaeda did prepare a credible large-scale plot against commercial aviation in August 2006 and nearly brought down an international flight over Detroit in December 2009,1 the organization went multiple years without a successfully executed terrorist attack in the West. For an organization that had to a certain extent staked its credibility on its ability to sustain an armed struggle against the “far enemy,” this hiatus damaged its reputation. Compounding these problems was al-Qaeda’s Iraq affiliate, which had stubbornly ignored the al-Qaeda leadership’s guidance to tone down what they deemed to be excessively violent methods. After overplaying its hand, which provoked an organized backlash from Iraqi Sunni communities, al-Qaeda in Iraq collapsed. In turn, its collapse was a blow to the al-Qaeda organization as a whole.In his 2008 book Leaderless Jihad, psychiatrist and former C.I.A. case officer Marc Sageman reflected on the al-Qaeda of the 2000s.2 Sageman argued that the capabilities of al-Qaeda’s senior leadership had declined sharply, and to such an extent that the organization no longer exercised command and control over either its nominal affiliates or over like-minded jihadists operating outside Afghanistan and Pakistan. With al-Qaeda now a marginalized organization, Sageman argued, the most potent jihadist threat to the West now emanated from “bunches of guys.” These were small groups of radicalized individuals inspired by salafi jihadist ideology, who planned attacks without coordinating with or receiving guidance from a broader organization like al-Qaeda.

While Leaderless Jihad both reflected and influenced the thoughts of a growing number of terrorism analysts and journalists,3 it also provoked a blistering rebuttal from Georgetown University terrorism scholar Bruce Hoffman. Hoffman objected to Sageman’s central claim that al-Qaeda’s senior leadership had become “neutralized operationally.”4Instead, he argued that al-Qaeda was a “remarkably agile and flexible organization,” and that its leadership had rebounded from personnel losses, retained operational control over affiliates, and sustained its ability to plan external operations against the West. While Hoffman acknowledged the threat posed by local and regional terrorist networks, he argued that al-Qaeda continued to pose a greater challenge to American and European security.

The Hoffman-Sageman debate remains largely unresolved a decade after the publication of Leaderless Jihad, as analysts continue to debate fundamental questions about the relevance of al-Qaeda’s senior leadership and the structure of the organization. Is al-Qaeda a top-down, centralized organization or a collection of flat, information-age networks? Do its leaders remain linked with and provide strategic direction to the organization’s affiliates or have they been reduced to a symbolic role? Is al-Qaeda even a single, coherent organization or is it more akin to a social movement, devoid of hierarchy and without a concrete structure?

The lack of consensus on these questions within the analytic community impedes our ability to anticipate the behavior of al-Qaeda and its affiliates, and to counter their future operations. If we do not accurately understand fundamental aspects of al-Qaeda’s structure, we will be unable to either identify and target the organization’s center of gravity or predict how strategic directives from its leadership will affect the behavior of affiliates. As documents recovered from Abbottabad become accessible and first-hand accounts from jihadist movement insiders proliferate, we now have enough information to more definitively answer pressing questions about al-Qaeda’s organizational design.

Close analysis of these primary source materials, which include a vast trove of documents produced by al-Qaeda’s top officials, has yielded two important findings that we present at length in this article. First, al-Qaeda remains a coherent and centralized organization, albeit one that is not perfectly centralized. Second, al-Qaeda’s leadership continues to be essential in determining both the trajectory of the organization as well as its strategic direction. While al-Qaeda sometimes fails to resolve its internal disputes before they boil over into the public eye—a phenomenon seen in earlier years as well (there were highly public disputes in the 1990s in both Sudan and Afghanistan over the state and trajectory of the global jihadist movement)—its affiliates generally continue to adhere to the goals, objectives and strategies outlined by the organization’s senior leadership.5 At the same time, al-Qaeda’s flexible organizational model allows affiliates to adapt their tactical approach to local dynamics.

Though al-Qaeda’s organizational structure has undergone several significant changes since its inception, the current structure continues to reflect the strategic vision of its founders. From the outset, al-Qaeda adopted a unique organizational design, whereby its senior leadership outlined a strategic course for the organization a whole, but empowered mid-level commanders to execute this strategy as they saw fit. “Centralization of decision and decentralization of execution,” as this organizational principle has been described, remains operative today.6  Indeed, in adhering to this principle, al-Qaeda has been able to maintain both organizational and strategic coherence even in the face of considerable internal and external challenges.

This article charts al-Qaeda’s development over its nearly thirty-year existence, placing special emphasis on its early history. The organization’s initial structure, we argue, would have an enduring influence on how the organization functioned and developed as time passed. This article begins with an exploration of the strategic and ideological rationale behind the establishment of al-Qaeda. We consider, in particular, how this rationale informed the organization’s early emphasis on “centralization of decision and decentralization of execution.” Next, we examine how al-Qaeda’s organizational structure was transformed both by new challenges, like its loss of Afghanistan as a safe haven after the 9/11 attacks, and by its expansion to include new affiliates. Finally, we explain the important ways in which our explanation of al-Qaeda’s organizational structure should shape future assessments of the challenges that al-Qaeda faces, and of the challenges that it poses.

Creating the Vanguard

Al-Qaeda’s raison d’être is rooted in the concept of an international vanguard charged with taking the first steps necessary to sweep an un-Islamic world order from power (including the secular governments of the Middle East and the influence of Western powers that support them), and usher in Islamic governance across the globe. The international jihadist army that al-Qaeda seeks to build bears close resemblance to the vanguards of early Islamic history, and also closely resembles the vanguard concept that features prominently in the writings of two prominent jihadist theorists of the twentieth century, Sayyid Qutb and Abdullah Azzam.

Qutb, an Egyptian scholar who is often considered the ideological forefather of the modern jihadist movement, believed that the Muslim world had descended into a state of jahiliyya, or ignorance, a pejorative term that Muslims identify with life in the Arabian Peninsula prior to the advent of Islam. Qutb argued that only a vanguard, composed of a small number of pious Muslims, could awaken the Ummah and rescue it from this state of darkness. In Qutb’s words: “It is necessary that there should be a vanguard which sets out and then keeps walking on the path, marching through the vast ocean of jahiliyya which has encompassed the entire world.”7

Qutb likely borrowed the term vanguard from Marxism, which averred that a small core of committed individuals was necessary to mobilize the masses to communist revolution. But in his estimation, as well as that of other influential Islamist thinkers, the concept of a vanguard can actually be traced back to the early years of Islamic history, when the Prophet Muhammad and a small coterie of followers overcame the opposition of Arab tribes, and spread Islam across the Arabian Peninsula. Muslim Brotherhood founder Hassan al-Banna drew an explicit comparison between the Prophet’s earliest followers and the movement he sought to build, explaining: “We try to make of this modern proselytizing a real echo to the early proselytizing.”8

Qutb’s discussion of how this vanguard would form and operate was, like much of his writing, heavy on theory, tending toward diagnosis rather than prescription. It was left to later figures, like Abdullah Azzam, to determine how to put the idea of a vanguard into practice.

Azzam—who was once bin Laden’s mentor, before running afoul of the young Saudi in the late 1980s9—emerged as the most influential jihadist theoretician and strategist of the 1980s. His writings touched on a wide array of subjects, but his most extensive discussion of the purpose and function of a vanguard appeared in an article titled “al-Qaeda al-Sulbah” (The Solid Base), which was published in 1988 in al-Jihad magazine, a publication Azzam founded to report on the mujahedin’s anti-Soviet war in Afghanistan. In the article, Azzam explained the need to have a vanguard to bring about revolution in the Islamic world:

For every invention there must be a vanguard to carry it forward and, while forcing its way into society, endure enormous expenses and costly sacrifices. There is no ideology, neither earthly nor heavenly, that does not require such a vanguard that gives everything it possesses in order to achieve victory for this ideology. It carries the flag all along the sheer endless and difficult path until it reaches its destination in the reality of life, since Allah has destined that it should make it and manifest itself. This vanguard constitutes the solid base (al-qaeda al-subah) for the expected society.10


This vanguard, Azzam wrote, would first galvanize the people, serving as the “spark that ignites the energies of the Ummah.”11 The vanguard’s job, according to Azzam, would not end there. As he explained in Join the Caravan, a short book published in 1987, once the Muslim community had been spurred to action, the vanguard would serve as the “beating heart and deliberating mind,” providing strategic and ideological guidance to the Ummah.12

Al-Qaeda sees itself as a manifestation of this vanguard. The organization’s goal, according to its founders and strategists, is to galvanize the Muslim masses to revolt against the existing international system, which is corrupt and impious, and to inspire the Ummah to replace this system with an Islamic caliphate. Al-Qaeda is to be the vanguard of this revolution, the “organization and leadership leading change,” as Ayman al-Zawahiri, al-Qaeda’s current emir, explained in Knights Under the Prophet’s Banner, his treatise on the history and future of the jihadist movement.13

Al-Qaeda’s perception of itself as a vanguard has clear implications for the group’s organizational structure. Al-Qaeda’s leaders agreed with Qutb and Azzam that the Islamic revolution could not be leaderless: A revolution that lacked both ideological and strategic guidance would exhaust itself. As Azzam explained in “al-Qaeda al-Sulbah,” an ideology without a vanguard to promote and propagate it would be “stillborn, perishing before it sees light and life.”14 Al-Qaeda viewed, and continues to view, the leaderless jihad model as strategically infeasible.

Instead, al-Qaeda sought to build a robust organizational structure that would enable it to fulfill its self-proclaimed role as the revolution’s vanguard. Three principles shaped the creation of this structure. First, al-Qaeda needed to establish a propaganda apparatus that would allow the group to convey its messages throughout the globe, and inspire the Ummah to join its revolution. Zawahiri articulated the importance of propaganda in a 2005 letter to al-Qaeda in Iraq (AQI) leader Abu Musab al-Zarqawi, explaining that “we are in a battle, and that more than half of this battle is taking place in the battlefield of the media.”15 Second, al-Qaeda needed command-and-control mechanisms to direct the activities of its subordinates, and to provide strategic guidance to those involved in its revolution, regardless of where they were operating. Third and finally, the organization would need to be resilient. Azzam recognized that the path to an Islamic revolution would be “endless and difficult.”16 If its ultimate objectives were to be achieved, al-Qaeda would need to be able to endure repeated challenges and great losses.

While al-Qaeda has undergone numerous transformations since its inception, the organization has held steadfastly to its overarching goal: to serve as the vanguard of an Islamic revolution. Further, the three core organizational principles that first shaped al-Qaeda continue to guide the group. Al-Qaeda’s propaganda efforts, though they remain essential, are largely beyond the scope of this paper. This paper focuses, instead, on how al-Qaeda has maintained its command-and-control mechanisms and continued to implement reforms aimed at improving its resilience, even as the group has expanded its geographic reach, suffered the loss of key leaders, and adapted its strategic approach in response to shifting geopolitical dynamics.

Building a Durable Organization

Al-Qaeda’s founding documents make clear that al-Qaeda leaders prioritized building a coherent and resilient organization. In contrast, the minutes from al-Qaeda’s first meetings in August 1988 are somewhat ambiguous about the group’s specific objectives. Though these minutes record that al-Qaeda’s overarching goal is to make Islam “victorious,” they lack any explanation of what victory means or how it might be achieved. The minutes reveal, however, that considerable attention was devoted to the organizational structure that al-Qaeda would adopt, attesting to the importance its founders placed on developing standard bureaucratic practices and procedures.

Al-Qaeda’s first meeting began with a discussion of the limitations of the Maktab al-Khidamat al-Mujahedin, an organization created and run by Abdullah Azzam that coordinated both international fundraising for the Afghan jihad and recruitment of Arab fighters. For al-Qaeda’s founders, the Maktab al-Khidamat’s history served as a cautionary tale. Bin Laden and other Arabs in Afghanistan were frustrated with the “mismanagement and bad treatment” that occurred within the Maktab al-Khidamat, which by 1988, had become mired in infighting.17 At their first meeting, therefore, al-Qaeda’s founders emphasized the need to establish a formal organization to avoid these kinds of deficiencies. Bin Laden and his colleagues sought to design an organization equipped to overcome the challenges that had plagued the Maktab al-Khidamat.

Al-Qaeda’s founders envisioned a hierarchical, rules-based organization. The minutes from al-Qaeda’s first meetings reveal that all members would have to obey the group’s “statutes and instructions.” They also show al-Qaeda’s early efforts to facilitate specialization through the establishment of committees, including an advisory council and a mobilization committee, each of which would be responsible for different tasks. A subsequent undated document, believed to have been written in the late 1980s or early 1990s, provides a more extensive description of the roles and responsibilities of each of al-Qaeda’s committees and sections.18 It explains, for example, that al-Qaeda’s military committee would consist of four sections: general combat, special operations, nuclear weapons, and the library and research section. It also stipulates that the commander of the military committee would be required to have a minimum of five years of military experience, be at least 30 years old, and hold a university degree.19

Another founding document, labeled by the Combating Terrorism Center at West Point as al-Qaeda’s structure and bylaws, goes into greater depth about al-Qaeda’s decision-making processes and command structure.20 It makes clear that al-Qaeda’s emir is the ultimate authority on strategic decisions and the appointment of leaders. One of the emir’s additional responsibilities is to “discuss and implement” al-Qaeda’s annual plan, budget, and internal structure. Additionally, the emir is given the authority to appoint all members of the leadership council, al-Qaeda’s most senior decision-making body. Though the leadership council is ostensibly authorized to replace the emir if he “deviates from sharia,” the emir’s ability to unilaterally hire or fire members of the council significantly blunts any potential curb on his power. Similarly, the emir wields full control over his deputy, whose duties, the document states, are “delegated by the emir.” These two clauses ensure that there are few checks on the emir’s power. Fazul Abdullah Mohammed (a.k.a. Fadil Harun), a high-ranking al-Qaeda official who helped orchestrate the 1998 Embassy bombings in East Africa, later confirmed that the emir’s authority was unrivaled, and that bin Laden was not bound by the decisions made by al-Qaeda’s leadership council.21

While the structure and bylaws make clear that the emir’s word on strategic matters is essentially irrefutable, it also limits the emir’s involvement in day-to-day operations. The emir should, according to the document, take a largely hands-off approach at the operational and tactical level. His involvement, furthermore, should be limited to participation in “periodic meetings” and to reviewing the performance of subordinates and committees. Responsibility for day-to-day operations fell to the chairmen of the various committees (e.g., military, security, political, economic) and to their deputies, who are generally referred to as supervisors. The chairman and chief of staff of the military committee are responsible for developing al-Qaeda’s military policy. Then, the leadership council is supposed to approve and oversee the implementation of this policy. Finally, the training and combat supervisors are tasked with developing operational plans through which to achieve the goals and policies articulated by the chairman and chief of staff.

Putting Doctrine into Practice

Relatively little is known about al-Qaeda’s internal dynamics during its early years in Afghanistan.22 However, an account of the organization’s first attempted international operation provides some insight into how its earliest external operations were arranged. In November 1991, Paulo Jose de Almeida Santos, a Portuguese al-Qaeda recruit, was arrested in Rome after he tried to assassinate Mohammed Zahir Shah, the former Afghan king. In an interview with the Portuguese magazine Expresso, Santos, who wanted to kill the king to prevent his return to Afghanistan, explained that he had proposed the plot to his commanders in al-Qaeda. He was then brought to Peshawar to meet Abu Hafs al-Masri and bin Laden, who asked about the rationale for the assassination, as well as Santos’s plans for carrying out the attack.23

Santos interpreted the fact that he was able to propose a plot directly to bin Laden as a sign that al-Qaeda, in 1991, was “disorganized” and lacked a “well-defined hierarchy.” There is undoubtedly some truth to Santos’s assessment. In 1991, al-Qaeda was in a state of flux as it tried to navigate the increasingly fissiparous and violent Afghan mujahedin landscape. Just months after Santos’s failed assassination attempt, al-Qaeda pulled a significant portion of its assets out of Afghanistan and Pakistan.24

There are, however, other possible interpretations of the facts that Santos describes. For one, the ease with which Santos, a largely insignificant foot soldier, was able to interact with bin Laden may have represented an intentional feature of al-Qaeda’s organizational design. Indeed, before 9/11, bin Laden sought to foster a culture of entrepreneurship, encouraging al-Qaeda’s rank and file, and even individuals who had not officially joined, to present him with ideas for plots and operations.25 Nasser al-Bahri, who served as bin Laden’s bodyguard prior to the 9/11 attacks, explained that individuals who developed attack plans could bypass al-Qaeda’s bureaucracy and present their proposals directly to bin Laden and his senior commanders.26 Bin Laden or one of his trusted deputies would then judge whether the proposed attack fit within the contours of al-Qaeda’s military strategy, and if the attack was approved, responsibility was delegated to a subordinate to plan and execute the operation.27

Bin Laden’s willingness to defer to subordinates on issues of operational planning is also consistent with Santos’s experience. In his interview with Expresso, Santos explained that bin Laden “did not give any orders,” and said that when it came to planning operations, Abu Hafs al-Masri “was the real chief of al-Qaeda.”28 On the basis of his interactions with these two men, Santos concluded that “whether bin Laden gave the green light or not is not important.” Santos’s interpretation of al-Qaeda’s power dynamics based on his limited interactions with its upper echelons, however, was inaccurate. While bin Laden rarely involved himself in the minutiae of operational planning, in 1991, while he was al-Qaeda’s supreme authority, his approval was required for all operations carried out in the organization’s name. This was certainly true for Santos’s plot as well, which marked the first time that al-Qaeda attempted an attack outside of Afghanistan. Again, there certainly was a degree of disorganization within al-Qaeda at the time. But the fact that Abu Hafs, rather than bin Laden, served as Santos’s primary point of contact may well have been an intended aspect of al-Qaeda’s design, rather than an indication of bin Laden’s insignificance.

Indeed, Santos’s narrative fits with al-Qaeda’s model of “centralization of decision and decentralization of execution,” as described by bin Laden’s former bodyguard Nasser al-Bahri.29 This phrase accurately explains al-Qaeda’s unique management structure, whereby bin Laden would assess the feasibility and strategic value of proposed missions and offer funding as well as institutional support for plots he approved, but would then allow his deputies to execute the mission as they saw fit.

The experiences of several other al-Qaeda operatives over the years closely mirror the model that Bahri described and Santos unknowingly echoed. Mohammed al-Owhali, one of the plotters involved in the 1998 attacks on United States embassies in Nairobi and Dar es Salaam, explained that mid-level commanders in al-Qaeda planned the attacks. He also reported that it would have been unusual for bin Laden to give instructions directly to low-level operatives like himself.30 Owhali conceded that he “was never specifically told that [the embassy attack] was bin Laden’s mission,” indicating the degree to which bin Laden removed himself from operational planning. The 9/11 Commission report, meanwhile, dedicated an entire section to “terrorist entrepreneurs,” who, according to the Commission, “enjoyed considerable autonomy” in their operational planning.31

The “centralization of decision and decentralization of execution” operational management model endures to this day. Indeed, it is a key source of al-Qaeda’s resilience and capacity for innovation. For one, the devolution of responsibility for day-to-day operations to mid-level commanders allows al-Qaeda to remain adaptive, enabling operatives to modify tactics and operational plans in response to shifting ground conditions. This management model also has a profound impact on al-Qaeda’s overall capacity for learning. It encourages what Assaf Moghadam describes as bottom-up innovation, wherein al-Qaeda’s foot soldiers and mid-level commanders are able to “experiment locally” without bureaucratic constraints.32 Experimentation at the local level increases the rate at which al-Qaeda can develop new tactics and strategies to overcome obstacles introduced by counterterrorism actors. It also prevents the group from falling into fixed patterns of behavior that can be identified and then disrupted by local security services.

Relatedly, al-Qaeda’s decentralized management model has positioned the organization to recover efficiently after leadership decapitation. Al-Qaeda empowers junior officials to take risks, bestowing responsibilities on commanders that may far exceed their experience and knowledge. This baptism by fire involves some risk, as some young commanders are ill equipped to handle these duties or may prove too zealous in executing them. Nevertheless, this approach also produces experienced young officials capable of filling a leadership vacuum should their superiors be removed from the battlefield. The oft-cited assessment that al-Qaeda has a “deep bench” should, therefore, be understood in the context of al-Qaeda’s management style.33 Al-Qaeda’s success in replacing key leaders is to a considerable extent a product of its focus on professional development of junior commanders.

Within the analytic community, Al-Qaeda’s decentralized operational model has created confusion about the relative influence of its senior leadership. The hands-off role played by bin Laden and other senior al-Qaeda commanders in operational planning has often been interpreted, especially in the post-9/11 era, as a sign of a growing disconnect between al-Qaeda’s leadership and regional affiliates.34 This interpretation, however, fundamentally misconstrues the nature of al-Qaeda’s decision-making processes. By design, Al-Qaeda’s senior leadership is not intimately involved in the day-to-day operations of affiliates and cells across the globe. Measuring the leadership’s involvement in operational planning is thus an inaccurate means of assessing the leadership’s overall role in the global network. The extent to which the operations and actions implemented by al-Qaeda’s various affiliates align with and advance broader strategic aims is a more meaningful metric. As al-Qaeda’s founding documents make clear, the primary role of the emir—and, by extension, deputy emir and leadership council—is to craft a strategic vision through the development of annual plans, budgets and structures. Once this vision has been articulated, the emir is expected to serve in an oversight capacity, “following up on the work of supervisors in the leadership, executive and regional councils in implementing the plans and resolutions.”35 Here, a distinction can be drawn between the individual who reigns and the individual who rules. The emir reigns by serving as the supreme authority, while designated subordinates rule by setting and executing policy.

Bin Laden and his successor, Ayman al-Zawahiri, have put this operational model into practice. They outline strategic priorities and guidelines, and give regional commanders broad leeway to adapt these priorities to local conditions. Many analysts, both in and outside government, have long argued that this management style has caused al-Qaeda to become increasingly decentralized and diffuse.36 But Fazul Abdullah Mohammed, one of the planners of the 1998 embassy bombings, presents a compelling counterargument. In his memoirs, Fazul claimed that al-Qaeda did possess a centralized organizational structure, but he distinguished al-Qaeda’s structure from “a dull form of centralization.” Fazul explained that “each person in al-Qaeda is responsible for his own work and has complete authority to carry out his tasks.”37 Assaf Moghadam has similarly argued that al-Qaeda’s management style is top down, in the sense that the top requires the bottom to execute missions. In other words, authority to carry forth a plan is delegated to subordinates.38 (You might recall that Moghadam was quoted earlier in this article explaining that al-Qaeda’s management model encourages bottom-up innovation. Far from contradicting himself, his point is that, for al-Qaeda, “innovation was a multi-directional process,” with both bottom-up and top-down elements.)39

Al-Qaeda operates more efficiently by empowering middle managers and junior commanders. On the one hand, this arrangement certainly creates opportunities for rogue subordinates to disobey the leadership’s dictates, a risk that has materialized in the occasional heated dispute between senior leadership and affiliates. In the case of the Islamic State (ISIS), there was a complete break between the leadership and an affiliate. But on the other hand, this structure can also—perhaps counterintuitively—amplify the influence of al-Qaeda’s leadership. When commanders responsible for implementation adhere to the strategic guidelines articulated by the leadership, al-Qaeda’s power projection capabilities are enhanced beyond what the leadership, on its own would, have been able to achieve.

To assess al-Qaeda Central’s command and control capabilities within its existing organizational framework, two factors are relevant. The first factor concerns al-Qaeda’s capacity for vertical communication, the organization’s ability to disseminate information between different levels of its hierarchy. Al-Qaeda’s senior leaders need to be able to communicate effectively with subordinates to ensure that decisions made at the operational level align with and support overarching objectives. Communication from subordinates to leadership is also essential. Though al-Qaeda’s battlefield commanders are given broad flexibility in adapting strategic plans, they still need to be able to engage with their superiors to convey changes in the operating environment and to discuss future plans. If vertical communication is disrupted or too sporadic, command and control capabilities will be compromised, opening up greater possibilities for operational commanders to deviate from al-Qaeda’s strategic priorities.

The second factor relates to al-Qaeda’s ability to ensure that subordinates act in a manner consistent with the group’s strategic interests. Al-Qaeda’s organizational model makes it susceptible to preference divergence. That is, the interests of actors tasked with implementing al-Qaeda’s strategic plan may be incongruent with those of the leadership, which designed the plan.40 Some degree of preference divergence is inevitable, as actors in different operating environments will have different priorities and concerns. Problems emerge when operational commanders undercut al-Qaeda’s broader objectives by consistently making decisions that further their own interests and contradict the leadership’s guidelines. In most organizations, this conflict between principal (al-Qaeda’s leadership) and agent (battlefield commanders) exists, but in al-Qaeda’s case, it is particularly pronounced. This is because the leadership delegates considerable responsibility to subordinates, and has constraints on its enforcement power outside its small geographic stronghold.

In order to contain and effectively manage preference divergence, Al-Qaeda leadership must carefully adhere to its organizational procedures while also retaining the loyalty of its subordinates. Before 9/11, al-Qaeda’s leadership systematically criticized and sanctioned operational commanders who strayed from strategic guidelines.41 Over time, however, al-Qaeda Central has become less able to effectively discipline its affiliates. The task of disciplining has grown more difficult as the organization continues to expand geographically to include more affiliates. Al-Qaeda Central’s reduced financial leverage also limits its direct coercive power over subordinates. Furthermore, since 9/11, al-Qaeda’s senior leadership has had to dedicate attention to protecting itself, as it is a major target of counterterrorism efforts. Notwithstanding these challenges, a public reprimand from a senior al-Qaeda leader still carries considerable weight in the organization.

Al-Qaeda cultivates loyalty and allegiance amongst its affiliates in order to manage the risk of preference divergence. Over the course of several decades, al-Qaeda’s leaders have built enduring relationships with jihadists across the globe. These personal relationships, which are often solidified on the battlefield or through marriage and extended family networks, serve as a binding force and a buffer against disobedience in al-Qaeda’s ranks. Al-Qaeda has been effective in building a brand and mission to which its affiliates are generally strongly committed. This allegiance has been a powerful source of organizational cohesion and one that analysts have underestimated. For example, analysts massively overestimated the draw of ISIS during its competition with al-Qaeda, which led them to overstate the likelihood of al-Qaeda branches defecting to their jihadist rival in between 2014 and 2016.42

In cultivating loyalty and allegiance amongst its affiliates, al-Qaeda Central gains indirect coercive power. A jihadist group that defects from al-Qaeda or clashes with its leadership may be unable to establish new relationships with regional jihadist groups that remain aligned with al-Qaeda. Both al-Qaeda in the Islamic Maghreb and al-Shabaab, for example, helped to bolster Boko Haram organizationally when the Nigerian government cracked down on it in 2009. Boko Haram subsequently defected to ISIS in 2015, a decision that may have impeded its ability to be succored by al-Qaeda-aligned jihadist organizations, particularly when the group confronted a four-country offensive against it.43

The history of al-Qaeda’s organizational structure is one of a struggle to maintain robust networks of communication, effectively discipline affiliates, and encourage unity in the face of significant internal and external challenges. As state actors improved their electronic surveillance capabilities, al-Qaeda’s ability to communicate across its network was noticeably impeded. Repeated physical displacement took its toll on the organization’s cohesion. Internal dissent has, at times, threatened to tear the organization apart. Despite these disruptions, however, the foundational organizational structure upon which al-Qaeda was built has remained intact. Indeed, al-Qaeda has frequently defied analysts’ predictions, and demonstrated the effectiveness of the “centralization of decision and decentralization of execution” model.

The First Test

It is often assumed that al-Qaeda’s organizational cohesion was first threatened following the United States invasion of Afghanistan in October 2001, but the first real test of al-Qaeda’s resilience actually occurred about a decade earlier. In 1989, bin Laden became persona non grata in Pakistan after he allegedly bribed parliamentarians to support a no-confidence vote against the government of Benazir Bhutto.44Following bin Laden’s return to Saudi Arabia, al-Qaeda’s infrastructure in Afghanistan and Pakistan remained largely intact only for a short time. Abu Ubaidah al-Banshiri and Abu Hafs al-Masri, both skilled Egyptian military commanders, ran the organization’s training camps after bin Laden left.45 But as tensions between mujahedin factions escalated into violence in 1992, after Mohammad Najibullah’s Communist government collapsed, Arab militants began leaving Afghanistan (though quite a few remained and thrived there). Another significant blow to al-Qaeda’s Afghanistan-Pakistan network came in 1993, when the Pakistani government, in response to accusations that it was harboring terrorists, began expelling Arabs from the country.46These two events significantly diminished al-Qaeda’s Afghanistan-Pakistan safe haven.

Al-Qaeda adapted to this setback relatively quickly, largely by shifting its operational hub to Sudan, where bin Laden had been living since 1992. From Sudan, bin Laden and other al-Qaeda commanders strengthened the organization through three lines of effort. First, bin Laden increased al-Qaeda’s involvement in Sudan’s licit economy through investments in the agricultural and construction industries.47 Second, al-Qaeda attempted to solidify relationships with other jihadist groups harbored in Sudan, including the Libyan Islamic Fighting Group (LIFG) and Egyptian Islamic Jihad (EIJ), two groups that had had previous contact with al-Qaeda in Afghanistan. These efforts to build bridges with other jihadist groups had mixed success during this period. The third and most important effort to strengthen the organization involved its international outreach efforts. Working through small reconnaissance teams and front organizations like those provided by the Benevolence International Foundation, al-Qaeda developed relations with like-minded militant groups, and assisted jihadists fighting military campaigns across the globe. As the 9/11 Commission Report explains, bin Laden accomplished this through the creation of what he dubbed the Islamic Army Shura:

In Sudan, he established an “Islamic Army Shura” that was to serve as the coordinating body for the consortium of terrorist groups with which he was forging alliances. It was composed of his own al Qaeda Shura together with leaders or representatives of terrorist organizations that were still independent. In building this Islamic army, he enlisted groups from Saudi Arabia, Egypt, Jordan, Lebanon, Iraq, Oman, Algeria, Libya, Tunisia, Morocco, Somalia, and Eritrea. Al Qaeda also established cooperative but less formal relationships with other extremist groups from these same countries; from the African states of Chad, Mali, Niger, Nigeria, and Uganda; and from the Southeast Asian states of Burma, Thailand, Malaysia, and Indonesia. Bin Ladin maintained connections in the Bosnian conflict as well. The groundwork for a true global terrorist network was being laid.48


These nascent engagements laid the groundwork for al-Qaeda’s later efforts to further expand through affiliations with jihadist groups across the globe.

One of al-Qaeda’s more robust international outreach efforts during this period took place in the Horn of Africa. In late 1992, bin Laden deployed a team of operatives, led by the Egyptian Abu Ubaidah al-Banshiri, to develop a new safe haven for al-Qaeda in the region. The Horn of Africa was to be used as a staging ground for operations in the Arabian Peninsula.49 Over the next few years, al-Qaeda sought to embed itself within the Somali militant landscape, and build operational and support networks in the region.50 The networks and relationships that al-Qaeda developed in East Africa in the early 1990s would prove useful several years later, when al-Qaeda deployed a new team to plan attacks against United States interests in the region. Their efforts ultimately led to the bombing of the United States embassies in Kenya and Tanzania in 1998, and also created the basis for the emergence of Somalia-based militant groups. Among these groups were the Islamic Courts Union (ICU) and al-Qaeda’s powerful Somali affiliate al-Shabaab, which itself grew out of the ICU’s youth wing.51 Despite the early challenges, al-Qaeda’s efforts in the Horn of Africa were overwhelmingly successful over the long term.

Contemporary analysts took a dim view of al-Qaeda’s organizational structure during the group’s time in Sudan, and of the jihadist movement’s cohesion during this period. A 1995 National Intelligence Estimate concluded that the jihadist movement was composed of “transient groupings of individuals” that lacked “b> organization but rather are loose affiliations.”52 Some United States officials also viewed bin Laden as a bit player on the jihadist scene, an ambitious and wealthy individual who gained little by throwing around his money. In 1998, Vince Cannistraro, who held a senior position at the CIA’s Counterterrorism Center until 1991, claimed that “a group can con someone like bin Laden for funds to carry out an operation on an individual basis… And [bin Laden] will do it as long as it fits with his religious objectives.”53 These dismissive assessments of al-Qaeda and bin Laden both during and just after his time in Sudan mark the first, but not the last occasion on which the analytic community underestimated the al-Qaeda organization. It should be noted that al-Qaeda’s organizational structure was, indeed, less robust, and its membership roll smaller, than would be the case after it moved back to Afghanistan. Even so, al-Qaeda proved capable of organizing international operations, fundraising for jihadist campaigns across the globe, and facilitating military training.

Court testimony given by Jamal al-Fadl, an al-Qaeda member who became an informant for the United States government after embezzling over $100,000 from the jihadist organization, provides insight into al-Qaeda’s reach and capabilities during its time in Sudan. Al-Fadl’s testimony indicates that the group was intimately involved in moving recruits, weapons, and materiel to battlefields across the globe. For instance, al-Fadl explained that al-Qaeda operated an office in Baku that purchased weapons and supplies, and smuggled materiel and recruits into Chechnya.54 To avoid drawing attention to its activities in Chechnya, al-Qaeda worked through the Benevolence International Foundation (BIF), which functioned as one of its front organizations in Baku. BIF also played a major role in supporting jihadist actors in Bosnia. The organization produced propaganda materials aimed at attracting donors to the Bosnia conflict; purchased weapons and other military material; provided financial support to the families of militants fighting in Bosnia; and organized training camps for local and foreign fighters.55

The strengths of al-Qaeda’s organizational capabilities in Sudan are further evidenced by its ability to adapt to different contexts, and sustain military training under difficult circumstances. According to al-Fadl, the Sudanese government grew leery of allowing al-Qaeda to conduct robust training programs in Sudan. This was likely due to the political fallout with the Egyptian government following the unsuccessful assassination attempt on Egyptian leader Hosni Mubarak in June 1995, which was linked to Sudan-based Egyptian militants.56Nonetheless, al-Qaeda, in tandem with other militant groups that sought refuge in Sudan, was able to establish several training facilities there. Al-Fadl noted that these facilities primarily provided refresher courses to militants who already had battlefield experience. Al-Qaeda also used its camps in Sudan to test chemical weapons, which, if developed, were to be provided to the Sudanese government to support its fight against rebels in southern Sudan.57 Along with their work in Sudan, al-Qaeda operatives maintained a training presence in eastern Afghanistan despite the group’s aforementioned reduction in presence in the country, provided assistance to Islamist militant groups in Somalia, and received training from Hizballah operatives in southern Lebanon.58 Thus, while it was based in Sudan, al-Qaeda conducted training in multiple countries, tailoring its activities to the demands and challenges of the local environments in which it operated.

Al-Qaeda’s international operations and growing profile ultimately drew unwanted attention to its presence in Sudan. As a result, in 1996, the Sudanese government, facing pressure from the United States and other countries, demanded that al-Qaeda leave the country. Losing its Sudanese safe haven was a setback, but the organizational infrastructure and global network that al-Qaeda had cultivated served as a foundation, which the jihadist group would continue to build upon its return to Afghanistan.

The Jihadist Behemoth

In Afghanistan from 1996 to 2001, al-Qaeda reached its high point as a hierarchical and bureaucratic organization. Operating from safe havens in southern and eastern Afghanistan, al-Qaeda further professionalized its bureaucratic structure and established a comprehensive, multi-phased training process for members and recruits. The infrastructure that al-Qaeda developed in Afghanistan allowed it to absorb hundreds of new recruits, improve the capabilities of current members, and orchestrate a series of complex operations, most prominently the 9/11 attacks. As al-Qaeda’s bureaucratic structure expanded, it retained the “centralization of decision and decentralization of execution” management model, and remained agile and innovative.

While the move to Afghanistan would eventually be a boon to al-Qaeda, the transition from Sudan was fraught with challenges. Al-Qaeda had to invest significant resources in rebuilding training camps in Afghanistan, while simultaneously navigating the country’s volatile political landscape. The power of some mujahedin commanders with whom al-Qaeda had developed a close rapport had waned, while the Taliban rapidly gained territory. Al-Qaeda also encountered financial difficulties as it relocated. Some of bin Laden’s assets in Sudan—over $30 million, according to one estimate59—were frozen when he left for Afghanistan, which offered few new economic opportunities.

Al-Qaeda’s successful expansion in the face of these obstacles is testament to its resilience. Within four years of moving to Afghanistan, al-Qaeda had established an extensive network of training camps that offered courses in explosives-making, guerilla warfare, and document forgery, among other specialties. Al-Qaeda also offered train-the-trainer courses aimed at enhancing its own capabilities, as well as those of other militant groups.60 As al-Qaeda’s network of training camps grew, senior leaders considered how they could improve management of the organization’s expanding activities. In a letter written in November 1998, Abd al-Hadi al-Iraqi, a senior al-Qaeda member and a trainer at several camps, urged prominent Egyptian military commander Saif al-Adel to establish a personnel management system to document incoming recruits and current members.61 Al-Iraqi noted that each member’s personnel file should include information on training and battlefield experience, as well as performance assessments from supervisors. This system, al-Iraqi hoped, would prevent an arbitrary promotion process, and streamline the handling of new recruits.

Numerous documents discovered after 9/11 demonstrate that al-Qaeda implemented al-Iraqi’s recommendations and also sought to further professionalize its personnel system. One document that provides insight into al-Qaeda’s bureaucratic practices is an application filled out by José Padilla, an American-born convert, in July 2000.62 This document, which was issued by the personnel branch of al-Qaeda’s military wing, required Padilla to provide information on his educational and religious background, foreign travels, health status and military experience, among other things. It also included a section to be filled out by al-Qaeda administrators, which required information on Padilla’s passport, visa and ticket status.

Wall Street Journal reporter Alan Cullison, who serendipitously obtained two of al-Qaeda’s most valuable computers after damage to his own laptop forced him to get to know Kabul’s computer dealers, discovered further evidence of al-Qaeda’s meticulous administrative practices.63Cullison explained that al-Qaeda’s digital files included a “network of folders and subfolders that neatly laid out the group’s organizational structure,” and discussed “budgets, training manuals for recruits, and scouting reports for international attacks.”64 Al-Qaeda integrated these bureaucratic processes into its day-to-day operations. Anne Stenersen notes that recruits had to pre-register for training camps at the Office of Mujahedin Affairs, before reporting to their camp on a “designated date.”65

The extensive training and organizational infrastructure that al-Qaeda developed in Afghanistan was integral to the organization’s efforts to expand its membership ranks. In the pre-9/11 period, al-Qaeda was one of several jihadist groups competing for recruits in Afghanistan. According to Abu Musab al-Suri’s estimate, fourteen different groups operated training camps in the country by the end of 1999.66 Al-Qaeda’s capacity to absorb new recruits, however, was superior to that of other groups. Al-Qaeda’s training programs were also more comprehensive, and its trainers more experienced, than what other militant groups offered.67 Moreover, al-Qaeda’s transnational vision appealed to fighters of all nationalities. For these reasons, al-Qaeda was able to capitalize on the influx of new recruits streaming into Afghanistan after the 1998 Embassy attacks.

From its safe haven in Afghanistan, al-Qaeda engaged in organizational learning and improved its operational capabilities. Cullison found that al-Qaeda operatives discussing sensitive operational issues used code words and a cryptographic system to communicate. Though al-Qaeda’s cryptographic system was rather basic, it still required coordination, indicating that the organization had established standard operating procedures for internal communications. One of the more chilling documents on the computers discussed al-Qaeda’s nascent efforts to develop a biological and chemical weapons program. In a letter to Abu Hafs al-Masri, Ayman al-Zawahiri outlined the “destructive power” of these weapons, and provided a brief review of articles that could help al-Qaeda improve its unconventional weapons capabilities.68 American forces later discovered a videotape documenting al-Qaeda testing chemical weapons on dogs.69

As al-Qaeda’s bureaucracy became more professionalized, it encountered an issue familiar to many growing organizations: micro-management. In one letter stored in the data files recovered by Cullison, Zawahiri took a Yemeni operative to task for failing to provide a comprehensive accounting of recent expenses. Zawahiri’s criticisms included questions about why the Yemeni had renovated a computer and bought a new fax machine, when, according to Zawahiri, the Yemeni cell already had two fax machines.70

Micro-management aside, al-Qaeda sought to maintain a culture wherein lower-level commanders were empowered to take initiative and shape the implementation of strategic plans. Indeed, the story behind the conception of the 9/11 attacks illustrates al-Qaeda’s efforts to maintain a bottom-up innovation model even as it pursued greater bureaucratization. In 1996, as al-Qaeda was getting settled in Afghanistan, Khalid Sheikh Mohammed approached bin Laden with a grandiose plan to hijack planes and crash them into prominent buildings in the United States.71 Bin Laden initially rejected Mohammed’s proposal, reportedly because al-Qaeda lacked the necessary funds. By early 1999, however, al-Qaeda had received an infusion of money from external sources, and when Mohammed approached bin Laden again with a less ambitious version of his initial plan, he was given a green light to proceed.72

Other al-Qaeda operatives were similarly empowered to innovate and think creatively about external operations planning. Abd al-Rahim al-Nashiri, the mastermind behind the USS Cole attack, was first dispatched to Yemen in 1998, and tasked with scoping out potential American targets. Over the next two years, Nashiri conducted reconnaissance and built his network in Yemen, regularly returning to Afghanistan to report to bin Laden. Bin Laden assisted Nashiri in his operational planning—when Nashiri struggled to find United States naval vessels off the western coast of Yemen, bin Laden suggested that he instead focus on the Port of Aden—but Nashiri “retained discretion in selecting operatives and devising attacks,” according to the 9/11 Commission Report.73

A close review of the three most prominent attacks engineered by al-Qaeda while the group was in Afghanistan—the 1998 Embassy bombings, the USS Cole attack, and the 9/11 operation—reveals another aspect of the organization’s management approach. The 9/11 Commission Report indicates that bin Laden personally selected the hijackers who would carry out that operation. Similarly, bin Laden attempted to replace the operatives whom Nashiri selected to carry out the USS Cole attack, though he was ultimately rebuffed by Nashiri.74These two actions seem to contradict al-Qaeda’s principle of “decentralization of implementation,” since picking foot soldiers for an attack is generally assumed to be a responsibility of the field commander. But bin Laden’s involvement in selecting operatives for these plots may in fact reinforce, rather than undercut, the al-Qaeda leadership’s hands-off approach to operational planning. Bin Laden planned to delegate almost all responsibilities for coordinating and preparing attacks to subordinates, but he had to ensure that the individuals who assumed these duties were competent and trustworthy. Hand picking operatives for an attack, therefore, was an exercise in quality assurance. That bin Laden appears not to have involved himself in selecting operatives for the 1998 embassy attacks may imply that he did not deem it necessary.75 At the time, al-Qaeda’s East Africa network was directed by Abu Muhammad al-Masri, one of the jihadist organization’s original members. He had been operating in East Africa for several years by that point, and had likely earned bin Laden’s confidence long before the attacks were launched. The logic behind selecting operatives for the aforementioned attacks is similar to that behind al-Qaeda leadership’s current involvement in picking or, at least, approving the emirs of regional affiliates.76

Despite al-Qaeda’s continued efforts to support decentralization of implementation, there should be little doubt that al-Qaeda functioned as a hierarchical, and increasingly professional, organization during its later years in Afghanistan. Yet some observers continued to view al-Qaeda as a diffuse network, and discounted its organizational capacity. Perhaps the most misleading characterization of how al-Qaeda functioned at the time appeared in a January 2000 New Yorker profile of bin Laden, which claimed that al-Qaeda lacked a robust internal structure.77 The article included several quotes from former State Department counterterrorism official David Long, who argued that al-Qaeda resembled “an informal brotherhood [rather than] a clear, sterling network,” and asserted that the group was best understood as a “clearing house from which other groups elicit funds, training, and logistical support.”78

The tendency among some government officials to downplay al-Qaeda’s organizational structure and capacity may have affected the ability of the United States intelligence community to anticipate a complex operation like 9/11. Some pre-9/11 intelligence assessments did make note of al-Qaeda’s training activities and budding organizational structure. For example, one CIA report, entitled Afghanistan: An Incubator for International Terrorism, determined that Afghanistan “provide[d] bin Laden a relatively safe operating environment to oversee his organization’s worldwide terrorist activities,” and emphasized that training camps in the country “form the foundation of the worldwide mujahidin network.”79 While desk officers at the CIA and other agencies documented al-Qaeda’s increasingly sophisticated training activities, it is not evident that senior policymakers fully appreciated “the gravity of the threat.”80 As the 9/11 Commission Report explained, government officials were still debating whether al-Qaeda was “a big deal” as late as September 4, 2001.81

Unsurprisingly, the 9/11 attacks eliminated any doubt about al-Qaeda’s capabilities. The attacks also quickly rendered obsolete the paradigm that had governed al-Qaeda’s activities and capabilities prior to September 2001. The United States invasion of Afghanistan rapidly dismantled al-Qaeda’s physical infrastructure, and disrupted the bureaucracy that the group had spent years building. Al-Qaeda’s senior leaders scattered across the Middle East and South Asia.

Remarkably, Al-Qaeda adapted to these challenges, maintaining its organizational cohesion and decision-making approach at the same time that it expanded its geographical presence and reach. The organization that analysts confronted in the aftermath of 9/11, however, would be significantly more difficult to interpret than the organization that had operated prior to 9/11.

Al-Qaeda in Flux

In November 2002, several senior al-Qaeda leaders and associates gathered for a meeting in Iran, where the organization had found space to continue operating after the U.S. invasion of Afghanistan.82 While the meeting was not a full gathering of al-Qaeda’s shura council—bin Laden, Zawahiri and other top members were in Pakistan at the time—it nonetheless marked a rare occasion on which multiple al-Qaeda leaders convened in person to discuss the organization’s affairs. One participant was Abu Musab al-Suri, who had urged al-Qaeda to cease planning external operations while the group was under the protection of the Taliban.83 Suri’s concerns about what would happen if al-Qaeda launched a major attack from Afghanistan had been borne out in the aftermath of 9/11. As he had predicted, the Taliban’s emirate collapsed following the United States invasion and al-Qaeda’s training camp infrastructure was crushed along with it. By the time of the November 2002 meeting in Iran, American and allied forces were hunting down al-Qaeda’s members.84 By then, several prominent jihadists, including general manager Abu Hafs al-Masri, had been killed or captured. Suri believed that under these circumstances, al-Qaeda could not survive as a centralized organization. He proposed that al-Qaeda dismantle its hierarchy, disperse its networks across the globe, and pursue a model of leaderless jihad, where individuals and small cells that were not directed by al-Qaeda would assume responsibility for continuing the military campaign.

Suri presented this proposal for leaderless jihad at what was likely the most vulnerable point in al-Qaeda’s history. Its leaders were dispersed and inter-organizational communication was growing increasingly perilous as the United States ramped up its electronic surveillance capabilities. United States Special Forces routinely conducted raids to kill or capture al-Qaeda commanders and used information gathered during one operation to prompt additional raids. A leaderless organizational model, which would have permitted members to sever ties with one another and operate autonomously, may have addressed these issues.

The fact that al-Qaeda did not adopt Suri’s proposal and has never considered such a policy since the November 2002 meeting in Iran is significant. Even when its organizational structure was under immense strain, al-Qaeda’s leadership never considered using its diminished influence as a justification for transforming the organization into a decentralized movement. Doing so would contradict its raison d’être. As the self-styled vanguard of the global jihadist revolution, al-Qaeda considers its strategic and ideological guidance essential to the global movement. In Zawahiri’s words, al-Qaeda must serve as the “organization and leadership leading change.”85

Instead of dismantling its hierarchy in the aftermath of the United States invasion of Afghanistan, al-Qaeda’s leadership regrouped. The best account of how al-Qaeda members escaped Afghanistan comes from Adrian Levy and Cathy Scott-Clark’s The Exile, a 2017 book that draws heavily from primary sources, including interviews with al-Qaeda members and associates. Levy and Scott-Clark found that most al-Qaeda members moved to one of three locations: Iran, the tribal areas of western Pakistan, and cities in the Pakistani provinces of Sindh and Punjab.

One group of al-Qaeda members, which included security chief Saif al-Adel, Abu Muhammed al-Masri (a key figure in the 1998 Embassy bombings), and Abu Khayr al-Masri, fled first to Pakistan, and then made its way to Iran via Quetta Province.86 Iran provided these militants a refuge from American forces, but also closely monitored their activities. The Iranian government’s relationship with al-Qaeda militants would oscillate over time. Though a complete story of the relationship between Iran and al-Qaeda has yet to be told, it is clear that the al-Qaeda contingent in Iran was often effectively incarcerated. Even under these controlled conditions, however, these al-Qaeda operatives managed to maintain frequent communications with their counterparts elsewhere,87 helped to facilitate the movement of fighters and funds between different conflict zones,88 and were even involved in directing attacks.89

A second contingent of al-Qaeda members fleeing Afghanistan found refuge in the tribal areas of western Pakistan, which would eventually become al-Qaeda’s new global command hub. Hassan Ghul, an al-Qaeda facilitator arrested by the United States in early 2004, told American officials that Ayman al-Zawahiri, Abd al-Hadi al-Iraqi and over 200 al-Qaeda fighters and associates had settled in the Shakai Valley in South Waziristan. This region was also home to Nek Mohammed, a Pakistani militant and al-Qaeda sympathizer who had become a major irritant to the Pakistani military.90 The Pakistani military and American drones targeted al-Qaeda safe havens in the tribal areas, forcing Zawahiri and his contingent out of the Shakai Valley. These al-Qaeda members were forced to resettle numerous times, but even as they moved locations, Zawahiri and other senior operatives continued to coordinate with al-Qaeda commanders outside the tribal areas. They coordinated, for example, with bin Laden, who himself had bounced between safe houses in Pakistan before settling in Abbottabad in 2005. They also oversaw the al-Qaeda network in Afghanistan, Pakistan, and the Middle East.

A key node in this transnational network was Khalid Sheikh Mohammed, who is believed to have taken over al-Qaeda’s external operations portfolio after the 9/11 attacks. Mohammed, drawing on pre-existing relationships with Pakistani militant groups and kinship ties with members of his Baluch ethnic group, developed a robust operational network based in Karachi and extending to cities across Pakistan. Almost immediately after 9/11, Mohammed mobilized the cells under his command, which executed a series of attacks across the globe. This network was eventually degraded, as Pakistani and United States operatives successfully worked their way through Mohammed’s couriers and facilitators, before finally ensnaring Mohammed himself in 2003. But Mohammed’s frenetic planning in the months leading up to his arrest demonstrated that al-Qaeda had retained its external operations capabilities despite having been displaced from Afghanistan.

That al-Qaeda managed to survive and then rebuild its organization after 9/11 reflects the organization’s penchant for adaptability. For instance, it quickly recognized that American and allied forces often identified operatives who used mobile phones. Many al-Qaeda members, including bin Laden, thus eschewed cell phones in favor of human couriers, radios and the like.91 For his part, Khalid Shaikh Mohammed secured his communications and protected his network by constantly switching sim cards in his cell phone, rotating between a vast number of safe houses, relying heavily on couriers and using email dead drops.92 Through these adaptations, al-Qaeda slowed the disruption of its network. The adaptations, though, also came at a cost to information flow within the organization, making it more difficult to coordinate strategy internally. This underscores the tension between security and efficiency that jihadist groups confront.93

Also contributing to al-Qaeda’s resurgence was the manner in which the group exploited territorial safe havens. The tribal areas of Pakistan offered an ideal location to rebuild the organization and reestablish structured decision-making processes. In the immediate post-9/11 period, the Pakistani army was reluctant to intervene in the tribal areas, and proved to be largely ineffective when it conducted military operations there. The ability of the United States to collect and act on intelligence in the tribal areas was also limited. Moreover, some of the local Pakistani population was sympathetic to the Arabic-speaking foreigners who sought shelter and protection there after the United States invasion of Afghanistan. In the tribal areas, therefore, al-Qaeda found a permissive environment in which to operate. Al-Qaeda commanders could conduct in-person meetings, reinitiate training exercises, and plan military operations without attracting the attention of counterterrorism forces.

Strategic errors that the United States committed during the early years of the “global war on terror” further enabled al-Qaeda to rebuild itself. The most glaring mistake was the diversion of critical resources from Pakistan and Afghanistan to Iraq. The negative consequences of the invasion of Iraq from a counterterrorism perspective are well established, and do not need to be reiterated here at length. Still, it is worth noting that the United States began to shift counterterrorism resources to Iraq in late 2002, several months before the invasion—and at a time when the hunt for al-Qaeda operatives in Afghanistan and Pakistan was just gaining momentum. This decision to divert resources away from Afghanistan and to Iraq slowed the hunt for al-Qaeda commanders still on the lam. According to retired general Wayne Downing, who helped lead the post-9/11 counterterrorism campaign, it left “reams of material waiting to be exploited.”94

The organizational structure to which al-Qaeda adhered was a final factor contributing to its recovery. United States officials continuously overestimated the strategic impact of the death or capture of al-Qaeda leaders. After the capture of Khalid Sheikh Mohammed (KSM), for instance, Porter Goss, then-chairman of the House Permanent Select Committee on Intelligence, declared that “the tide has turned in terms of al-Qaeda.”95 It is true that the capture of Mohammed helped slow al-Qaeda’s external operations, given his outsize role in coordinating and supporting attacks across the globe. But the U.S. government has consistently overestimated the impact that the loss of a single leader, regardless of how senior, would have on al-Qaeda’s organizational capacity. Al-Qaeda had cultivated a cadre of skilled commanders in Afghanistan, many of whom gained battlefield experience fighting against the Northern Alliance. Al-Qaeda’s “deep bench” allowed the group to replace commanders who had been taken off the battlefield without sacrificing institutional knowledge or suffering major disruptions to its operations.

Other key post-KSM external operations planners include Younis al-Mauritani, Abd al-Rahim al-Sharqi, and Faruq al-Qahtani.99 Many analysts, however, have discounted al-Qaeda’s structural resilience, and have argued that its post-9/11 losses heralded the organization’s collapse. Journalist Jason Burke articulated an extreme version of this theory, claiming that al-Qaeda as an organization had “existed for a short period, between 1996 and 2001,” and met its demise in the mountains of Tora Bora in late 2001. Al-Qaeda had been replaced by “a broad and diverse movement of radical Islamic militancy,” according to Burke.100

While more extreme than widely held contemporary views of al-Qaeda, Burke’s argument relates to another theory about al-Qaeda that retains some popularity among analysts. This theory holds that al-Qaeda had evolved from a hierarchical organization into a networked social movement. According to this theory, after the U.S. invasion of Afghanistan, al-Qaeda’s leaders no longer maintained and commanded a formal organizational structure. Instead, bin Laden and others served as spiritual and ideological guides for a motley crew of militant groups, small cells and radicalized individuals, all of which adhered to a salafi jihadist worldview but maintained their own parochial interests.

There were important implications of this networked social movement theory for jihadist strategy. Decentralized movements, especially those that are transnational, do not possess the organizational structure, communications capabilities, and internal discipline needed to coordinate and pursue a common strategy. Adherents to such movements share a common worldview, but both their goals and their means of pursuing those goals differ and may even conflict with one another. In short, an implication of this argument was that as al-Qaeda’s organizational structure withered, the jihadist movement would no longer have an actor able to coordinate the activities of disparate groups and cells.

This theory of al-Qaeda as a social movement became the prevailing wisdom within the analytic community within a few years the 9/11 attacks. An August 2003 symposium featuring five RAND Corporation terrorism scholars and produced in coordination with FrontPage Magazine (a publication that was then less strident than is the case in 2018), illustrates the prevalence of this view. When the symposium moderator asked panelists how to define al-Qaeda, almost all of them offered some version of the social movement theory.101 To William Rosenau, al-Qaeda was a “worldview, not an organization.” John Parachini argued that since 9/11 al-Qaeda had “evolved from a loosely aligned network of militant Islamic terrorists who shared the formative experience of expelling Soviet forces from Afghanistan to a movement with adherents around the world enabling a global reach.” Even Bruce Hoffman—who, as we referenced in our introduction, is well known for his arguments against the leaderless jihad hypothesis—said, “Al Qaeda is an ideology more than army; a transnational movement and umbrella-like organization, not a monolithic entity.”102 Although Rohan Gunaratna had produced a rather comprehensive account of al-Qaeda’s pre-9/11 organizational structure, by 2004 he suggested that al-Qaeda had fulfilled its goal of spearheading a jihadist uprising, and had transformed into a movement.103

The “al-Qaeda as a movement” theory is flawed, because it relies on incomplete and inaccurate information about the organization. The theory is based on the assumption that al-Qaeda had no involvement in several prominent terrorist attacks carried out between 2001 and 2004, and that these attacks were, instead, orchestrated by local militant groups that shared a common worldview with al-Qaeda but little else. These attacks include the 2002 Bali bombings, the 2002 attacks on an Israeli-owned hotel and airline in Mombasa, multiple attacks in Turkey in 2003, the 2003 Riyadh bombings, and the 2004 Madrid bombings. The claim that al-Qaeda was not involved in these attacks appears less credible when each attack is scrutinized:

  • Hambali, the 2002 Bali bombings mastermind, admitted in interrogations that al-Qaeda provided $30,000 to fund the attack, and gave him another $100,000 afterward to support new operations.104
  • The suicide bomber who killed 19 in an attack on the El Ghriba synagogue in Djerba was in regular contact with Khalid Sheikh Mohammed and Christian Ganczarski, an al-Qaeda member who maintained close ties with bin Laden, Saif al-Adel and Abu Hafs al-Masri.105
  • Al-Qaeda’s East African network, which was led by Fazul Abdullah Mohammed and answered directly to al-Qaeda’s senior leadership, perpetrated the Mombasa attacks.106
  • The operatives who carried out the 2003 bombings in Turkey had met with bin Laden and Abu Hafs al-Masri in Afghanistan prior to 9/11, and had received training in bomb construction during that time. Luayy Sakka, a veteran al-Qaeda member who also maintained close ties with Abu Musab al-Zarqawi, financed the operations, and housed some of the operatives who fled Turkey to Syria after the attacks.107
  • An al-Qaeda cell in Yemen, which had been operating in the country prior to 9/11 and had perpetrated the USS Cole attack, carried out the 2003 Riyadh bombings. Those bombings may in fact have been ordered by Saif al-Adel and other al-Qaeda commanders based in Iran.108
  • Fernando Reinares, Spain’s foremost scholar of jihadism, has documented al-Qaeda’s role in supporting and approving the Madrid attacks at length in his 2014 book Al-Qaeda’s Revenge.109

While the degree of al-Qaeda’s importance differs from one plot to another, some of the aforementioned attacks clearly reflected the creativity and expertise of Khalid Sheikh Mohammed. Though KSMenjoyed significant autonomy while he was in Karachi, he continued to coordinate with and seek approval from bin Laden. According to The Exile, bin Laden surreptitiously traveled to Karachi in late 2001 to meet with Mohammed.110 During these meetings, bin Laden and KSMdiscussed current and future operational planning, and bin Laden signed off on a plot to hijack planes and crash them into Heathrow airport.111 Bin Laden allegedly also met with Richard Reid and Saajid Badat in Karachi before they departed for Europe, where they were charged with bringing down planes by detonating bombs implanted in their shoes.112 Bin Laden’s trip to Karachi indicated that the al-Qaeda emir maintained some degree of influence over external operations even while the organization had made a strategic decision to significantly limit its communications in an effort to avoid detection. (It also highlights his extraordinary freedom of movement in the settled areas of Pakistan.)

At best, the premises upon which the theory that al-Qaeda had been transformed into a movement are based are oversimplified. Recently declassified evidence recovered from bin Laden’s Abbottabad hideout cuts against this hypothesis. Al-Qaeda actually played a role in most of the major jihadist attacks that occurred between late 2001 and 2005. The organization leveraged its financial, logistical and operational networks to enable and direct attacks on multiple continents. Sometimes, however, al-Qaeda’s involvement in plots was not discovered until months or even years after the attacks occurred.

Even as new evidence emerged that contradicted the “al-Qaeda as a movement” theory, the theory continued to flourish, clouding future analysis. The notion that al-Qaeda’s organizational structure had been dismantled featured heavily in the investigation into the July 7, 2005 terrorist attacks on London’s mass transit system. British Foreign Secretary Jack Straw noted on the day of the attacks that the bombings bore “the hallmarks” of al-Qaeda.113 A subsequent New York Times article about the investigation, however, noted that many intelligence officials interviewed described al-Qaeda as a “badly hobbled, barely functioning organization.” A senior counterterrorism official claimed, “Al Qaeda is finished. But there is Al Qaedaism. This is a powerful ideology that drives local groups to do what they think Osama bin Laden wants.”114 Some intelligence services considered Abu Musab al-Suri’s Call to Global Islamic Resistance to be the new blueprint for the jihadist movement. This was the 1600-page treatise in which Suri articulated his theory of leaderless jihad, which, as explained earlier, al-Qaeda explicitly rejected.

Though intelligence agencies were initially skeptical that al-Qaeda possessed the organizational capacity to carry out the 7/7 attacks, subsequent evidence demonstrated that the group played a central role in the plot. Mohammed Siddique Khan and Shehzad Tanweer, the ringleaders of the 7/7 cell, had traveled to Pakistan. There, they met with senior al-Qaeda member Abu Ubaydah al-Masri, who convinced the two men to carry out an attack in England. Rashid Rauf, a British al-Qaeda operative, then took responsibility for overseeing the logistical and operational aspects of the plot, remaining in contact with Tanweer and Khan after they returned to the UK, and coaching the men as they built their explosives.115 On the one-year anniversary of the bombings, Al Jazeera posted a video from al-Qaeda featuring footage of the attackers before they struck. Ayman al-Zawahiri appeared on the tape, explaining that Khan and Tanweer had visited an al-Qaeda camp “seeking martyrdom.” Comparing the revelations in this tape to the conclusions of officials’ inquiry into the 7/7 attacks, Bob Ayers, a security expert at London’s Chatham House think tank, commented, “It makes the police look pretty bad. It means the investigation was either wrong, or they identified links but were reluctant to reveal them.”116

A Global Organization

Despite evidence that connected the 7/7 attacks to al-Qaeda, the theory that al-Qaeda was organizationally fragmented remained popular. To the contrary, the theory gained new life as al-Qaeda embarked on its next phase of organizational development.

In bin Laden’s words, the Iraq war presented the organization a “golden and unique opportunity,” particularly at a time when al-Qaeda leadership was under immense pressure in Pakistan and Afghanistan.117 As the insurgency gained momentum, al-Qaeda recognized an opportunity to capitalize on widespread popular discontent, attack U.S. forces in Iraq, and galvanize a new generation of jihadists. Al-Qaeda’s decision to formalize its relationship with Abu Musab al-Zarqawi’s organization in 2004 was thus both opportunistic and prudent. The relationship between Zarqawi and al-Qaeda dated to the late 1990s, when al-Qaeda funded Zarqawi’s training camp in Herat, and had grown stronger after Zarqawi and his men fought alongside al-Qaeda members at the battle of Tora Bora. Senior leaders of al-Qaeda always had trepidations about Zarqawi. They harbored reservations about his background as a street thug, as well as his lack of formal education, and bin Laden found Zarqawi’s boisterous and brazen nature off-putting.118Ultimately, these concerns gave way to the attractive strategic position that Zarqawi had achieved in Iraq, as al-Qaeda’s senior leaders chose to capitalize on the robust network that Zarqawi had built. Zarqawi’s group became known as al-Qaeda in Iraq (AQI).

Al-Qaeda’s senior leaders, however, quickly found themselves at odds with Zarqawi. Zarqawi’s proclivity for extreme violence, his reluctance to cooperate with other militant groups in Iraq, and his slaughters of the Iraqi Shia were all incongruent with al-Qaeda’s preferred methodology for the Iraq jihad. Fearing that al-Qaeda’s reputation in the Muslim world would be tarnished by AQI’s actions, al-Qaeda Central’s leaders sent at least two letters to Zarqawi counseling him to moderate his approach. In the first letter, Ayman al-Zawahiri urged Zarqawi to build public support, and to avoid inflaming tensions with the Shia.119Zawahiri was no pacifist—he advised Zarqawi to shoot prisoners rather than behead them—but he feared that Zarqawi’s proclivity for brutality would alienate the population. Zawahiri stated, “the strongest weapon which the mujahedeen enjoy … is popular support from the Muslim masses.” Jihadists, therefore, “must avoid any action that the masses do not understand or approve.” Later that year, senior al-Qaeda official Atiyah Abd al-Rahman wrote a harsher letter to Zarqawi echoing Zawahiri’s advice.120 Atiyah told Zarqawi that military policy was subordinate to political objectives, and exhorted the Jordan-born leader to rein in his violent tendencies or risk eroding public sympathy for al-Qaeda. He counseled Zarqawi to overlook the “mistakes and flaws” of the population, and to tolerate “a great deal of harm from them for the sake of not having them turn away and turn into enemies on any level.” He also criticized Zarqawi for failing to consult with al-Qaeda’s leadership before acting on any “comprehensive issues.”

The interactions between Al-Qaeda Central, Abu Musab al-Zarqawi, and AQI illustrate both the organizational opportunities and challenges that al-Qaeda faced then and continues to face now, as it continues to expand its geographical reach and formalize its relationship with allied jihadist groups across the globe. On the one hand, the strategy of developing alliances made it possible for al-Qaeda to project its influence into new theaters, demonstrate (or, in some cases, simply create the perception of) momentum, and expand the pool of resources on which it could draw. It also helped al-Qaeda move closer to its foundational goal of becoming the vanguard organization. Al-Qaeda could provide strategic and ideological guidance to organizations under its umbrella, thus giving it greater influence and control over the trajectory of the jihadist movement. On the other hand, this strategy complicated al-Qaeda’s efforts to maintain organizational cohesion and strategic unity.

One challenge that al-Qaeda encountered, for example, was its ability to establish and then maintain lines of communications with an ever-growing number of affiliates. While the organization employed couriers to communicate in Afghanistan and Pakistan, the courier strategy has proven riskier and less reliable when communicating with affiliates in Iraq and other countries further afield from the senior leadership. Couriers tasked with passing letters between al-Qaeda leadership and its affiliates were sometimes arrested, and the content of their communications were revealed to the public. In some cases, security conditions actually prevented al-Qaeda from dispatching envoys (who, in contrast to couriers, are formal representatives) to meet with affiliates. In his letter to Zarqawi, for example, Atiyah Abd al-Rahman explained that al-Qaeda’s leadership was unable to send an envoy to Iraq, and, therefore, encouraged Zarqawi to send a courier to Pakistan, instead, to reopen lines of communication.121 Zarqawi did send the requested courier, and al-Qaeda Central sent Zarqawi’s successor multiple envoys once the security situation improved.

The challenges associated with establishing reliable lines of communication increased the likelihood that al-Qaeda’s affiliates would deviate from the strategic course outlined by al-Qaeda Central. Affiliates could, in certain circumstances, also be left unaware of dictates issued by al-Qaeda Central, and thus, adopt measures that unintentionally undercut the interests of the organization as determined by senior leaders. Such communications barriers could similarly inhibit al-Qaeda Central’s ability to effectively advise affiliates on how to respond to events as they unfolded. This could then result in missed opportunities and strategic confusion. For affiliates that disagreed with and wanted to ignore strategic advice from al-Qaeda Central, real communications issues served as an ideal excuse for actions that contravened the dictates of senior leadership.

The decision to acquire affiliates also raised the possibility that al-Qaeda would experience preference divergence and strategic incoherence. Prior to its geographic expansion, the risk and potential impact of preference divergence between al-Qaeda and its affiliates were limited. Field commanders tasked with conducting attacks abroad were often hand-picked by bin Laden or by one of his lieutenants. Even if a commander deviated from the operational playbook while carrying out an attack, the impact this single attack would have on either al-Qaeda’s image or its strategy would be minimal.

But geographic expansion increased the possibility that affiliates would have interests that differed significantly from those of al-Qaeda Central. Local cultural, social and political dynamics have a profound effect on the strategy, tactics, and concerns of affiliates. Affiliates may be inclined to prioritize their local considerations over the global agenda of al-Qaeda Central. Preference divergence may also result from regional commanders who begin to view themselves as autonomous from—or even superior to—the core organization. Al-Qaeda Central can use sticks and carrots—like withholding funds and other resources—to deter affiliates from going rogue, but such coercive power is greatly diminished when affiliates develop alternative sources of funding.122

The potential impact of preference divergence on al-Qaeda’s image and long-term prospects also increases as the organization expands geographically. Some affiliates have control over their own media outlets, which can effectively restrict the ability of al-Qaeda Central to sustain a common narrative across all public lines of communication. Should affiliates choose not to comply with al-Qaeda’s agenda, or unknowingly engage in behavior that undercuts it, the consequences for al-Qaeda Central can be considerable. For this reason, some scholarship argues—incorrectly, in our judgment—that al-Qaeda’s expansion, both before and after the Arab Spring, should be understood to reflect the organization’s weakness, rather than its strength.123

This skeptical view of al-Qaeda’s expansion has been rather consistent over time. By 2004, al-Qaeda was widely perceived as deeply fragmented and decentralized. The decision to establish a formal alliance with Zarqawi’s group in Iraq was interpreted by many observers as a last-ditch effort to allow al-Qaeda to remain relevant in the eyes of its followers. During AQI’s period of strength, many observers believed that Zarqawi had eclipsed bin Laden. Indeed, one analyst asserted that al-Qaeda’s base had shifted from Afghanistan to Iraq.124 To be clear, al-Qaeda’s senior leadership clearly did have trouble controlling AQI at key times, particularly when al-Qaeda Central tried to reign in its affiliate’s ultraviolent methods.

But arguments that al-Qaeda’s decision to ally with Zarqawi was a sign of weakness do not consider the wide variety of factors that may be indicative of its organizational strength. For example, a powerful Iraqi-based militant group thought it advantageous to bring the al-Qaeda brand to Iraq. Further, while al-Qaeda’s association with AQI did ultimately damage its brand, what were the intermediate benefits to al-Qaeda? What were the immediate financial implications of this decision?

Many analysts also interpreted al-Qaeda Central’s decision to formalize its relationship with al-Qaeda in the Islamic Maghreb in 2007 and with al-Qaeda in the Arabian Peninsula in 2009 in a similar manner. Bin Laden’s death in May 2011 cemented the view of many observers that al-Qaeda Central wielded little to no control over its affiliates. An August 2011 New York Times article entitled “Al Qaeda Affiliates Growing Independent” articulated the conventional wisdom in that regard.125Terrorism experts both within and outside of government, the article reported, had come to view al-Qaeda Central as increasingly marginalized, while the affiliates were “gaining in stature.” Brian Fishman, then at the New America Foundation, said, “it’s increasingly likely that the Al Qaeda affiliate groups are just going to start doing their own thing,” and added that “at some point, the guys in Pakistan might be reduced to issuing a lot of public statements and hoping for the best.” Scholar Barak Mendelsohn wrote, “rather than a demonstration of al-Qaeda’s prowess, as some scholars view it,” the organization’s expansion was “in fact a sign of great difficulties.” Through expansion, he continued, al-Qaeda “has been considerably weakened.”126

But the principle of “centralization of decision and decentralization of execution” proved to be well suited to the organization’s strategy of establishing affiliations. The primary responsibilities of al-Qaeda’s leadership, according to this model, are to provide strategic guidance to affiliates and to advise them on major personnel and operational decisions, including the appointment of local leaders. The affiliates are then charged with putting al-Qaeda’s strategic plan into action. In doing so, the affiliates are given considerable autonomy with only limited oversight. This management structure, which closely mirrors al-Qaeda leadership’s relationship with cell leaders tasked to carry out specific attacks, has allowed the group to maintain command and control of the expanding organization. The leadership’s role in determining the military, political and propaganda strategy of the organization allows it to shape the behavior of affiliates, to mitigate preference divergence, and to avoid the kind of strategic incoherence that could taint al-Qaeda’s global image. Al-Qaeda Central’s involvement in selecting or at least approving the appointment of its affiliates’ emirs similarly reduces the likelihood that commanders will deliberately deviate from al-Qaeda’s strategic guidance.

Meanwhile, al-Qaeda’s decentralized approach positioned the organization to more effectively deal with communications barriers between the leadership and its affiliates. Since al-Qaeda Central’s role is restricted to providing guidance to affiliates on strategy and major personnel and operational issues, the amount of communication needed between the leadership and affiliates is fairly limited. It seems, though, that in the post-Edward Snowden world, al-Qaeda may be capable of communicating with its affiliates daily if need be.127 Moreover, because al-Qaeda has authorized its affiliates to adapt strategic plans to local contexts, the organization as a whole remains flexible. This “glocalized” model—a global strategy and outlook integrated into a local environment—has also served as an additional buffer against preference divergence.

Al-Qaeda Central has, in many regards, effectively managed its affiliates. But some affiliates have engaged in behavior that contravenes al-Qaeda’s objectives and the group’s overall brand. In the mid-2000s, AQI’s brutal violence and sectarian tendencies illustrated how harmful such deviance could be to the organization. Al-Qaeda Core attempted to “rebrand” the organization after AQI’s failure. Extreme preference divergence emerged again under ISIS, ultimately producing a complete breakup between al-Qaeda and ISIS.

Rather than over-interpreting well-known cases in which preference divergence between al-Qaeda and its affiliates produced open conflict, it is worth asking why this does not occur more frequently. Al-Qaeda’s internal documents, including the trove of information seized from bin Laden’s Abbottabad compound, contain the strongest evidence of how al-Qaeda maintained relative organizational cohesion with its affiliates. A small subset of the Abbottabad documents –17 documents released in 2012—was initially used to advance the theory that al-Qaeda’s senior leadership was out of touch with and had lost control of its affiliates.128This early theory proved to be misleading. At the time, Bruce Hoffman argued that public pronouncements by individuals who did not have the opportunity to view the entirety of the Abbottabad document collection should have been far more cautious, especially since their assessments were at odds with the initial conclusions drawn by intelligence officials. Indeed, the early pronouncements by intelligence officials who reviewed the documents, which appeared in print even before the theory emerged that the documents showed that al-Qaeda Core had lost touch, held that they showed bin Laden to be highly involved and perhaps even a “micro-manager.”129

These discrepancies were resolved when new tranches of documents were released—in 2015, 2016, and 2017. The new documents illustrated bin Laden and other core al-Qaeda leaders’ extensive involvement in—and sometimes micro-management of—affiliates’ strategic and operational decisions. It also became clear that al-Qaeda’s chain of command was still intact, despite leadership losses suffered by the group prior to 2011, and that affiliates and operational commanders generally considered bin Laden’s directives and advice binding. The insights that the Abbottabad documents have provided include the following revelations:

  • Around May 2010, bin Laden ordered a senior al-Qaeda commander to establish external operations wings throughout Africa that would allow al-Qaeda to target Western and U.S. interests across the continent.130Abdelmalek Droukdel was charged with directing external operations in North Africa, while Shabaab was given responsibility for the Horn of Africa, and Yunis al-Mauritani was given control of the rest of Africa. In the years following bin Laden’s directive, al-Qaeda affiliates in Africa carried out several sophisticated attacks against Western targets, including the Westgate Mall massacre in Nairobi and the siege on the In Amenas gas facility in southern Algeria.
  • Bin Laden was directly responsible for determining al-Qaeda’s policy toward state actors, including their truce negotiations with Pakistan’s Inter-Services Intelligence Agency, as well as separate talks with Nawaz Sharif’s brother in his capacity as the Governor of Punjab. Bin Laden also often instructed affiliates to refrain from targeting states with which al-Qaeda was not engaged in active conflict. In an October 2007 letter to Abu Ayyub al-Masri, AQI’s war minister, bin Laden called for AQI to avoid carrying out attacks in Turkey, “unless there is a chance for a large operation against the Jews or the Crusaders.”131 He also advised Masri not to target or threaten the Iranian regime, as Iran served as a “main artery for funds, personnel, and communication” for al-Qaeda.132  In several other letters written around 2010, al-Qaeda’s senior leadership and affiliates discussed the merits and religious legitimacy of a truce, which was ultimately approved, between al-Qaeda in the Islamic Maghreb (AQIM) and the Mauritanian government.133 Both AQIMand AQI appear to have followed Bin Laden’s guidance. Abu Muhammad al-Adnani, a former AQI member who became ISIS’s chief spokesman, said in a May 2014 statement that AQI had complied with bin Laden’s request not to target Iran, prior to that organization splitting from al-Qaeda.134 Similarly, AQIM refrained from targeting Mauritania for several years following internal deliberations about the truce.135
  • Al-Qaeda’s senior leadership engages in an extensive process of internal deliberation before making decisions, and sometimes consults leaders of affiliates about other affiliates’ affairs. A 2010 letter from Shabaab emir Ahmed Abdi Godane explained that Atiyah Abd al-Rahman and Abu Yahya al-Libi, two senior al-Qaeda officials based in Afghanistan/Pakistan, were “tasked” (presumably by bin Laden or Zawahiri) to write a report on the prospective Mauritanian truce from an Islamic legal perspective.136 The report was to be submitted to al-Qaeda’s leadership, which would discuss the matter further and convey its decision to Abdelmalek Droukdel. In the letter, Godane weighed in on the prospective truce as well, which indicated that the leaders of al-Qaeda’s affiliates were consulted on major strategic issues, even if these issues did not directly impact them. As documents related to al-Qaeda Core’s recent dispute with Syrian affiliate Hayat Tahrir al-Sham make clear, this practice continues today.
  • Bin Laden involved himself in tactical and operational decisions, which is why some in the intelligence community characterized him as a micromanager. For instance, in late 2010, bin Laden wrote two letters to Atiyah instructing his subordinates to move al-Qaeda operatives out of North and South Waziristan, two tribal agencies that were under constant surveillance by American drones, and to safer locations in Pakistan and the eastern Afghan provinces of Nuristan, Kunar, Ghazni and Zabul.137
  • Relatedly, bin Laden was intimately involved in personnel decisions, including the vetting of emerging leaders. One telling exchange involved Anwar al-Awlaki, the prominent American-born cleric who had joined AQAPin the late 2000s. With Awlaki’s star rising, AQAP emir Nasir al-Wuhayshi suggested that he step aside and allow Awlaki to take over as AQAP’s leader. Wuhayshi argued that this would allow al-Qaeda to capitalize on Awlaki’s popularity.138 Bin Laden responded in an August 2010 letter to Atiyah, instructing him to tell Wuhayshi to remain AQAP’s leader. Bin Laden also requested that Wuhayshi provide bin Laden with Awlaki’s resume, as well as specific reasons why Wuhayshi recommended Awlaki.139 This letter reflected bin Laden’s cautious approach to the selection of al-Qaeda leaders, as well as his wariness of Awlaki.
  • Though bin Laden and other al-Qaeda leaders based in Pakistan experienced challenges trying to communicate with affiliates and operatives in the Middle East and North Africa, they developed a way to overcome these difficulties. For instance, Atiyah served as an intermediary between bin Laden and al-Qaeda’s affiliates in Yemen, Somalia and North Africa. The decision to create a degree of distance between bin Laden and al-Qaeda’s affiliates was probably intended to reduce the chances that bin Laden’s communications would be intercepted and his location revealed. In a letter, bin Laden explained that the two couriers whom he used to pass statements to the media were only willing to carry messages every three months, and he asked a subordinate to identify other means of publicizing his statements.140

The Abbottabad documents, as well as other primary source materials, offer additional insight into the relationship between AQI and al-Qaeda’s senior leadership. AQI’s insubordination at the height of the Iraq war, which prompted rebukes from Zawahiri and Atiyah, has long been cited as evidence that al-Qaeda Central maintained little to no control over its affiliates. Indeed, some have argued that even after Zarqawi’s death and prior to Abu Bakr al-Baghdadi’s ascendance, al-Qaeda Central could not rein in its Iraqi affiliate. Further, some observers have argued that al-Qaeda’s Iraqi affiliate declared the establishment of an Islamic state in Iraq in October 2006 without consulting bin Laden, Zawahiri or other al-Qaeda leaders.141 The Abbottabad documents, however, suggest that coordination between al-Qaeda Central and AQI after Zarqawi’s death and prior to bin Laden’s was more robust than previously assumed. For instance, as previously noted, Abu Muhammad al-Adnani said in a 2014 statement that the Iraqi affiliate had eventually complied with bin Laden’s 2007 mandate to stop targeting or threatening Iran.142 (While ISIS’s idea of compliance may differ from our own, Adnani’s statement at least shows that al-Qaeda’s directives were able to influence its actions while it remained an affiliate.) In another 2007 letter, bin Laden instructed Zawahiri to “remove ambiguity” concerning al-Qaeda’s ties with the Islamic State of Iraq (ISI)—the name by which al-Qaeda in Iraq was known at the time—and to come to the defense of ISI in his future public statements.143 A letter from bin Laden to an unknown recipient, written sometime after April 2010, reveals the most about continuity in the al-Qaeda-ISIrelationship.144 In the letter, bin Laden commented on reports of the deaths of ISI’s emir and war minister, and discussed al-Qaeda’s succession plan for its affiliate, wherein ISI would establish a “temporary administration” to manage the organization’s affairs while ISI and al-Qaeda Central worked to appoint a new emir.

These revelations from the Abbottabad documents highlight the need for a more nuanced assessment of the historical relationship between al-Qaeda Central and its Iraqi affiliate. There is little doubt that al-Qaeda’s senior leadership faced persistent struggles in preventing AQI/ISI from acting on its more destructive impulses. Similarly, al-Qaeda’s leadership experienced difficulties communicating with its Iraqi affiliate, which likely further affected the former’s ability to shape events in Iraq. At the same time, though, AQI still complied with some key instructions from al-Qaeda Central, and bin Laden retained the ability to appoint the group’s leaders. Only in late 2013, when Abu Bakr al-Baghdadi openly defied Ayman al-Zawahiri’s guidance concerning the organization’s expansion into Syria, did the relationship between al-Qaeda Central and its Iraqi affiliate fray completely.

The Abbottabad documents also clarify the details of another relationship: al-Qaeda Central’s relationship with Shabaab prior to the latter’s February 2012 announcement of affiliation with al-Qaeda. The Combating Terrorism Center’s report, Letters from Abbottabad, concluded that bin Laden was wary of formalizing al-Qaeda’s relationship with Shabaab because he saw Shabaab’s “poor governance and inflexible administration of hudud” as a potential liability for al-Qaeda’s brand.145 The report, which based its findings on an August 2010 letter from bin Laden to Godane, also suggested that bin Laden may have been stringing Shabaab along in order to ensure that Shabaab continued to provide al-Qaeda with funding, even though al-Qaeda had no intention of making it an affiliate.

Subsequently released documents show that at the time of bin Laden’s letter to Godane, al-Qaeda Central had already privately accepted Shabaab’s bayat, thus making it an undeclared—but nonetheless official—al-Qaeda affiliate. For instance, Godane was consulted on the merits of the Mauritanian truce proposal, a sensitive subject that would have only been shared with official affiliates.146 Similarly, in a letter to Atiyah written in 2010, bin Laden discussed how Shabaab and AQIM could work to obtain pledges of bayat from other actors in their respective theaters who supported the jihadist cause.147 The fact that bin Laden mentioned Shabaab alongside AQIM, which had publicly joined al-Qaeda in 2007, and wished to advise Shabaab on expanding its network, makes clear that al-Qaeda already considered the Somali group to be a bona fide affiliate.

These findings cast bin Laden’s directive to Shabaab to conceal its ties with al-Qaeda in a different light. Bin Laden’s efforts to mask the Shabaab-al-Qaeda relationship were likely intended to help Shabaab develop its network without attracting the attention of counterterrorism forces or scaring off local allies. Evidence gathered prior to the Abbottabad raid also supports this interpretation. In August 2010, the Long War Journal reported that al-Qaeda officials told Shabaab to “maintain a low profile on al Qaeda links,” and that al-Qaeda reasoned that any public statements linking it to Shabaab would “draw international scrutiny” to the Somali group’s activities.148 Bin Laden’s words in his letter to Godane in 2010 are consistent with this view. He wrote that once al-Shabaab’s relationship with al-Qaeda “becomes declared and out in the open, it would have the enemies escalate their anger and mobilize against” it.149

Al-Qaeda’s Covert Growth Strategy

Al-Qaeda’s efforts to mask its ties with Shabaab foreshadowed the strategy that al-Qaeda would adopt after the Arab Spring. The collapse of autocratic regimes in Egypt, Tunisia, and Libya presented al-Qaeda with an unprecedented opportunity to expand its presence into countries that had previously been difficult to penetrate. Al-Qaeda also understood that it had to be cautious as it built its networks in North Africa. Any public advertisement of its activities in the region risked triggering attention from local and international security forces. Al-Qaeda did not want to risk having its nascent affiliates outlawed before they hit a critical mass. Al-Qaeda, therefore, opted for a covert growth strategy. The group would deploy envoys to countries affected by the Arab Spring and establish affiliates there, but no public announcement about these new relationships would be made. The covert affiliates—which included Ansar al-Sharia in Tunisia, the Ansar al-Sharia factions in the eastern Libyan cities of Benghazi and Derna, and Jabhat al-Nusra in Syria—were instructed to mask their links with al-Qaeda.

Today, a sizable body of evidence highlights al-Qaeda’s covert growth strategy in the post-Arab Spring period and its ties with affiliates, all of which were once covert. In 2013, Zawahiri wrote a letter scolding Abu Muhammad al-Julani, the emir of Jabhat al-Nusra, for publicly revealing the Syrian organization’s ties with al-Qaeda without first asking permission from al-Qaeda Central.150 Meanwhile, al-Qaeda’s ties with Ansar al-Sharia in Tunisia became increasingly clear by 2013. The Tunisian government had captured documents, subsequently reported in the Tunisian media, showing that Abu Iyadh al-Tunisi, Ansar al-Sharia’s emir, had secretly pledged allegiance to Abdelmalek Droukdel, AQIM’s emir.151 Additionally, a 2012 report produced by the Federal Research Division of the Library of Congress detailed al-Qaeda’s extensive activities and network in Libya, including its ties with Ansar al-Sharia.152

In the immediate post-Arab Spring period, however, analysts were slow to recognize the relationship between al-Qaeda Central and its covert affiliates. Ansar al-Sharia groups in both Tunisia and Libya were labeled localized jihadist groups that shared al-Qaeda’s ideology, but operated independent of al-Qaeda’s command structure.153 The question of al-Qaeda’s links with its covert affiliates in Libya became highly politicized following the 2012 attack on the U.S. consulate in Benghazi. While the intelligence community immediately concluded that al-Qaeda had been involved in the attack,154 spokespeople for the Obama administration initially declared that the attack occurred when spontaneous protests escalated into violence. Numerous journalists and analysts subsequently repeated the line that Ansar al-Sharia in Benghazi and Derna were “purely local extremist organizations.”155

Why did some observers initially conclude that the Ansar al-Sharia factions in Libya and Tunisia were not linked organizationally to al-Qaeda? At least three factors explain this error. First, al-Qaeda was largely successful in masking its ties, at least initially, with its covert affiliates. As one of the authors of this article noted at the time, terrorism analysts were “stuck reading shadows” as they tried to assess the relationship between al-Qaeda and jihadist groups that had popped up in Libya, Tunisia and Syria.156 With only incomplete and ambiguous information about Ansar al-Sharia’s origins and relationships, observers resorted to what had become a default assessment about the jihadist movement: that al-Qaeda Central possessed little control over militant groups operating outside Afghanistan and Pakistan.

Second, the analytic community’s misguided view of how the Arab Spring would impact the jihadist movement may have led many to overlook key shifts in al-Qaeda’s strategy. As autocratic regimes in Egypt and Tunisia succumbed to the pressure of largely peaceful protest movements, analysts, pundits and journalists came to an early consensus that al-Qaeda’s revolutionary model, which revolved around the notion that only violence could uproot regimes, had lost its appeal in the Muslim world. The Arab Spring and bin Laden’s death were perceived as the “final bookends” to the war against al-Qaeda.157 Such an optimistic view failed to seriously consider how al-Qaeda might seek to exploit the tumult and instability that followed the Arab Spring revolutions. This impulse to view regional events through an optimistic lens where jihadism was concerned, coupled with the assumption that the organization was struggling to assert its relevance in this new environment, may well have helped lead the analytic community to miss critical signs that al-Qaeda was pursuing a covert growth strategy as it sought to gain a foothold in post-revolutionary countries.

Third, analysts adopted an overly simplistic view of al-Qaeda’s global strategy, which prevented them from understanding how Ansar al-Sharia in Tunisia and other covert affiliates fit into the organization’s growth model. Many observers asserted that al-Qaeda was exclusively focused on striking the “far enemy” (i.e., the United States and its allies in Western Europe), and was largely disinterested in carrying out governance projects in the Middle East. Ansar al-Sharia in Tunisia, however, had a locally-oriented strategy—which one of us analyzed as a progression from dawa to hisba to jihad in one of the earliest full-length studies on the group158—that appeared incongruent with al-Qaeda’s global activities and aims. President Obama articulated this sentiment in a May 2013 speech on terrorism in which he noted that the jihadist movement in the post-Arab Spring period consisted of “collections of local militias or extremists interested in seizing territory” that operated “perhaps in loose affiliation with regional networks.”159

This limited view of al-Qaeda’s strategy persists to this day. In a 2016 monograph heralding al-Qaeda’s decline, scholar Jarret Brachman argued: “Al-Qaeda’s primary affiliates have turned inward and are concentrating more on making territorial gains locally, appealing to the local populous [sic] and consolidating themselves through low-level criminality than they are on advancing al-Qaeda’s grandiose global agenda.”160 Georgetown University scholar Daniel Byman has similarly asserted that al-Qaeda is on the decline because its “affiliate organizations focus on their local and regional concerns rather than attacking the West.”161

Such assessments define al-Qaeda’s strategy in the post-Arab Spring period too narrowly, and thus overlook both the organization’s rationale for violence against the West, as well as the possible ways in which the Arab Spring may have altered these dynamics. Al-Qaeda’s strategy of attacking the “far enemy” was motivated by a strategic belief that al-Qaeda could only topple local regimes and establish Islamic emirates if it first crippled the West, because Western military and economic support would prevent “near enemy” regimes from falling. The “far enemy” strategy was, in other words, a means to an end, rather than an unalterable commitment to prioritize attacks against the West. The events of the Arab Spring shifted al-Qaeda’s calculus, because it revealed that Western states would not necessarily step in to save the autocratic regimes against which al-Qaeda also wages jihad. In the case of Libya, Western governments actually stepped in to topple Qaddafi; while they did not intervene at all when Hosni Mubarak fell in Egypt. The enormous opportunities that exist for al-Qaeda in the post-Arab Spring world mean that attacks against Western countries may be deprioritized for the time being, as the jihadist movement exploits opportunities in the region.


Al-Qaeda’s new opportunities for growth, of course, presented their own set of challenges. Following a period of mounting tensions between al-Qaeda and ISIS, in February 2014, al-Qaeda expelled its Iraqi affiliate from the organization. The dramatic rise of ISIS thereafter led many observers to conclude that the breakaway group had usurped its parent organization between 2014 and 2016, and that various al-Qaeda branches would likely break away and join ISIS. We have already written a lengthy analysis in these pages about how al-Qaeda survived the ISISchallenge, after having survived two other significant challenges (the black mark on the organization’s reputation after AQI’s 2007-09 defeat and the Arab Spring revolutions).162 In successfully navigating the ISISchallenge, al-Qaeda again proved resilient. This time, however, it showed resilience in an area where analysts had previously been skeptical about its capabilities: in the relationship between parent organization and affiliates.

There are again storm clouds surrounding al-Qaeda’s core-affiliate relations, as its leadership clashes with Syrian affiliate Hayat Tahrir al-Sham (HTS).163 Most analysts have interpreted this dispute in a manner consistent with the field’s ingrained tendency to perceive al-Qaeda’s senior leadership as marginal. But one immutable lesson of past struggles within al-Qaeda and other jihadist organizations is that their meaning is not best understood through the lens of analysts’ immediate response, but their significance becomes clearer over time. Suffice it to say that disputes like this raise the risk for al-Qaeda that, if insubordination and rebellion goes unpunished, other branches will perceive the cost of acting against al-Qaeda Core’s directives as lower.164Conversely, al-Qaeda’s multiple networks are interlocking. See, for example, the relationship between Shabaab and al-Qaeda in the Arabian Peninsula, or between AQIM and the Sahelian jihadists. If al-Qaeda’s affiliates step out of line, as Boko Haram did, then al-Qaeda Core can withdraw its support and invest its resources with competitor organizations. Only time will tell which of these two countervailing considerations will prove more decisive in resolving the conflict with HTS, and managing other affiliate relationships beyond Syria.

While questions persist about the direction that the jihadist movement will take—questions magnified by the fact that jihadist organizations are clandestine in nature—al-Qaeda has, thus far, been able to sustain an overall trend toward greater relevance. This article outlines the formula that the organization has followed to remain important. As we examine current and future challenges facing the organization, it is crucial to bear in mind the logic of al-Qaeda’s organizational design, and also the various advantages that spring therefrom. In order to stop almost willfully perceiving al-Qaeda as weak, we must continue to work towards better understanding how the organization actually functions. Equipped with more accurate analyses, we will put ourselves in a position to more effectively weaken al-Qaeda.

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