Al-Qaeda’s Second Wind: The Post-Withdrawal Resurgence and Its Threat to U.S. Security

Uma Miskinyar

Introduction

The power vacuum left by the U.S. withdrawal from Afghanistan has reshaped Central Asia’s balance of power in ways that pose significant challenges to U.S. national security, causing a tumultuous disruption to the West. The rise of militant Islamist groups has exponentially grown along the Afghanistan-Pakistan border, resulting in hundreds of civilian casualties, posing the question: does the resurgence of Al-Qaeda mean anything to America?

The Reconstitution of Al-Qaeda and the Role of Iran

Al-Qaeda, once thought of as fractured, has quietly reconstituted under de-facto leader Saif al-Adel, now operating from Iran, a nation whose nuclear ambitions and proxy networks challenge U.S. interests. Tehran’s sheltering of Al-Qaeda’s leader appears to be a calculated strategy to use terrorism as a geopolitical pressure valve while maintaining plausible deniability. Such a collaboration accentuates a dangerous convergence between state and non-state actors, blurring the line between statecraft and subversion.

For the United States, Iran’s covert facilitation of Al-Qaeda’s leadership structure introduces a dual-front security concern: a nation already challenging U.S. interests through its nuclear ambitions and proxy militias now becomes an indirect enabler of terrorism, effectively multiplying the threat landscape confronting Washington. It not only weakens U.S. deterrence but also erodes on-the-ground intelligence reach across the Middle East and South Asia. If Iran’s quiet protection of Al-Qaeda signals a new axis of convenience, Russia and China have ensured that the vacuum surrounding Afghanistan becomes a proving ground for their own ambitions.

Whether Al-Qaeda’s resurgence leads to another era of global terror or remains a contained insurgency will depend not on military strength, but on whether great powers can sustain the political will to act collectively against a shared threat.

Regional Power Shifts: Russia, China, and Iran’s Expanding Influence

Russian influence remains entrenched through the deployment of the 201st Motor Rifle Division and disinformation campaigns that exploit Tajikistan’s dependence on Moscow for security and economic support, reinforcing a regional status quo favorable to Moscow. At the same time, Beijing’s expanding footprint through infrastructure investments, security partnerships, and diplomatic engagement, combined with Iran’s soft power initiatives, further erodes Western influence, creating a complex web of competing actors in which U.S. strategic interests are increasingly challenged. This convergence of adversarial strategies underscores that Al-Qaeda’s resurgence is not merely a local phenomenon but is being shaped and shielded by broader regional power dynamics, complicating counterterrorism efforts and the projection of U.S. influence.

The Taliban’s Return and the Rebirth of Safe Havens

Meanwhile, the Taliban’s return has turned Afghanistan into permissive terrain for extremist resurgence, with training camps, weapons caches, and smuggling routes rebuilding under the radar of a limited U.S. on-the-ground intelligence presence. Among dozens of militant factions, the Baluchistan Liberation Army (BLA), operating under its militant wing known as the Majeed Brigade, has expanded rapidly since 2024. Responsible for the March 2025 hijacking of the Jaffar Express and a series of suicide attacks near Karachi, it was designated as a Foreign Terrorist Organization by the U.S. Department of State in August 2025. The BLA is a singular example of growing insurgency within Central and South Asia, a telltale sign of the Taliban’s tolerance of militant groups despite repeated pledges and U.S. counterterrorism efforts to curb resurgence and ultimately crack down on militant networks operating in the region. For Washington, this resurgence reflects the difficulties of sustaining regional visibility in the absence of a direct presence. With limited on-the-ground access, understanding the pace and direction of militant activity becomes increasingly dependent on indirect sources. Even if technical intelligence capabilities in the region could remain strong, such monitoring offers a different kind of awareness– one that lacks the texture and immediacy of human insight on the ground.

Afghanistan’s Deepening Instability

The instability radiates inward to Afghanistan, where Al-Qaeda, sheltered by the Taliban, reestablished eight new training camps and five madrasas along the Panjshir Valley north of Kabul, a number suspected to have risen since August 2024. Maisam Nazary, top diplomat for Afghanistan’s National Resistance Front (NRF), warned, “The Taliban have even allowed al-Qaeda to build bases and munitions depots in the heart of the Panjshir Valley…something unheard of, even in the 1990s.”

Since the Taliban’s return to power in 2021, militant activity across Central and South Asia has surged. Afghanistan’s porous borders and mountainous terrain have created a sanctuary for fighters moving in from the Arab world, Central Asia, and parts of Europe. Intelligence estimates now suggest at least 21 active terrorist organizations inside the country. The result is a state governed by disorder: an unmonitored battlespace where regional militias, foreign fighters, and transnational jihadist movements coexist under minimal scrutiny. What was once a fragmented insurgency has evolved into a layered ecosystem of militancy, capable of projecting instability far beyond Afghanistan’s borders.

International Spread of Affiliated Terror Networks

Since its initial expansion following the Taliban’s resurgence in Afghanistan, terror groups have gained control over much of the country’s northern border. According to the Special Inspector General for Afghanistan Reconstruction, the Taliban has targeted Islamic State elements and other factions, while also tolerating the presence of Al-Qaeda and the TTP. In 2024, de-facto Al-Qaeda leader Saif al-Adel explicitly called for foreign fighters to migrate to the Panjshir Valley, preparing to launch attacks against the West.

Beyond Afghanistan, efforts to counter Al-Qaeda affiliates have met with mixed success, illustrating that the group’s threat extends far beyond U.S. borders. On October 2, U.S. Central Command targeted Ansar Islam in Syria, killing Muhammad Abd al Wahhab al Ahmad, a senior Al-Qaeda attack planner traveling through Idlib province. Meanwhile, the United States and France have largely disengaged from direct counterterrorism operations in the Sahel to combat Jama'at Nasr al-Islam wal-Muslimin (JNIM), an Al-Qaeda affiliate that has grown fivefold since its inception in 2017, marking a complete withdrawal from Mali and neighboring states after years of deteriorating relations with regional juntas. Using weaponized religious narratives and corrupt funding networks to consolidate power, JNIM has become one of Africa’s deadliest militant groups and seeks to expand into West African coastal states. Preventing the emergence of another Al-Qaeda-affiliated quasi-state has never been more complicated, as external disengagement leaves regional regimes increasingly dependent on Russian-backed forces whose priorities center on regime protection rather than civilian security, stretching U.S. counterterrorism efforts and resources whilst creating space for Russian-backed forces to fill the security vacuum.

To the public, this proliferation underscores Al-Qaeda’s decentralized model. Each offshoot stretches U.S. counterterrorism efforts thinner, turning a global network of terror into a constantly shifting, multi-front challenge.

The Return of the Homeland Threat

Now, just over 24 years after the tragic day of September 11, 2001, the United States faces a troubling question: is history in danger of repeating itself?

Following the U.S. withdrawal of troops from Afghanistan in 2020, emerging terror threats posed by Al-Qaeda were among the key factors shaping America’s renewed emphasis on lethality and domestic security over global partnerships. A power vacuum with far-reaching effects, Al-Qaeda’s resurgence has not always received full attention, despite repeated warnings from counterterrorism experts to refocus on Central and South Asia. The boundaries between international and domestic terrorism have blurred. Historically, the United States has strengthened its defense capabilities abroad to prevent threats from reaching its civilians. With such an advanced defense posture, the United States continues its role as a global protector, but threats inevitably follow to challenge it.

In a press release from the Office of the Director of National Intelligence (ODNI) in September 2025, the U.S. National Counterterrorism Center named Al-Qaeda as an urgent threat to our homeland, stating: “Al-Qa‘ida’s resurgence of calls for attacks in the homeland highlights its persistent and enduring threat to the country… [Al-Qaeda in the Arabian Peninsula] celebrating recent attacks in the U.S. and calling on its supporters in the homeland to conduct attacks using simple attack methods, such as firearms, explosives, knives, vehicle-rammings, or Molotov cocktails.” Many of the suggested target themes in Al-Qaeda’s warnings align with the group’s post-9/11 plots in the homeland. As Al-Qaeda’s propaganda often underscores these concepts, they indicate potential targets that must be closely monitored. A wake-up call to the public, the release communicates the need for the United States to recalibrate its counterterrorism posture, merging domestic resilience with international. These developments suggest that the boundaries between global and domestic security are increasingly porous, demanding a more integrated policy response. 

Current U.S. counterterrorism engagement appears to operate through a decentralized framework, combining over-the-horizon capabilities, selective intelligence coordination, and economic measures such as targeted sanctions. However, with weakened ground networks and diminished local cooperation, Washington’s ability to preempt threats has eroded. NATO’s disengagement and the EU’s limited capacity for joint counterterrorism further exacerbate this gap, allowing extremist networks to exploit political vacuums faster than they can be filled.

What makes this new phase of terrorism particularly insidious is not simply Al-Qaeda’s persistence, but its transformation. Today’s threat does not mirror the centralized structure of the pre-9/11 network, but rather a diffuse constellation of semi-autonomous affiliates operating within digital, financial, and ideological gray zones. From Saif al-Adel’s coordination from within Iran to JNIM’s consolidation across the Sahel and AQAP’s renewed media outreach in Yemen, Al-Qaeda’s adaptability lies in its ability to weaponize instability itself. This decentralization could complicate U.S. intelligence collection, as traditional metrics, training camps, leadership councils, and financing nodes no longer define the battlefield. In a world saturated by online radicalization, encrypted communication, and proxy warfare, the threshold for operational capability has drastically lowered. Consequently, the line between a “foreign” and a “domestic” threat has blurred, creating a strategic paradox: America’s success in dismantling centralized networks has birthed a new era of horizontal, self-sustaining extremism—one far harder to detect, deter, or destroy.

Strategic Reflection: Lessons, Costs, and Future Direction

The National Counterterrorism Center’s press release communicates the importance of understanding adversaries, emphasizing that the U.S. ability to safeguard our nation relies on its ability to define its motives. Military strategists argue there is no excuse for strategic surprise, but in practice, ambiguity persists. Countering terrorism remains more opaque than ever in the realm of foreign affairs. Yet even in ambiguity, cooperation has yielded pockets of clarity, and some efforts have proven effective.

The U.S. spent trillions on the War on Terror and lost nearly 7,000 service members. Washington’s awareness of these costs has shaped counterterrorism strategy, making targeted drone strikes, a low-risk method of conventional warfare, the new norm for addressing direct threats. The vacuum left by the U.S. withdrawal from Afghanistan reshaped not only the balance of power in Central Asia, but also the psychology of the global security landscape. Where American presence once imposed a fragile order, ambiguity now reigns. The Taliban’s internal divisions, coupled with the competing ambitions of Iran, China, and Russia, have created overlapping spheres of influence where authority is contested and extremism quietly recalibrates. In this shifting terrain, Al-Qaeda has learned to adapt, not by rebuilding what it once lost, but by weaving itself into the fault lines of fragile states and unresolved conflicts.

This new iteration of Al-Qaeda is less visible, more patient, and far more integrated into regional dynamics than before. It thrives not on attention, but in areas with limited oversight. With U.S. on-the-ground operation-focused intelligence networks degraded and local partnerships weakened, the group has reemerged in the spaces between rival interests, exploiting gaps in coordination and trust. The Majeed Brigade’s designation is not merely symbolic of this trend but emblematic of a larger strategic evolution—one where jihadist movements have traded spectacle for endurance, choosing to survive within the noise of competing power plays rather than stand apart from them.

The United States now faces a paradox: the same restraint meant to end “forever wars” has created permissive conditions for terrorism’s quiet return. Washington must therefore recalibrate—not through military surge, but by rebuilding regional intelligence networks, strengthening multilateral counterterrorism frameworks, and investing in local governance resilience. The challenge ahead is not to reoccupy, but to reengage.

For U.S. national security, the implications reach beyond counterterrorism. The erosion of ground presence has left a void in situational awareness that technology alone cannot fill. The threat has become more abstract: measured less by immediate attacks and more by the slow diffusion of influence, ideology, and access. The danger is not that Al-Qaeda will strike tomorrow, but that by the time its next move is recognized, it will already have reshaped the terrain on which the United States must respond. The most dangerous threats often grow unseen, shaping the battlefield long before they are recognized.