The Threat of Al Qaeda and ISIS-K in Taliban-Controlled Afghanistan


November 4, 2021

A year and a half before their takeover of Afghanistan in August, the Taliban signed a deal with the U.S. stipulating that they would not allow any individuals or groups to use Afghan soil “to threaten the security of the United States and its allies.”

Today, with the Taliban in control and U.S. troops withdrawn after two decades of war and insurgency — a moment that FRONTLINE correspondent Najibullah Quraishi examined in the October 2021 documentary Taliban Takeoverthose concerns remain. On Oct. 26, a top Pentagon official said terrorist groups in Afghanistan could be capable of launching attacks on the West and its allies within six months to two years.

Among them: Al Qaeda, the terrorist group previously harbored by the Taliban that orchestrated the Sept. 11, 2001, attacks on the United States; and ISIS-Khorasan, the South Asian affiliate of the self-declared Islamic State.

How much of a threat do these groups pose to the U.S. and its allies, as well as to regional stability? What kind of counterterrorism strategy has President Joe Biden said the U.S. will pursue in Afghanistan? Here’s a look at the current situation.

The Taliban

While the Taliban is considered a threat to the rights and liberties of women and minorities within Afghanistan, the group isn’t likely to launch direct attacks on the West. The danger, for the region and the world, is reflected in the 2020 deal with the U.S., in which the U.S. called on the Taliban to “send a clear message that those who pose a threat to the security of the United States and its allies have no place in Afghanistan.”

But experts told FRONTLINE that expecting the Taliban to prevent Afghanistan from being used as a staging ground by terrorist groups is not realistic.

“I think any promises along those lines were meaningless,” said Seth Jones, a counterterrorism expert and the director of the International Security Program at the Center for Strategic and International Studies, a bipartisan think tank.

Jones pointed out that Al Qaeda fighters fought alongside the Taliban in offensives. And when the Taliban formed its de facto government, at least two men in the cabinet, Sirajuddin Haqqani and Khalil Haqqani, were on the U.S. State Department’s most wanted list and described as having close ties to Al Qaeda.

Amira Jadoon, assistant professor at the Combating Terrorism Center, part of the U.S. Military Academy at West Point, said the Taliban’s current quest to be recognized by the international community as a legitimate government might make them “steer clear from actively harboring terrorist groups, because logically it doesn’t serve their political goals.”

But even if the Taliban were willing to prevent terrorist groups from using Afghan soil to launch attacks, experts said they have limited capacity. Jadoon noted that the Taliban are focused on figuring out how to govern the country, and their experience as a successful insurgent group doesn’t necessarily translate to becoming a state actor in charge of constraining terrorism.

Read more: ‘Brink of Collapse’: How Frozen Assets & Halted Foreign Aid Are Impacting the Afghan People 

Other obstacles to the Taliban successfully monitoring terrorist activity include the Taliban’s demonstrated inability to prevent terrorist attacks within Afghanistan’s borders, such as the deadly Aug. 26 bombings claimed by ISIS-K that killed 13 U.S. troops and at least 170 Afghans at and near Kabul’s airport, and Afghanistan’s terrain of deserts, mountains and caves.

“It’s very difficult to keep people outside of Afghanistan if people want to come in,” said M. Lyla Kohistany, a former U.S. naval intelligence officer and CEO of Task Force Pineapple, an effort by U.S. veterans and volunteers to help evacuate and resettle at-risk Afghans, especially Afghan special operations forces. “The borders are porous.”

In addition to the airport bombings, Kohistany pointed to a series of bombings carried out inside Afghanistan by ISIS-K in recent weeks, including an Oct. 15 explosion in the southern city of Kandahar, long considered the Taliban’s stronghold.

“This is ISIS-K showing through force that, in fact, it’s virtually impossible for a group like the Taliban — without the kinds of assets that the United States and the international community have — to keep them from using Afghanistan in the future as a safe haven, a sanctuary to conduct transnational terrorist attacks,” Kohistany said.

“What is likely to happen is that Afghanistan will end up being a passive sponsor of terrorism,” Jadoon said.

Al Qaeda

How much of a danger Al Qaeda — the transnational terrorist group that launched the deadliest terror attacks on U.S. soil in American history — poses to the U.S. has evolved over the past 20 years. Counterterrorism efforts undertaken by the U.S. and its international and Afghan allies have diminished the group, especially through the targeting of senior leaders.

“Capacity-wise, Al Qaeda is not the Al Qaeda it was around 9/11,” Jadoon said. “The problem is that its ideology is strong, and its resolve is really strong, and it’s also become more decentralized and localized.”

A June United Nations report predating the withdrawal of U.S. troops estimated the current membership of Al Qaeda and its South Asian affiliate, Al Qaeda in the Indian Subcontinent, at anywhere from several dozen to 500 people, with Al Qaeda present in at least 15 provinces of Afghanistan. Kohistany said numbers alone don’t accurately reflect capability because they don’t account for different groups working together.

The report noted that historically strong ties between Al Qaeda and the Taliban — which have included leaders of Al Qaeda pledging their allegiance to the leaders of the Taliban — “remain close, based on ideological alignment, relationships forged through common struggle and intermarriage.”

Experts told FRONTLINE there has been no evidence those ties have been weakened or broken. In fact, Al Qaeda’s senior leadership released a statement after the last U.S. troops left Afghanistan congratulating the Taliban for its “historic victory.”

Read more: 17 Essential Documentaries on the War in Afghanistan — and Its Consequences

The Taliban taking charge of Afghanistan could provide Al Qaeda the opportunity to reconsolidate and strengthen, which could pose an increased threat to U.S. interests. “In the near-term, [Al Qaeda is] probably not a significant threat. But as time goes by, I think that threat is likely to increase,” said CSIS’ Jones. He said he was worried about Al Qaeda’s ability to launch external attacks increasing by 2022. “How much [the Taliban are] able to limit Al Qaeda activity will be a question mark.”


While the Taliban and Al Qaeda historically have had close ties and a mutually beneficial relationship, ISIS-K has viewed the Taliban as its strategic rival. ISIS-K labeled the Taliban a nationalist entity for wanting to govern Afghanistan only, Jadoon said, whereas ISIS-K’s goals have included transnational jihad and establishing a caliphate that supersedes national boundaries.

ISIS-K sees Afghanistan as a potential staging ground and “like a beacon, in essence, for their ideology,” Kohistany said.

Since its inception, ISIS-K attracted disaffected members of the Afghan Taliban, Pakistani Taliban and other regional militant groups who felt their original organizations were not extreme enough, according to Madiha Afzal, a fellow at the Brookings Institution whose work focuses on the U.S. relationship with Afghanistan and Pakistan, as well as on extremism in South Asia.

In the 2015 documentary ISIS in Afghanistan, a senior ISIS-K commander told FRONTLINE correspondent Quraishi that he and others had been fighting a “holy war” as part of the Taliban, “But God says when there is a caliphate, you must join the caliphate.” Quraishi found that militants also defected from other groups because ISIS-K paid its fighters more.

“In some ways, the takeover of the Taliban makes it even more vulnerable to defections away from it to ISIS-K,” Afzal said.

Since the U.S. withdrawal, ISIS-K has sought to undermine the Taliban’s legitimacy in the eyes of Afghan citizens and the world by showing the Taliban incapable of constraining terrorism within Afghanistan, Jadoon said. ISIS-K’s instigation of sectarian violence — suicide bombings targeting ethnic minorities and Shiite mosques, ambitions of establishing a global caliphate, poaching militants ­— all make the group a threat to the Taliban, Jadoon said. “None of these goals or tactics are in the Afghan Taliban’s interests.”

The June U.N. report estimated ISIS-K’s core group at approximately 1,500 to 2,200 fighters. Jadoon said the number has grown since then — up to 5,000. Jadoon said ISIS-K also has formed logistical and operational alliances with other militant groups in the region, such as the Pakistan-based Lashkar-e-Jhangvi, which allows them to claim credit for more attacks.

If ISIS-K were to also leverage resources from the estimated thousands of remaining adherents of core ISIS, “you’re looking at a pretty sizable capability,” Kohistany said.


On Aug. 31, after the last U.S. troops left Afghanistan, President Biden said the fight against terrorism in Afghanistan would continue without a “ground war.”

“We have what’s called over-the-horizon capabilities, which means we can strike terrorists and targets without American boots on the ground — or very few, if needed,” he said in an address to the American public.

Jones, of CSIS, said there are distinct differences between the situation in Afghanistan and other places where the U.S. has used aerial surveillance and drone strikes to target suspected terrorists from the air. First, in countries including Somalia, Libya, Syria and Yemen, the U.S. has worked with partner forces on the ground to carry out counterterrorism strikes. Second, the U.S. has used bases in neighboring countries or on maritime vessels to launch aircrafts. Last, the U.S. has relied on existing intelligence infrastructures within the countries, sometimes with an American presence on the ground.

In Afghanistan, Jones said, the U.S. currently has none of these: no partner force, no nearby air bases and no intelligence network to tap into.

“This is unlike any major U.S. operation I have seen to conduct counterterrorism,” said Jones, who previously advised U.S. special operations in Afghanistan. “It’s a fiction that you can conduct any kind of a meaningful counterterrorism campaign based on purely flying aircraft over territory without nearby basing, without partner forces and without much intelligence infrastructure.”

Such conditions can carry “huge risks” and lead to “huge mistakes,” he said.

On Aug. 29 in Kabul, the U.S. launched a drone strike targeting members of ISIS-K, after the deadly bombings at Kabul’s airport. Investigations by The New York Times and other news organizations uncovered that the strike had instead killed Zemari Ahmadi, a worker for a U.S. aid group, as well as several children. On Sept. 17, the Pentagon acknowledged the strike was a “tragic mistake” and said it killed up to 10 civilians, including seven children.

While human rights groups have long criticized U.S. drone strikes for killing civilians, Afzal, of Brookings, said that because the Aug. 29 strike was so public and well-documented by media, it opened over-the-horizon operations to what could be a new era of scrutiny.

She also said over-the-horizon counterterrorism operations can only do so much. “Killing a target doesn’t do anything to the ideology of the group. It doesn’t target extremism.”

Priyanka Boghani

Priyanka Boghani, Digital Editor, FRONTLINE



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