The Return of Al Qaeda to Afghanistan: How Seriously to Take the Threat

Under Taliban rule, terrorist groups are once again flourishing.

Security forces control vehicles at a checkpoint as security measures tightened after a U.S. drone strike killed al-Qaeda leader Ayman al-Zawahiri in the capital Kabul, Afghanistan on August 3, 2022. (Photo by Haroon Sabawoon/Anadolu Agency via Getty Images)

MY PHONE BLEW UP in April 2021 after President Joe Biden ordered the withdrawal of American forces from Afghanistan. My contacts throughout the Afghan government asked for immediate meetings. While those of us working in the U.S. embassy in Kabul knew of the president’s deliberations, nobody was warned of his decision before he announced it to the world.

As a military diplomat, I tried to reassure jittery allies that we would continue to stand by them. Some Afghans were cocksure, predicting the Afghan government would defeat the Taliban, al Qaeda, and their Pakistani sponsors. Many senior-ranking Afghan National Army officers asked for visas to ensure the safety of their families so they could continue fighting. Other officials panicked, bargained, or eventually disappeared.

The reaction of Abdullah (not his real name) was different. He was a mid-ranking official at Afghanistan’s National Directorate of Security, the government’s premiere intelligence service, a mix of the FBI and CIA. As a young man, he was trained by the Soviets during their Afghan war. He survived the bloody infighting between the warring factions inside the Afghan Communist government, but left Afghanistan after the Taliban came to power, not returning until after 9/11. Of all my contacts, Abdullah, now in his sixties, knew Americans the best. He didn’t fawn over us, and he didn’t suffer fools.

As we sat inside the embassy, Abdullah sipped on his favorite scotch. I danced around the elephant in the room: our pending withdrawal. Finally, after a few minutes of small talk, Abdullah, in his usual blunt manner, asked me, “Will, when are you going to ask me about the U.S. withdrawal?”

I chuckled. “I’ll do it right now, brother. What do you think?”

“I think it is a mistake, obviously,” he told me matter-of-factly. “But that’s not important. What is important is this: When the Taliban take over again, they will bring al Qaeda with them, and you will be back to square one. This decision will eventually lead to a river of blood for everyone.”

Abdullah not only foretold his government’s fall but also the resurgence of al Qaeda in Afghanistan and the lack of options available to the United States to do anything about it. According to a recent United Nations report, al Qaeda is operating eight training camps in Afghanistan and maintains strong ties to the Taliban. Of course, the Taliban denies all of this, but there’s no reason to distrust the U.N. report—and no reason to be surprised by it.

“Afghanistan is al Qaeda’s crown jewel. They use it as a base to train and run their network,” said terrorism expert Sara Harmouch.

True to its name, al Qaeda (the base) uses its home territory in Afghanistan as a base to run its worldwide network, which has franchises in Africa, the Middle East, and throughout South Asia. While al Qaeda’s purported leader, former Egyptian special forces officer Saif al-Adel, is likely in Iran, other senior al Qaeda leaders, like Amin ul Haq, arrived in Afghanistan shortly after the Taliban’s victory.

Haq has deep ties to the region. He served as the head of Osama bin Laden’s elite Black Guard. In 2011, Pakistan released Haq because they “failed to prove any charge with his association” with bin Laden, a laughable statement considering his storied connections to the group. Haq, a trained doctor, is from Afghanistan’s restive Nangarhar province and fought the Soviet Union with Hezb-e Islami Khalis under Yunus Khalis, a man whom bin Laden affectionately referred to as “Father Sheikh.”

Haq is far from the only al Qaeda leader in Afghanistan. Others are members of the Afghan government. Sirajuddin Haqqani, the minister of interior and son of longtime bin Laden ally Jaluluddin Haqqani, has extensive and longstanding ties to al Qaeda. His ministry not only controls all of Afghanistan’s police but is also responsible for issuing passports—a fact that should send shivers down every American’s spine. Al Qaeda members are not just in Kabul; they’re in the provinces, too. Kapisa Governor Qari Baryal, who led an IED cell that killed one of my airmen, has extensive connections to al Qaeda.

It’s easy to overlook al Qaeda’s influence because figures like Haqqani and Baryal are mainly associated with the Haqqani Network and the Taliban, respectively. This is a fundamental error. Westerners often imagine that these groups are built like Western organizations, with clear organizational charts and chains of command. In reality, they mutually permeate each other. They share a history of fighting the Soviet Union, other Afghans, and the United States.

“Al Qaeda, the Taliban, and the Haqqani Network are inseparable, especially Taliban commanders on the ground, who are linked with al Qaeda through familial connections, like marriage,” said Ahmad Zia Seraj, the former head of Afghanistan’s National Directorate of Security, now a visiting professor at King’s College London. He could have also mentioned ethnic and tribal ties, as well as those based on friendship or political convenience or pledges of allegiance. As Mary Habeck, a scholar of Islamic extremism, noted shortly after the withdrawal,

every leader of al Qaeda has stated they are part of the Taliban; not “guests,” but made men in the Taliban with oaths of fealty (bay’at) to the head of the Taliban; oaths that al Qaeda’s leaders hold to be legally and religiously binding. These oaths bind the swearer into a hierarchical relationship with a commander that one must “hear and obey.”

Despite these groups’ close working relationships, the Biden administration feels confident about their over-the-horizon counterterrorism strategy, especially after the drone strike that killed former al Qaeda leader Ayman al-Zawahiri in August 2022. That strike, while tactically successful, should have alarmed the administration about the feasibility of their long-term strategy to keep America safe from terrorist threats emanating from Afghanistan.

First, Zawahiri was killed in a safe house owned by Sirajuddin Haqqani, underscoring their close ties. The Taliban still denies that Zawahiri was killed in Afghanistan, because doing so would admit that they violated (again) the Doha agreement with the United States by sheltering al Qaeda’s leader.

Biden’s over-the-horizon strategy also has fundamental flaws. While America’s intelligence community excels at the skills required to target, track, and fix targets, it no longer has the same capability to track terrorists in Afghanistan that it had when the United States had a presence in the country. No amount of technology makes it easier to see Afghanistan from the outside than from inside Afghanistan. The current strategy partly relies on kinetic strikes to keep terrorists at bay. But future drone strikes, like the one that killed Zawahiri, will almost certainly be launched from Pakistan. This essentially puts the strategy in the hands of a country that helped kill thousands of American soldiers throughout America’s twenty-year war in Afghanistan.

The current U.S. strategy also relies on the Taliban’s assistance in keeping a lid on al Qaeda and the Islamic State. (That’s a little like saying the FBI needs the KKK’s help to control the Aryan Nations.) The $2 billion in humanitarian aid sent to the Taliban since the fall of Kabul might be considered a bribe for peace—a similar gambit to the one Israel used to try to control Hamas before October 7. While al Qaeda has pledged not to conduct attacks from Afghanistan, they will almost certainly use their freedom of movement to train operatives and funnel them to their franchises. The United States has also likely joined forces with the Taliban to fight a mutual enemy, the Islamic State Khorasan Province. But ISKP’s staying power in Afghanistan highlights the fact that Afghanistan has once again become a breeding ground for terrorists.

“The Taliban’s victory in Afghanistan inspired other terrorist groups. They now think, if they can do it, so can we,” says Seraj, who reported last month that fifteen terrorist groups are operating in Afghanistan.

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THERE ARE CURRENTLY NO GOOD counterterrorism options, and with the return of great power competition, America’s national security bureaucracy has other priorities, as evidenced by the Defense Department’s decision not to teach any more personnel Pashto. Nevertheless, the first step in constructing a long-term strategy is admitting that the current one is bound to fail.

“How can we craft a viable counterterrorism policy without admitting the facts on the ground? In the long term, the only viable counterterrorism policy is resistance to the Taliban,” said Bill Roggio, editor of the Long War Journal. For twenty years, that resistance took the form of the Afghan government backed by the United States and our allies and partners, but that’s no longer an option. Now the Taliban are the government, and forces that are more sympathetic to America are in the resistance.

There are a few anti-Taliban groups currently operating in Afghanistan. The National Resistance Front is likely the strongest. Ahmad Massoud, son of the legendary mujahedeen leader Ahmad Shah Massoud, is the group’s leader. There are also other groups, like former Chief of General Staff Yasin Zia’s Afghan Freedom Front and the Afghan Liberation Movement. While their attacks against the Taliban have increased, the opposition is still splintered, despite some recent progress.

This lack of cohesion is not new. It partly explained the fall of the previous government, and it was true of the anti-Taliban forces before 9/11. But often unity is easier in resistance than in government. With the Taliban back in power, creating a unified opposition should be more attainable.

The United States would be foolish not to aid these resistance groups with money, small arms, and intelligence. They will not need nearly as much aid as Ukraine or Israel. Every hour and dollar the Taliban has to spend securing its hold on Afghanistan can’t be spent helping al Qaeda and other extremist groups plot international terrorism.

And the United States can help in one way that is public. Instead of sending high-ranking officials to meet with the Taliban, the United States and its allies could help foster a government in exile, and should give it the $40 million it sends the Taliban every week. Our meetings with the Taliban also lend legitimacy to a gender apartheid regime that is still killing our Afghan allies. Instead, we should spend our time and resources on Afghan leaders who actually represent the aspirations of the Afghan people.

While the over-the-horizon counterterrorism strategy may survive, with small tweaks, for the short term, it is not a long-term strategy against an adversary that has survived a two-decade-long war with the United States. The threat from Afghanistan is getting worse, and al Qaeda is still intent on attacking the United States. The Taliban is stronger and more unified than ever before, but they are not invincible.

Creating a government in exile that can provide legitimacy to Taliban resistance groups would require patience, persistence, and guile—the same traits the Taliban, al Qaeda, and their Pakistani patrons used to defeat the United States and the Afghan government.

Abdullah was right. We are back at square one. The United States made numerous mistakes during the war in Afghanistan, and many more during and after the withdrawal. But it’s not too late to devise a long-term strategy that denies al Qaeda a sanctuary to plot attacks against the West. When it is too late, we’ll know it—just like we did on September 11.