Why Are Al Qaeda Leaders in Iran?

What a Prisoner Exchange Reveals About an Unlikely Relationship

On January 12, during an event at the National Press Club in Washington, D.C., outgoing U.S. Secretary of State Mike Pompeo delivered an address accusing Iran of being al Qaeda’s “new home base.” Pompeo alleged that after 30 years of cooperation, Iran and al Qaeda had taken their relationship to a new level in recent years. In 2015, Tehran supposedly “decided to allow al Qaeda to establish a new operational headquarters” on its territory and now the terrorist organization “is operating under the hard shell of the Iranian regime’s protection.”

Pompeo was hardly the first American political figure (or analyst, or pundit) to charge Iran with providing support for al Qaeda, but his allegation was of a different kind entirely. Many listeners dismissed the outgoing secretary of state’s remarks as propaganda aimed at interfering with the Biden administration’s hoped-for rapprochement with Tehran. But Pompeo’s claim—however exaggerated—in fact rests on a grain of truth: something did happen in 2015 between al Qaeda and Iran. At the time, Iran was detaining certain al Qaeda leaders on its territory. In a prisoner exchange with the terrorist group, Tehran granted those leaders freedom of movement that allowed them to oversee al Qaeda’s global operations with greater ease than in the past. A more careful examination of this arrangement, however, complicates any notion of an “Iran–al Qaeda axis.” The regime and the terrorist organization may coordinate with each other on some matters, but they are not the kind of operational partners that some would like to believe they are.

“THE OPPRESSIVE IRANIAN INTELLIGENCE PRISON”

A pattern of cooperation between Iran and al Qaeda is a well-established fact. According to the 9/11 Commission Report, in the 1990s, “senior al Qaeda operatives and trainers traveled to Iran to receive training in explosives,” while others “received advice and training from Hezbollah” in Lebanon. And in the years before 9/11, a number of the al Qaeda hijackers traveled through Iranian territory. “Sunni-Shia divisions,” the report found, “did not necessarily pose an insurmountable barrier to cooperation in terrorist operations” between al Qaeda and Iran.

The al Qaeda leadership, although it belongs to the virulently anti-Shiite Sunni jihadi movement, has long sought to minimize sectarian tensions in pursuit of its overriding strategic objective: expelling the U.S. military presence from the Middle East. That objective is of course shared with Tehran, and so a certain level of cooperation might be expected.

And yet, as the counterterrorism scholar Assaf Moghadam has convincingly argued, al Qaeda’s relationship with Iran has never risen above the level of “tactical cooperation.” Iran has permitted al Qaeda to use its territory as a “facilitation hub”—as the al Qaeda founder Osama bin Laden put it in a 2007 letter, “Iran is our main artery for funds, personnel, and communication”—but it has also put restrictions on al Qaeda leaders living there. The relationship has been marked by periods of extreme strain and tension.

Following the 9/11 attacks, numerous al Qaeda operatives sought and received refuge in Iran but were subject to varying levels of detention and house arrest. The operatives found the conditions of their detention, which included limitations on their ability to communicate with the outside world, to be unacceptable. The political scientist Nelly Lahoud studied the thousands of internal al Qaeda documents recovered at the compound in the Pakistani city of Abbottabad, where bin Laden was killed in 2011, and observed that the men, “far from being operational in Iran . . . were in despair.” They staged violent protests against their Iranian captors and urged their comrades abroad to intervene on their behalf.

In a 2010 letter to the al Qaeda leadership in the Afghanistan-Pakistan region, some of these men bemoaned their custody “in the oppressive Iranian intelligence prison,” professing to want nothing more than to leave. They called on their “brothers in Khurasan”—a reference to a historic region that included parts of Afghanistan and Iran—to take action to secure their release: “What we want you to do is to kidnap Iranian officials, then negotiate with their government without publicizing it.” Al Qaeda had already set about doing exactly that.

THE PRISONER EXCHANGE

In 2011, Iran and al Qaeda agreed to a prisoner exchange that saw the release of several key al Qaeda members, including bin Laden’s son Hamza, in exchange for an Iranian diplomat abducted in Pakistan in 2008. Several years later, in 2015, another exchange took place, involving an Iranian diplomat whom al Qaeda’s branch in Yemen had kidnapped in 2013. This second swap explains why certain al Qaeda leaders have been able to live freely in Iran.

As The New York Times and other outlets reported, the prisoner exchange in 2015 involved the release from Iranian detention of five “senior members” of al Qaeda, including three Egyptians (Sayf al-Adl, Abu Muhammad al-Masri, and Abu al-Khayr al-Masri) and two Jordanians (Abu al-Qassam and Sari Shihab), in exchange for the Iranian diplomat in Yemen. But this was not the complete story.

In 2017, more details about the deal emerged in the course of an internal jihadi dispute over the decision by al Qaeda’s branch in Syria, Jabhat al-Nusra, to leave al Qaeda and become an independent group. This group, known as Hayat Tahrir al-Sham (HTS), now administers a swath of territory in Syria’s northwest and has tense relations, at best, with al Qaeda’s main line.

In October 2017, the al Qaeda leader Ayman al-Zawahiri gave a speech in which he condemned HTS for breaking its oath of loyalty to the mother organization and for pursuing a nationalist struggle in Syria. There followed a written war of words between a senior HTS official, Abd al-Rahim Atun, who sought to defend the group’s decision to go its own way, and two senior al Qaeda members in Syria, Sami al-Uraydi and the aforementioned Abu al-Qassam. In the course of this exchange, the three men drew attention to the 2015 deal between al Qaeda and Iran, which had led to the release of the al Qaeda leaders who oversaw Jabhat al-Nusra’s break from its parent organization.

According to Atun, the prisoner exchange in 2015 involved six al Qaeda members detained by the Iranians. Four were given their freedom and allowed to leave Iran, relocating to Syria, while two were freed from Iranian detention but barred from leaving the country. The four Syria-bound leaders were the Egyptian Abu al-Khayr al-Masri, the Jordanian Abu al-Qassam, and two unidentified “companions.” The two who stayed in Iran were the Egyptians Sayf al-Adl and Abu Muhammad al-Masri.

At the time of their release, Abu al-Khayr al-Masri acted as Zawahiri’s principal deputy. In Zawahiri’s absence—he was incommunicado for more than two years, according to Atun—Abu al-Khayr formed a leadership council with the Iran-based Sayf al-Adl and Abu Muhammad al-Masri to consider important decisions. When it came to the Syrian branch’s proposed breaking of ties with al Qaeda, the council was split: Abu al-Khayr, in Syria, approved the move while the two men in Iran rejected it. The breaking of ties proceeded over the latter’s objections.

In the view of Atun, the positions of the Iran-based leaders were irrelevant, as they were “being held captive . . . in the enemy state of Iran.” Abu al-Qassam, in his response, objected to the characterization of the men’s status in Iran as one of captivity or detention (ihtijaz). “Following the prisoner exchange that you know about,” he wrote, “they [Sayf al-Adl and Abu Muhammad al-Masri] left prison and they are not being held captive in the sense that is understood and brought to mind by this word. Rather they are prohibited from traveling until such time as God grants them departure. They are moving about and living their normal lives apart from not being allowed to travel.”

These assertions appear to support Pompeo’s allegation that “Ayman al-Zawahiri’s deputies . . .  are living a normal al Qaeda life” in Iran today. But the agreement ends there. According to Pompeo, Iran has allowed Zawahiri’s deputies to live freely in Iran because it seeks to facilitate al Qaeda’s terrorist operations: “They are partners in terrorism, partners in hate,” he claimed. Yet Abu al-Qassam portrays a relationship with Iran that is nothing like a partnership. According to him, the al Qaeda leaders’ freedom of movement in Iran was hard won—the result of the 2015 prisoner exchange. Iran did not grant it willingly but was coerced into doing so. Furthermore, Zawahiri’s deputies are in Iran not voluntarily but rather because they are forbidden to leave under the terms of their release from Iranian detention.

Why would Iran insist on keeping those al Qaeda leaders in the country? The likely answer is that Iran wants to ensure that al Qaeda does not carry out terrorist attacks against Iran. Al Qaeda forces have battled Iranian-backed groups across the Middle East, including the Lebanese Hezbollah and the Houthis in Yemen, and many al Qaeda members harbor deep resentment toward the Iranians. Meanwhile, the group’s ideological cousins in the Islamic State (or ISIS) have claimed operations on Iranian territory, including attacks on the Iranian parliament and the mausoleum of Ayatollah Khomeini in 2017. The presence of al Qaeda leaders in the country thus serves as a kind of insurance policy or collateral.

But the presence of these figures in Iran does not necessarily entail the conclusion that Tehran is currently providing material support to al Qaeda operations. No evidence has been made public to support such a claim. The killing of Abu Muhammad al-Masri in Tehran—reportedly at the hands of Israeli agents—last August shows only that he was in fact living freely in Iran, as the 2015 prisoner exchange made possible. Sayf al-Adl is presumably the only remaining deputy of Zawahiri’s who enjoys that level of freedom in Iran today, though other al Qaeda members are also believed to be in the country.

AFGHANISTAN, NOT IRAN

Iran should be held accountable for tolerating al Qaeda activity on its territory. It is no small matter that al Qaeda’s presumed number two enjoys free rein in the Iranian capital. But the new U.S. administration should refrain from conflating the threats posed by Iran and al Qaeda and exaggerating the extent of their cooperation. These are separate challenges that need to be assessed independently of each other. The challenge of Iran centers on its nuclear program and its regional adventurism, that of al Qaeda on threats to the U.S. homeland and the several insurgencies being waged by affiliate groups in central and eastern Africa, among other places.

The new administration should also avoid politicized assessments of the threat that al Qaeda poses. The last administration portrayed al Qaeda as a fading concern when it sought to minimize the risks of withdrawing from Afghanistan but as a gathering force when it sought to underscore the menace of the Iranian regime. Both characterizations can’t be accurate, though something of the reverse may be closer to the truth.

Al Qaeda stands to benefit greatly from a U.S. withdrawal from Afghanistan, while it seems to have gained little from its presence in Iran. The Taliban, with which the United States reached a deal in February 2020 whereby U.S. forces will fully withdraw by May 2021, has maintained a relationship with al Qaeda despite promises of cutting off support. Al Qaeda even presents the Taliban as its supreme authority and imagines Afghanistan as the seat of a future caliphate, notions the Taliban has not refuted.

The 2015 prisoner exchange between Iran and al Qaeda, meanwhile, does not appear to have advanced the terrorist group’s cause. Rather than providing al Qaeda with a new safe haven in which it is “poised to gain strength” (in Pompeo’s words), the agreement with Iran actually seems to have hurt the group more than it has helped it. Of the six al Qaeda leaders who were freed in the swap, at least four have been killed—three in Syria and one in Iran. These are just some of the many targeted killings in recent years that have decimated the organization’s overarching leadership. If al Qaeda is to regain strength in the coming years, it is more likely to happen in Afghanistan than in Iran.

All publishing rights and copyrights reserved to MENA Research and Study Center