Virtually unnoticed, since late 2001, Iran has held some of al Qaeda's most senior leaders. Several of these operatives, such as Yasin al-Suri, an al Qaeda facilitator, have moved recruits and money from the Middle East to central al Qaeda in Pakistan. Others, such as Saif al-Adel, an Egyptian that served as head of al Qaeda's security committee, and Abu Muhammad al-Masri, one of the masterminds of the 1998 U.S. embassy bombings in East Africa, have provided strategic and operational assistance to central al Qaeda. The Iranian government has held most of them under house arrest, limited their freedom of movement, and closely monitored their activities. Yet the organization's presence in Iran means that, contrary to optimistic assessments that have become the norm in Washington, al Qaeda's demise is not imminent. 

Perhaps more disturbing, Iran appears willing to expand its limited relationship with al Qaeda. Just as with its other surrogate, Hezbollah, the country could turn to al Qaeda to mount a retaliation to any U.S. or Israeli attack. To be sure, the organization is no Iranian puppet. And the two have sometimes been antagonistic, as illustrated by al Qaeda in Iraq's recent attacks against Shias. But both share a hatred of the United States. U.S. policymakers should think twice about provoking a closer relationship between them and should draw greater public attention to Iran's limited, but still unacceptable, cooperation with al Qaeda. 

Evidence of the Iranian-al Qaeda partnership abounds -- and much of it is public. This past year, I culled through hundreds of documents from the Harmony database at West Point; perused hundreds more open-source and declassified documents, such as the U.S. Department of Treasury's sanctions against al Qaeda leaders in Iran; and interviewed government officials from the United States, Europe, the Middle East, and South Asia.

Through that research, the history of al Qaeda in Iran emerges as follows: over the past several years, al Qaeda has taken a beating in Iraq, Pakistan, Yemen, the Horn of Africa, and North Africa. In particular, an ongoing campaign of drone strikes has weakened -- although not eliminated -- al Qaeda's leadership cadre in Pakistan. But the group's outpost in Iran has remained almost untouched for the past decade. In late 2001, as the Taliban regime collapsed, most al Qaeda operatives fled Afghanistan. Many of the leaders, including Osama bin Laden and Ayman al-Zawahiri, bin Laden's deputy and future successor, headed for Pakistan. But some did not, choosing instead to go west. And Iran was apparently more than willing to accept them. Around October 2001, the government dispatched a delegation to Afghanistan to guarantee the safe travel of operatives and their families to Iran. 

Initially, Iran's Quds Force -- the division of the Revolutionary Guard Corps whose mission is to organize, train, equip, and finance foreign Islamic revolutionary movements -- took the lead. Between 2001 and 2002, it helped transport several hundred al Qaeda-linked individuals. By 2002, al Qaeda had established in Iran its "management council," a body that bin Laden reportedly tasked with providing strategic support to the organization's leaders in Pakistan. Key members of the council included Adel, Sulayman Abu Ghayth, Abu al-Khayr al-Masri, Abu Muhammad al-Masri, and Abu Hafs al-Mauritani. All five remained influential over the next several years and retained close ties to bin Laden. Among the most active of the council, Adel even helped organize groups of fighters to overthrow Hamid Karzai's regime in Afghanistan and provided support for the May 2003 terrorist attacks in Riyadh. 

According to U.S. government officials involved in discussions with Iran, over time, the growing cadre of al Qaeda leaders on Iranian soil apparently triggered a debate among senior officials in Tehran. Some worried that the United States would eventually use the terrorist group's presence as a casus belli. Indeed, in late 2002 and early 2003, U.S. government officials held face-to-face discussions with Iranian officials demanding the regime deport al Qaeda leaders to their countries of origin. Iran refused, but around the same time, the country's Ministry of Intelligence took control of relations with the group. It set to work rounding up al Qaeda members and their families. 

By early 2003, Tehran had detained all the members of the management council and their subordinates who remained in the country. It is not entirely clear what conditions were like for al Qaeda detainees. Some apparently suffered through harsh prison confinement, while others enjoyed informal house arrest with freedom to communicate, travel, and fundraise. Over the next several years, bin Laden, Zawahiri, and other leaders apparently sent messages to Tehran threatening to retaliate if al Qaeda personnel and members of bin Laden's family were not released. Iran did not comply. Bin Laden did not follow through.

After that, the details of al Qaeda's relationship with the Iranian government are hazy. It seems that many of the operatives under house arrest petitioned for release. In 2009 and 2010, Iran did begin to free some detainees and their family members, including members of bin Laden's family. And the management council remained in Iran, still under limited house arrest. Tehran appears to have drawn several red lines for the council: Refrain from plotting terrorist attacks from Iranian soil, abstain from targeting the Iranian government, and keep a low profile. As long as it did so, the Iranian government would permit al Qaeda operatives some freedom to fundraise, communicate with al Qaeda central in Pakistan and other affiliates, and funnel foreign fighters through Iran.

Today, Iran is still an important al Qaeda hub. Suri, who was born in 1982 in al-Qamishli, Syria, is a key operative. According to U.S. Treasury Department accounts, Tehran has permitted Suri to operate discretely within Iran since at least 2005. He has collected money from donors and transferred it to al Qaeda's leadership in Pakistan and other locations; facilitated the travel of extremist recruits from the Gulf to Pakistan and Afghanistan; and according to U.S. State Department accounts, "arranges the release of al-Qaeda personnel from Iranian prisons."

On the surface, the relationship between Shia Iran and Sunni al Qaeda is puzzling. Their religious views do differ, but they share a more important common interest: countering the United States and its allies, including Israel, Saudi Arabia, and the United Kingdom. Iran's rationale might be compared to that of British Prime Minister Winston Churchill, who declared, "If Hitler invaded Hell, I would make at least a favorable reference to the devil in the House of Commons."

Iran is likely holding al Qaeda leaders on its territory first as an act of defense. So long as Tehran has several leaders under its control, the group will likely refrain from attacking Iran. But the strategy also has an offensive component. If the United States or Israel undertook a bombing campaign against Iran, Tehran could employ al Qaeda in a response. Tehran has long used proxies to pursue its foreign policy interests, especially Hezbollah in Lebanon, and it has a history of reaching out to Sunni groups. In Afghanistan, for example, Iran has provided limited support to the Taliban to keep the United States tied down. Al Qaeda's proven willingness and ability to strike the United States make it an attractive partner. 

Al Qaeda is probably making similar calculations. To be sure, some revile the Ayatollahs. Abu Mus'ab al-Zarqawi, the now-deceased head of al Qaeda in Iraq, actively targeted Shias there. In a 2004 letter, Zarqawi explained that they are "the insurmountable obstacle, the lurking snake, the crafty and malicious scorpion." Yet, in a sign of Churchill-esque pragmatism, Zawahiri chastised Zarqawi in 2005, writing that the Shias were not the primary enemy -- at least not for the moment. It was crucial, Zawahiri explained, to understand that success hinged on support from the Muslim masses. One of Zarqawi's most significant mistakes, Zawahiri chided him, was targeting Shia communities, because such a strategy would cripple al Qaeda's support among the broader Muslim community. And most al Qaeda operatives since the debacle in Iraq have cautiously followed Zawahiri's lead.  

Moreover, Iran is in many ways a safer territory from which al Qaeda can operate. The United States has targeted al Qaeda in Iraq, Pakistan, Yemen, and other countries, but it has limited operational reach in Iran. In addition, Iran borders the Persian Gulf, Iraq, Turkey, Afghanistan, and Pakistan, making it centrally located for most al Qaeda affiliates. No wonder that Suri has been able to move money and recruits through Iran to various theaters, including al Qaeda central in Pakistan. Although most governments in the region have clamped down on al Qaeda, Iran's willingness to allow some activity sets it apart. 

With the management council still under limited house arrest, Iran and al Qaeda remain at arm's length. But that could change if Washington's relationship with Tehran does. So far, the conflict between Iran and the West has been limited to diplomatic pressure and economic sanctions. It has also occasionally deteriorated into cyber attacks, sabotage, assassinations, kidnappings, and support to proxy organizations. But much like the struggle between the U.S. and Soviet Union during the Cold War, it has not spilled into overt conflict. Should an increase of those activities cause a broad deterioration in relations, however, or should the United States or Israel decide to attack Iranian nuclear facilities, Iran and al Qaeda could come closer together. 

For one, Iran would likely respond to an attack by targeting the United States and its allies through proxies in Iraq, Afghanistan, and other countries. The regime might increase its logistical support to al Qaeda by providing money, weapons, housing, travel documents, and transit to operatives -- some of which it is already doing. In a worse scenario, Tehran might even allow al Qaeda officials in Iran to go to Pakistan to replenish the group's depleted leadership there, or else open its borders to additional al Qaeda higher-ups. Several of the operatives already in Iran, including Adel and Abu Hafs al-Mauritani, would be especially valuable in this regard, because of their prestige, experience in paramilitary and external operations, and religious credentials. In an even more extreme scenario, Iran could support an al Qaeda attack against the United States or one of its allies, although the regime would surely attempt to hide its role in any plotting. Based on Iran's cautious approach over the past decade, Tehran's most likely strategy would be to gradually increase its support to al Qaeda in response to U.S. actions. That way it could go slowly, and back away at any time, rather than choosing an all-or-nothing approach from the start. 

It would be unwise to overestimate the leverage Tehran has over al Qaeda's leadership. The terrorist organization would almost certainly refuse Iranian direction. But given the group's current challenges, any support or tentative permission to plot on Iran's soil would be helpful. It could set about restoring its depleted senior ranks in Pakistan and other countries, or else rebuild within Iran itself. The organization might thus be amenable to working within Iranian constraints, such as seeking permission before planning attacks in the West from Iranian soil, as long as the taps were flowing. 

It is true that the United States has limited leverage with Iran, but it still has several options. The first, and perhaps easiest, is to better expose the existence and activities of al Qaeda leaders in Iran. Al Qaeda has killed tens of thousands of Sunnis, Shias, and non-Muslims over the past two decades and has unified virtually all governments in the world against it. Iran, too, has become an international pariah. Its limited aid to al Qaeda is worthy of further public condemnation. But Iran has largely escaped such scrutiny. 

The United States could encourage more countries to prohibit citizens and companies from engaging in commercial and financial transactions with al Qaeda leaders and their networks in Iran. The U.S. Treasury and State Departments have taken steps against some al Qaeda operatives and their supporters in Iran, including against Suri and his circle. But those efforts have not been coupled with robust diplomatic efforts to encourage other countries to do the same. Nor have they been successful in eliminating al Qaeda's sanctuary in Iran. 

Finally, the United States should think twice about actions that would push Iran and al Qaeda closer together -- especially a preemptive attack on the country's nuclear program. Thus far, Iran and al Qaeda have mutually limited their relationship. It would be a travesty to push the two closer together at the very moment that central al Qaeda in Pakistan has been severely weakened. 

Thankfully, there is still time to deal with the problem. But the stakes are too high for the United States to remain quiet any longer.

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  • SETH G. JONES is Senior Political Scientist at RAND and author of Hunting in the Shadows: The Pursuit of al Qaeda Since 9/11. Between 2009 and 2011, he served at U.S. Special Operations Command, including as a Plans Officer and Senior Adviser to the Commanding General of U.S. Special Operations Forces in Afghanistan.
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