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.

The Iran-Pakistan border. (snotch / flickr)

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