There has always been some sort of relationship between the Sunni terrorist group and the Shia theocracy. After 9/11, several al-Qaeda leaders were placed under "house arrest" in Tehran. There have also been occassional reports of meetings between the two wary adversaries - specifically about how to fight Americans in Afghanistan.
But this seems altogether different. Foreign Relations reports:
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.
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.
This points to evidence of a more pragmatic Iranian leadership than we sometimes give them credit for. And it suggests another reason for regime change in Iran.