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More evidence is emerging of the cooperation between Iran and al Qaeda. Last June, the Obama Treasury Department named six al Qaeda facilitators operating in Iran under a “secret deal” between al Qaeda and the Iranian regime. Then, in December, a federal court found that Iran had “aided, abetted and conspired with” al Qaeda in the 1998 bombings of the U.S. embassies in Kenya and Tanzania.

Now, RAND scholar Seth Jones has published an important new essay in Foreign Affairs detailing the evolution of the Iran-al Qaeda relationship. Jones spent much of the past year at West Point culling through hundreds of open-source and declassified documents, and interviewed government officials from the United States, Europe, the Middle East, and South Asia. Based on this research, he concludes, “Evidence of the Iranian-al Qaeda partnership abounds” and that “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.”

Jones writes:

[O]ver 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.

He notes that:

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.

As for al Qaeda:

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. …. Although most governments in the region have clamped down on al Qaeda, Iran’s willingness to allow some activity sets it apart.

Jones is clearly sensitive to the possibility that the evidence he has produced could strengthen the hand of those who argue for military action against Iran’s nuclear facilities. He concludes that a pre-emptive attack on Iran’s nuclear facilities could backfire by pushing Iran and al Qaeda 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. … 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.

This is certainly a risk that must be weighed before any military action is taken. But policymakers could reasonably conclude that the risk of a closer Iran-al Qaeda alliance does not, in the long run, outweigh the risk of an Iranian regime armed with nuclear weapons.

You can read the full essay here.