Double Cross

09.25.14 9:55 AM ET

Will Iran Sell Out Al Qaeda for Nukes?

The Iranians want to make a deal with the U.S.: They help us fight terror in exchange for nuclear concessions. Tehran could start by giving up the al Qaeda leaders it’s harboring.

On Wednesday in New York, Iranian President Hassan Rouhani offered to help the West fight terrorism—and play a more “active role” in the Middle East—as long as the West is willing to do it Iran’s way and also come to a deal on its nuclear program.

The Iranian offer has been widely interpreted as one to fight ISIS alongside the U.S. After all, Iranian-backed militias and American airpower earlier this month helped drive ISIS out of the Iraqi town of Amerli.

But there’s a second possibility. Iran has long been harboring senior al Qaeda, al Nusra, and so-called Khorasan Group leaders as part of its complicated strategy to influence the region and keep itself off the terrorist target list, according the U.S. government, intelligence agencies, and terrorism experts.

Now, with a potential nuclear deal and rapprochement with the West in sight, the Shiite regime in Tehran could be looking to sell its Sunni terrorist friends down the river.

“The Iranians have kept a lot of these guys as a point of protection. They are explosive bargaining chips,” said Trita Parsi, president of the National Iranian American Council. “If they would have handed them over to the United States years ago without getting anything in return, they would have become a greater target for al Qaeda and they would have less cards to play with the U.S. now.”

U.S. officials have insisted all week that although U.S. and Iranian officials have been discussing the war on ISIS and Tehran’s nuclear program on the sidelines of the U.N. General Assembly this week, the two issues are not linked and never should be. But Iranian officials told Reuters that Iran would help the U.S. fight ISIS in Iraq and Syria only if the U.S. made concessions on Tehran’s nuclear program. The White House publicly rejected the offer.

On Wednesday, Rouhani connected the issues again and said that if only the U.S. struck a deal with Iran on the nuclear issue, Iran could really start to help on ISIS and other terrorist organizations.

“If Iran could reach a comprehensive deal on its nuclear program and leave sanctions behind, it would be able to assume a more active position on interregional dialogue in the Islamic world,” Rouhani told an audience at an event hosted by the New America Foundation.

“No one is justified in helping terrorists, whether they are taking action in Syria, or Iraq, or Lebanon, it really doesn’t matter,” he said. “Terrorism must be driven out and eradicated from the region.”

Washington experts often point out that Iran has more to lose than any country from the spread of ISIS and al Qaeda. The predominantly Shiite country is ideologically opposed to the Sunni terror groups, and ISIS threatens Iran’s dominance over neighboring Iraq. In 2003, Iran handed over to the United Nations the names of hundreds of al Qaeda suspects.

Yet the relationship between the Shiite mullahs and the Sunni extremists isn’t that simple. The question now is whether Iran is willing to trade those bargaining chips in exchange for the ability to preserve its nuclear program.

“The Iranian regime has nurtured al Qaeda for many years. There are links, there are contacts, they know these people,” said Fouad Hamdan, executive director of the Netherlands-based Rule of Law Foundation, which funds Naame Shaam, an NGO focused on Iran’s role in Syria.

Naame Shaam has produced a 105-page report on Iran’s mischief inside Syria and its ties to al Qaeda, al Nusra, and ISIS. Al Qaeda and ISIS are under orders not to attack inside Iran in order to preserve their supply network there, the report states. The U.S. government concurs.

According to the U.S. Treasury Department, Muhsin al Fadhli, a longtime al Qaeda member and the leader of the newly public Khorasan Group, lived in Iran from 2009 until 2013 with the knowledge and support of the Iranian government. (Jihadist web forums reported that Fadhli was killed Tuesday by U.S. airstrikes.) Treasury said Fadhli took over as head of al Qaeda’s operations in Iran in late 2011 in place of Yasin al-Suri, another senior al Qaeda leader who was detained briefly by the Iranian regime.

Fadhli was considered a major facilitator for Abu Musab al-Zarqawi, the founder of al Qaeda in Iraq, which eventually gave rise to ISIS. Al Qaeda’s network in Iran also is suspected of having planned attacks on foreign interests, including a thwarted 2013 plot to bomb the U.S. Embassy in Cairo.

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As recently as this past February, the Treasury Department reported that Suri had resumed control of the al Qaeda branch in Iran, after Fadhli returned to Syria to take over the al Nusra Front following its public split with ISIS.

“As head al Qaeda facilitator in Iran, Yasin al-Suri is responsible for overseeing al Qaeda efforts to transfer experienced operatives and leaders from Pakistan to Syria, organizing and maintaining routes by which new recruits can travel to Syria via Turkey, and assisting in the movement of al Qaeda external operatives to the West,” the Treasury Department said. “Al Qaeda’s network in Iran has facilitated the transfer of funds from Gulf-based donors to al Qaeda core and other affiliated elements, including the al-Nusra Front in Syria. The Iran-based al Qaeda network has also leveraged an extensive network of Kuwaiti jihadist donors to send money to Syria via Turkey.”

But recently, Hamdan said, Iran’s ties to al Qaeda and al Nusra have become less valuable. Al Nusra is more dependent on its Gulf patrons and the al Qaeda offshoot ISIS is running wild, fighting Iraqi and Iranian forces in Iraq. That’s why Iran might be willing to deal them away to the U.S.

“These guys, when they are totally out of the control of the Iranians, they are of no longer of use to the Iranians. The Iranians are the masters of creating monsters, using them against their enemies, and then selling them,” he said. “It’s a good card in your hand when you are in a de facto war with the U.S. since 1979 and when you are deep into negotiations over the nuclear program.”

Iran’s complicated relationship with al Qaeda stretches back to at least the late 1990s. The 9/11 Commission’s final report, for example, said, “There is strong evidence that Iran facilitated the transit of al Qaeda members into and out of Afghanistan before 9/11, and that some of these were future 9/11 hijackers.”

After the fall of the Taliban in 2001, several senior al Qaeda leaders fled to Iran, including a former Egyptian special operations officer named Saif al-Adel. Adel and others helped facilitate the movement of Zarqawi to Iraq from Afghanistan, where he became the first leader of al Qaeda’s franchise in Iraq, the predecessor organization to ISIS.

Nonetheless, in 2003 Iranian and U.S. negotiators discussed a possible trade of al Qaeda operatives in Iran in exchange for members of the People’s Mujahadin, an anti-Iranian terrorist organization that was based in Iraq after being expelled from Iran in the early 1980s.

In recent years Iran’s relationship with al Qaeda has soured. Al Qaeda leaders began leaving Iran in late 2008, including Osama bin Laden’s son Saad bin Laden. Today, Iran supports the governments of Syria and Iraq in their fight against al Qaeda franchises and ISIS.

Nonetheless, some al Qaeda senior managers remain in Iran. Seth Jones, the director of the International Security and Defense Policy Center at the Rand Corporation, said Iran could help the new U.S. campaign against ISIS and al Qaeda by rounding up the remaining al Qaeda operatives on its own territory.

“They could capture and hand over the remaining al Qaeda officials on Iranian soil,” he said. “A few, including Saif al Adel, remain in Iran.”

Thomas Joscelyn, a senior fellow at the Foundation for Defense of Democracies and senior editor of The Long War Journal, said Iran’s government could hand over intelligence on al Qaeda operatives and leaders it has hosted over the years.

“The Iranians probably have dossiers on most, if not all, of these guys because some of the key leaders were harbored by them in recent years,” he said. “All of that intelligence should be put on the table if they want to help us out on this. If there really is a deal on this, then why wouldn’t they offer this up?”

If Iran is ready to forgo its long-standing relationship with al Qaeda and help the U.S. and West fight against ISIS and al Qaeda, that could be a game changer in the overall relationship. It could make a nuclear deal more possible, said Jim Smith, an expert on Iran’s nuclear program at MIT.

“The U.S. is going to want to keep these as separate issues and not link them formally with a quid pro quo,” he said. “But the reality is that those issues with ISIS change the incentive structure. It gives the parties all the more reason to cooperate.”