For many years, major U.S. institutions ranging from the Pentagon to the 9/11 Commission have been pushing the line that Iran secretly cooperated with Al Qaeda both before and after the 9/11 terror attacks. But the evidence for those claims remained either secret or sketchy, and always highly questionable.
In early November, however, the mainstream media claimed to have its “smoking gun”—a CIA document written by an unidentified Al Qaeda official and released in conjunction with 47,000 never-before-seen documents seized from Osama bin Laden’s house in Abbottabad, Pakistan.
The Associated Press reported  that the Al Qaeda document “appears to bolster U.S. claims that Iran supported the extremist network leading up to the September 11 terror attacks.” The Wall Street Journal said  the document “provides new insights into Al Qaeda’s relationship with Iran, suggesting a pragmatic alliance that emerged out of shared hatred of the United States and Saudi Arabia.”
NBC News wrote that the document reveals that, “at various points in the relationship… Iran offered Al Qaeda help in the form of ‘money, arms’ and “training in Hezbollah camps in Lebanon in exchange for striking American interests in the Gulf,” implying that Al Qaeda had declined the offer. Former Obama National Security Council spokesman Ned Price, writing for The Atlantic, went even further, asserting  that the document includes an account of “a deal with Iranian authorities to host and train Saudi-Al Qaeda members as long as they have agreed to plot against their common enemy, American interests in the Gulf region.”
But none of those media reports were based on any careful reading of the document’s contents. The 19-page Arabic-language document, which was translated in full for TAC, doesn’t support the media narrative of new evidence of Iran-Al Qaeda cooperation, either before or after 9/11, at all. It provides no evidence whatsoever of tangible Iranian assistance to Al Qaeda. On the contrary, it confirms previous evidence that Iranian authorities quickly rounded up those Al Qaeda operatives living in the country when they were able to track them down, and held them in isolation to prevent any further contact with Al Qaeda units outside Iran.
What it shows is that the Al Qaeda operatives were led to believe Iran was friendly to their cause and were quite taken by surprise when their people were arrested in two waves in late 2002. It suggests that Iran had played them, gaining the fighters’ trust while maximizing intelligence regarding Al Qaeda’s presence in Iran.
Nevertheless, this account, which appears to have been written by a mid-level Al Qaeda cadre in 2007, appears to bolster an internal Al Qaeda narrative that the terror group rejected Iranian blandishments and were wary of what they saw as untrustworthiness on the part of the Iranians. The author asserts the Iranians offered Saudi Al Qaeda members who had entered the country “money and arms, anything they need, and training with Hezbollah in exchange for hitting American interests in Saudi Arabia and the Gulf.”
But there is no word about whether any Iranian arms or money were ever actually given to Al Qaeda fighters. And the author acknowledges that the Saudis in question were among those who had been deported during sweeping arrests, casting doubt over whether there was ever any deal in the offing.
The author suggests Al Qaeda rejected Iranian assistance on principle. “We don’t need them,” he insisted. “Thanks to God, we can do without them, and nothing can come from them but evil.”
That theme is obviously important to maintaining organizational identity and morale. But later in the document, the author expresses deep bitterness about what they obviously felt was Iranian double-dealing in 2002 to 2003. “They are ready to play-act,” he writes of the Iranians. “Their religion is lies and keeping quiet. And usually they show what is contrary to what is in their mind…. It is hereditary with them, deep in their character.”
The author recalls that Al Qaeda operatives were ordered to move to Iran in March 2002, three months after they had left Afghanistan for Waziristan or elsewhere in Pakistan (the document, by the way, says nothing of any activity in Iran before 9/11). He acknowledges that most of his cadres entered Iran illegally, although some of them obtained visas from the Iranian consulate in Karachi.
Among the latter was Abu Hafs al Mauritani, an Islamic scholar who was ordered by the leadership shura in Pakistan to seek Iranian permission for Al Qaeda fighters and families to pass through Iran or to stay there for an extended period. He was accompanied by middle and lower-ranking cadres, including some who worked for Abu Musab al Zarqawi. The account clearly suggests that Zarqawi himself had remained in hiding after entering Iran illegally.
Abu Hafs al Mauratani did reach an understanding with Iran, according to the Al Qaeda account, but it had nothing to do with providing arms or money. It was a deal that allowed them to remain for some period or to pass through the country, but only on the condition that they observe very strict security conditions: no meetings, no use of cell phones, no movements that would attract attention. The account attributes those restrictions to Iranian fears of U.S. retribution—which was undoubtedly part of the motivation. But it is clear Iran viewed Al Qaeda as an extremist Salafist security threat to itself as well.
The anonymous Al Qaeda operative’s account is a crucial piece of information in light of the neoconservatives’ insistence that Iran had fully cooperated with Al Qaeda. The document reveals that it was more complicated than that. If Iranian authorities had refused to receive the Abu Hafs group traveling with passport on friendly terms, it would have been far more difficult to gather intelligence on the Al Qaeda figures who they knew had entered illegally and were hiding. With those legal Al Qaeda visitors under surveillance, they have could identify, locate and ultimately round up the hidden Al Qaeda, as well as those who came with passports.
Most of the Al Qaeda visitors, according to the Al Qaeda document, settled in Zahedan, the capital of Sistan and Baluchistan Province where the majority of the population are Sunnis and speak Baluchi. They generally violated the security restrictions imposed by the Iranians. They established links with the Baluchis—who he notes were also Salafists—and began holding meetings. Some of them even made direct contact by phone with Salafist militants in Chechnya, where a conflict was rapidly spiraling out of control. Saif al-Adel, one of the leading Al Qaeda figures in Iran at the time, later revealed that the Al Qaeda fighting contingent under Abu Musab al Zarqawi’s command immediately began reorganizing to return to Afghanistan.
The first Iranian campaign to round up Al Qaeda personnel, which the author of the documents says was focused on Zahedan, came in May or June 2002—no more than three months after they have had entered Iran. Those arrested were either jailed or deported to their home countries. The Saudi Foreign Minister praised Iran in August for having transferred 16 Al Qaeda suspects to the Saudi government in June.
In February 2003 Iranian security launched a new wave of arrests. This time they captured three major groups of Al Qaeda operatives in Tehran and Mashad, including Zarqawi and other top leaders in the country, according to the document. Saif al Adel later revealed  in a post on a pro-Al Qaeda website in 2005 (reported in the Saudi-owned newspaper Asharq al-Awsat), that the Iranians had succeeded in capturing 80 percent of the group associated with Zarqawi, and that it had “caused the failure of 75 percent of our plan.”
The anonymous author writes that the initial Iran policy was to deport those arrested and that Zarqawi was allowed to go to Iraq (where he plotted attacks on Shia and coalition forces until his death in 2006). But then, he says, the policy suddenly changed and the Iranians stopped deportations, instead opting to keep the Al Qaeda senior leadership in custody—presumably as bargaining chips. Yes, Iran deported 225 Al Qaeda suspects to other countries, including Saudi Arabia, in 2003. But the Al Qaeda leaders were held in Iran, not as bargaining chips, but under tight security to prevent them from communicating with the Al Qaeda networks elsewhere in the region, which Bush administration officials eventually acknowledged. 
After the arrests and imprisonment of senior al Qaeda figures, the Al Qaeda leadership became increasingly angry at Iran. In November 2008, unknown gunmen abducted  an Iran consular official in Peshawar, Pakistan, and in July 2013, al Qaeda operatives in Yemen kidnapped an Iranian diplomat. In March 2015, Iran reported ly released five of the senior al Qaeda in prison, including Said al-Adel, in return for the release of the diplomat in Yemen. In a document taken from the Abbottabad compound and published by West Point’s Counter-Terrorism Center in 2012, a senior Al Qaeda official wrote,  “We believe that our efforts, which included escalating a political and media campaign, the threats we made, the kidnapping of their friend the commercial counselor in the Iranian Consulate in Peshawar, and other reasons that scared them based on what they saw (we are capable of), to be among the reasons that led them to expedite (the release of these prisoners).”
There was a time when Iran did view Al Qaeda as an ally. It was during and immediately after the war of the mujahedin against Soviet troops in Afghanistan. That, of course, was the period when the CIA was backing bin Laden’s efforts as well. But after the Taliban seized power in Kabul in 1996— and especially after Taliban troops killed 11 Iranian diplomats in Mazar-i-Sharif in 1998—the Iranian view of Al Qaeda changed fundamentally. Since then, Iran has clearly regarded it as an extreme sectarian terrorist organization and its sworn enemy. What has not changed is the determination of the U.S. national security state and the supporters of Israel to maintain the myth of an enduring Iranian support for Al Qaeda.
Gareth Porter is an independent journalist and winner of the 2012 Gellhorn Prize for journalism. He is the author of numerous books, including Manufactured Crisis: The Untold Story of the Iran Nuclear Scare (Just World Books, 2014).