Jones’ assertion on a nefarious Iran-al-Qaeda nexus is the stuff of official conspiracy theories arising from the 9/11 Commission report and from accusations made by Bush-era neocons. Much of the information used to establish the Iran-al-Qaeda relationship was gained during the interrogation of supposed al-Qaeda detainees. The U.S. claims a number of alleged 9/11 hijackers and al-Qaeda operatives traveled to Iran to and from Afghanistan, but does not offer any direct evidence of links between flights and the Iranians.
It should also be noted that Iran had attempted to work with the Bush administration on delivering al-Qaeda members held in Iran to the newly installed government in Afghanistan in exchange for information on Guantanamo detainees suspected of killing nine Iranian diplomats in Kabul, Afghanistan, in 1998. The Iranian request was denied after Bush declared Iran part of the Axis of Evil. Prior to Bush’s snub, Iran had turned over hundreds of al-Qaeda suspects to U.S. allies following the defeat of the Taliban. It provided valuable intelligence, names, photographs, and fingerprints on suspected al-Qaeda members it held.