Despite the 9-11 Commission's mandate to provide a “full and complete accounting” of the attacks of September 11, many key points were omitted from the final report. One of these important omissions attempted to cover up the role of Pakistan and whether or not Pakistani intelligence helped to fund the 9-11 attacks.Ties between Washington DC and the Pakistani intelligence agency, the ISI have been documented in media reports before and after the September 11th attacks. In March 2001, Pakistani regional expert and member of the Woodrow Wilson International Center for Scholars, Selig Harrisson, said “the CIA still has close links with the Pakistani intelligence service ISI.” Just one day before the attacks, a Pakistani newspaper in Islamabad reported that the head of the ISI was meeting with unspecified members of the Pentagon, National Security Council, and CIA Director George Tenet.On May 18th, 2002 the Washington Post reported that:"On the morning of Sept. 11, Porter Goss and Bob Graham were having breakfast with a Pakistani general named Mahmud Ahmed -- the soon-to-be-sacked head of Pakistan's intelligence service. Ahmed ran a spy agency notoriously close to Osama bin Laden and the Taliban."

Specific details of that meeting have still not been released and may never have been recorded.In 2001, various media outlets (CNN, Fox News, ABC, and AP) reported that $100,000 was wired from Pakistan to Mohammed Atta, the 9-11 lead hijacker. A "senior law enforcement source" told CNN that the paymaster was believed to be Ahmed Omar Saeed Sheikh, who was working for the Pakistani ISI at the time.Several media outlets reported in 2002 that the US government believed Saeed Sheikh to be an asset of the ISI, and that senior ISI officers knew him well. Also reported was the allegation by Indian intelligence that General Mahmud Ahmed ordered the wire transfer and that Indian intelligence claimed they had assisted the FBI during the investigation. Various mainstream Indian papers reported this in 2001 along with a mainstream Pakistani newspaper. In the West - the Wall Street Journal and Agence France Press picked up on the story in October. On October 7th 2001, Mahmood Ahmed was fired from his role at the ISI. The official explanation was because he was too close to the Taliban. This claim has been met with criticism by some analysts given the fact that there were several pro-Taliban officers that kept their jobs.During the 9/11 Commission hearings, the Family Steering Committee asked the Commissioners to investigate the ISI connection. However, the commission did little to "follow the money" and the 9/11 Commission Report made no mention of these allegations. Furthermore, the commission made the absurd statement that the question of who financed the terrorist attacks was "of little practical significance" [and that it had] "seen no evidence that any foreign government--or foreign government official--supplied any funding."