More than a month after the money transfer was discovered, the head of ISI, General Mehmood Ahmed resigned from his position. It was reported that the FBI was investigating the possibility that Gen. Ahmed ordered Saeed Sheikh to send the $100,000 to Atta <2>; there were also claims that Indian intelligence had already produced proof for the Pakistani administration that this was so.The Wall Street Journal was one of the only Western news organizations to follow up on the story, citing the Times of India: "US authorities sought removal after confirming the fact that $100,000 wired to WTC hijacker Mohammed Atta from Pakistan by Ahmad Umar Sheikh at the instance of Gen Mehmood."<3> Another Indian newspaper, the Daily Excelsior, quoting FBI sources, reported that the "FBI’s examination of the hard disk of the cellphone company Omar Sheikh had subscribed to led to the discovery of the "link" between him and the deposed chief of the Pakistani ISI, Gen. Mehmood Ahmed. And as the FBI investigators delved deep, sensational reports surfaced with regard to the transfer of 100,000 dollars to Mohammed Atta, one of the kamikaze pilots who flew his Boeing into the World Trade Centre. Gen. Mehmood Ahmed, the FBI investigators found, fully knew about the transfer of money to Atta."<4>
The Pittsburgh Tribune notes that "There are many in Musharraf's government who believe that Saeed Sheikh's power comes not from the ISI, but from his connections with our own CIA."<5>
Sheikh rose to prominence with the 2002 killing of Wall Street Journal reporter Daniel Pearl, who at the time was in Pakistan investigating connections between the ISI and Islamic militant groups. In Pakistan, Sheikh was sentenced to death for killing Pearl, however his complicity in the execution and the reasons behind it are in dispute.
In an opinion piece published by the Wall Street Journal, Tunku Varadarajan has claimed that “It is a fact that Gen. Mehmood Ahmed, then head of the ISI, wired $100,000 to Mohamed Atta before 9/11 through an intermediary."