In August 2005, President George W. Bush appointed Charles E. Allen, to the dual role of Assistant Secretary for Information Analysis at the Department of Homeland Security as well as the DHS Chief of Intelligence.

In October 2008, Allen warned that Anwar al-Awlaki "targets US Muslims with radical online lectures encouraging terrorist attacks from his new home in Yemen.

He said that at the advice of Mr. Allen, he created a special unit with officers from the C.I.A., the National Security Agency and the NGA to meet daily and focus on Al Qaeda in Afghanistan.

[10] Mark Perry offers this commentary about Allen based on information from colleagues:[11] From an August 2004 U.S. News & World Report article: "…more of a legend than a man around the CIA.

[14] Director of Central Intelligence William Webster formally reprimanded Allen for failing to fully comply with the DCI's request for full cooperation in the agency's internal Iran-Contra scandal investigation.

Supporters of Allen pointed out that Webster reprimanded the one person in the CIA who had brought his suspicions of a funds diversion to Robert Gates.

Satellite photos and electronic intercepts indicating this alternative use were regarded as circumstantial and unconvincing to Brigadier General Buster Glosson, who had primary responsibility for targeting.

A human source in Iraq, who had previously proven accurate warned the CIA that Iraqi intelligence had begun operating from the shelter.