One of the first official acts of the current Bush administration was to downgrade the office of national coordinator for counterterrorism on the National Security Council - a position held by Richard Clarke. Clarke had served in the Pentagon and State Department under presidents Reagan and Bush the elder, and was the first person to hold the counterterrorism job created by President Clinton. Under Clinton, he was elevated to cabinet rank, which gave him a seat at the principals' meeting, the highest decision-making group for national security.

By removing Clarke from the table, Bush put him in a box where he could speak only when spoken to. No longer would his memos go to the president; instead, they had to pass though a chain of command of national security adviser Condoleezza Rice and her deputy, Stephen Hadley, who bounced each of them back.

Terrorism was a Clinton issue: "soft" and obscure, having something to do with "globalisation", and other trends ridiculed from the Republican party platform. "In January 2001 the new administration really thought Clinton's recommendation that eliminating al-Qaida be one of their highest priorities, well, rather odd, like so many of the Clinton administration's actions, from their perspective," Clarke writes in his new book, Against All Enemies. When Clarke first met Rice and immediately raised the question of dealing with al-Qaida, she "gave me the impression she had never heard the term before".