From November 1999 to November 2001, he was Director for Transnational Threats on the National Security Council (NSC) staff, where he was responsible for the coordination and implementation of US counter-terrorism policy. During this period, he managed the U.S. Government's response to the Millennium terror alert, the USS "Cole" attack, and the September 11 attacks. During his time at the NSC, Cressey called for steps to be taken against al-Qaeda and Bin Laden, which were largely ignored until 9/11.