 Following his Air Force retirement, Gordon was chosen as the first administrator of the National Nuclear Security Administration and also Under Secretary of Energy, responsible for the U.S. nuclear weapons program, a position he filled from June 2000 to June 2002.He next served as the Deputy National Security Advisor for Combating Terrorism, then assumed duties as Homeland Security Advisor from June 2003 to June 2004.On September 16, 2004, he was inducted into the Naval Postgraduate School Hall of Fame.