Ralston became Vice Chairman of the Joint Chiefs of Staff in 1996. He was favorite to become Chairman of the Joint Chiefs of Staff in 1997, however following revelations of a secret affair he remained Vice Chairman until May 2000. He then became Supreme Allied Commander for the North Atlantic Treaty Organization (NATO) in Europe until January 2003 when he retired.Bill Clinton writes in his memoirs "My Life" that Ralston was used to resolve a potentially sticky situation with Pakistan in which the US would use Pakistani airspace to strike at the Al-Qaeda organization meeting in Afghanistan following the US Embassy bombings in Kenya and Tanzania. There was US concern that Pakistan's intelligence services would tip off the targets or even worse assume the missiles over Pakistan came from India, potentially triggering a nuclear conflict on the Indian sub-continent. As Clinton writes on page 799 of "My Life", "we decided to send the vice chairman of the Joint Chiefs of Staff, General Joe Ralston, to have dinner with the top Pakistani military commander at the time the attacks were scheduled. Ralston would tell him (the Pakistani general) what was happening a few minutes before our missiles invaded Pakistani airspace, too late to alert the Taliban or Al-Qaeda, but in time to avoid having them shot down or sparking a counterattack on India."