In 1990, while now Ugandan president Museveni was in New York City at a United Nations conference, the RPF took many Ugandan arms and supplies and invaded Rwanda. Karegeya stayed behind in Uganda to serve as a liaison between intelligence agencies of Uganda and the RPF. Following the war and the genocide, Karegeya took up a position as head of intelligence for the RPF's new government in Rwanda. From 1994 to 2004, he held the post of Director General, External Intelligence in the Rwandan Defence Forces.