Like other Tutsi exiles, including RPF founder Fred Rwigyema, Karegeya joined the National Resistance Army (NRA) in Uganda. The NRA had been fighting the Ugandan Bush War. The war was led by Yoweri Museveni who was attempting to overthrow Ugandan president Milton Obote. According to his own account, he was arrested in June 1982 and charged with treason, spending three years in jail. After serving his sentence he rejoined the NRA as a lieutenant in Ugandan military intelligence. He claims the decision to invade Rwanda was made at this time by the Tutsi exiles while Kagame was studying in the United States.