In April 1975, Hussein was promoted to head of the entire Gaddafi Battalion by President Amin during a meeting at Nakasero officers' mess, succeeding Isaac Maliyamungu. When the Uganda–Tanzania War broke out, the Gaddafi Battalion helped to secure eastern Uganda. Rebels crossed the border and attacked the town of Tororo on 2–4 March 1979. The Gaddafi Battalion helped to repulse the raid. Regardless, the war turned against Uganda, and the country's capital Kampala fell to the Tanzania People's Defence Force (TPDF) and allied rebels on 10–11 April 1979. The new Ugandan government was installed and appealed to the remaining Uganda Army forces to give up. Hussein was reportedly inclined to do so, and addressed his men at the Gaddafi Battalion barracks. A police officer later claimed that many soldiers were violently opposed to surrender, as they belonged to the West Nile tribes and feared execution as partisans of Amin. Fighting broke out among the troops, and the battalion disintegrated. With his troops no longer following orders, Hussein deserted his post and fled to Kenya in early April, accompanied by "many" other soldiers of the battalion. He surrendered at the border crossing of Malaba. The Kenyan government granted him asylum, and he consequently relocated to Nairobi. According to journalist Jonathan C.R., Hussein's defection was "the final proof that Amin was abandoned by all but the diehards". His flight reportedly left "no one" in control of Jinja. Regardless, some troops of the Gaddafi Battalion continued to resist until Jinja was captured by the TPDF on 22 April 1979.