The capital Kampala fell to the TPDF and its Ugandan rebel allies on 10–11 April 1979, followed by Jinja on 22 April 1979. Initially unsure about what to do, Mukooza decided to surrender to the new Tanzanian-backed government in Kampala on 24 April. He travelled to the capital using a friend's motorcycle to avoid being arrested at military checkpoints. When Mukooza arrived at Kampala's Nile Mansions, he was escorted to the office of David Oyite-Ojok, the Uganda National Liberation Army's chief of staff. Oyite-Ojok angrily asked Mukooza why he had not joined Bazaalaki's old plot to kill Amin in 1977, prompting the pilot to respond that he had only followed his professional code of conduct as soldier. After this interrogation, Oyite-Ojok ordered Radio Uganda journalist Mukalazi Kyobe to record Mukooza's surrender. Afterwards, the UAAF commander was secretly executed, and his body dumped at the Mbuya Military Hospital compound. According to researcher Muwonge Magembe, Bazaalaki convinced Oyite-Ojok to arrange his execution. The police eventually collected his body and identified him based on his driving permit. The police did not inform anyone, however, and instead registered "an unidentified male-dark-tall body" which they handed over to Mulago Hospital's mortuary. He was probably buried in a mass grave at Bukasa near Kirinya, Jinja District on 2 May 1979.