Long-standing tensions between Uganda and Tanzania resulted in open warfare in late 1978, when the Ugandan military invaded the Kagera salient under unclear circumstances. The Uganda Army Air Force assisted the invasion by attacking military and civilian targets in northern Tanzania. President Amin personally ordered Mukooza and his co-pilot Levi Mugyenyi to fly a bombing mission with their MiG-17. The two carried out the mission, but were almost shot down by Tanzanian anti-aircraft fire. Despite the efforts of the UAAF, the Tanzanians repulsed the Kagera invasion and counter-attacked. Uganda suffered several major defeats, and its air force was gradually worn down. The UAAF suffered catastrophic losses in February 1979, and its chief commander Christopher Israel Umba Gore disappeared. Gore's fate is unclear; he either fled to Sudan or was killed in an ambush, leaving Mukooza as acting commander of the Uganda Army Air Force. Mukooza realized that Amin's regime was collapsing. To keep his family out of harm's way, he sent them to Kaababbi in Busiro on 25 February 1979. As the Tanzania People's Defence Force (TPDF) approached Entebbe, Mukooza fled the town with a helicopter on 6 April 1979, relocating to Kimaka in Jinja. Lieutenant Colonel Cyril Orambi was left in charge of Entebbe's defenses. The Battle of Entebbe on 7 April 1979 resulted in the destruction of most of the UAAF. Panic spread at the other air bases, and what remained of the Uganda Army Air Force completely disintegrated. This left Mukooza with no means to continue the fight, and he stayed in Jinja. By the Uganda–Tanzania War's end, the UAAF was left completely destroyed.