In 1979 Tanzanian forces and Ugandan rebels invaded Uganda and overthrew Amin. Lumago fled from his mansion in Koboko, which was subsequently destroyed. He went to Zaire, from where he organised remnants of the Uganda Army into a rebel force. Together with other pro-Amin groups, Lumago's force invaded the West Nile region in 1980, starting the Ugandan Bush War. He eventually rose to commander of the pro-Amin insurgent group known as Former Uganda National Army (FUNA). In July 1985, the Ugandan government under Tito Okello invited him and about 1,500 FUNA fighters to return. He accepted, joined Okello's government, and consequently began to fight against another rebel movement, the National Resistance Army (NRA) of Yoweri Museveni. Lumago set up his headquarters in a hotel in Kampala from where he gave interviews and directed his troops. Meanwhile, FUNA was accused of gross indiscipline, reportedly raping and murdering civilians in the capital and other areas, though Lumago denied these charges. He also lobbied for an amnesty to allow Idi Amin to return to Uganda. Lumago's troops fought with the UNLA to defend Kampala from a NRA offensive in January 1986, but were defeated. He was forced to flee back into Zaire. Lumago still served as one of the commanders of FUNA by 1990, serving alongside Dusman Sabuni and Abdulatif Tiyua. He later became an associate of the West Nile Bank Front. Despite appeals by Ugandan government officials to peacefully return to Uganda, Lumago initially refrained from laying down his weapons out of fears of reprisals due to his long opposition against Museveni. He continued to live in exile until 1997.