The military government of General Tito Lutwa Okello ruled from July 1985 to January 1986 with no explicit policy except the natural goal of self-preservation--the motive for their defensive coup. To stiffen the flagging efforts of his army against the NRA, Okello invited former soldiers of Amin's army to reenter Uganda from the Sudanese refugee camps and participate in the civil war on the government side. As mercenaries fresh to the scene, these units fought well, but they were equally interested in looting and did not discriminate between supporters and enemies of the government. The reintroduction of Amin's infamous cohorts was poor international public relations for the Okello government and helped create a new tolerance of Museveni.

In 1986 a cease-fire initiative from Kenya was welcomed by Okello, who could hardly expect to govern the entire country with only war-weary and disillusioned Acholi troops to back him. Negotiations dragged on, but with Okello and the remnants of the UNLA army thoroughly discouraged, Museveni had only to wait for the regime to disintegrate. In January 1986, welcomed enthusiastically by the local civilian population, Museveni moved against Kampala. Okello and his soldiers fled northward to their ethnic base in Acholi. Yoweri Museveni formally claimed the presidency on January 29, 1986. Immense problems of reconstruction awaited the new regime.