In February 1981, shortly after the new Obote government took office, with Paulo Muwanga as vice president and minister of defense, a former Military Commission member, Yoweri Museveni, and his armed supporters declared themselves the National Resistance Army (NRA). Museveni vowed to overthrow Obote by means of a popular rebellion, and what became known as "the war in the bush" began. Several other underground groups also emerged to attempt to sabotage the new regime, but they were eventually crushed. Museveni, who had guerrilla war experience with the Front for the Liberation of Mozambique (Frente de Libertaçâo de Moçambique--Frelimo), campaigned in rural areas hostile to Obote's government, especially central and western Buganda and the western regions of Ankole and Bunyoro.

...In early 1983, to eliminate rural support for Museveni's guerrillas the area of Luwero District, north of Kampala, was targeted for a massive population removal affecting almost 750,000 people. These artificially created refugees were packed into several internment camps subject to military control, which in reality meant military abuse. Civilians outside the camps, in what came to be known as the "Luwero Triangle," were presumed to be guerrillas or guerrilla sympathizers and were treated accordingly. The farms of this highly productive agricultural area were looted--roofs, doors, and even door frames were stolen by UNLA troops. Civilian loss of life was extensive, as evidenced some years later by piles of human skulls in bush clearings and alongside rural roads.

...In this deteriorating military and economic situation, Obote subordinated other matters to a military victory over Museveni. North Korean military advisers were invited to take part against the NRA rebels in what was to be a final campaign that won neither British nor United States approval. But the army was warweary , and after the death of the highly capable General Oyite Ojok in a helicopter accident at the end of 1983, it began to split along ethnic lines.

...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 [and sought national reconciliation among the warring rival groups (tribal and political)]. Immense problems of reconstruction awaited the new regime.