Yusuf Lule, chair of the UNLA's political arm, formed the new government. He called for law and order and outlined a strategy to rehabilitate Uganda. To improve the military's reputation, he set new standards of literacy and political education for army and police recruits. To reduce the army's political role and build a truly national force, he proclaimed his intention to draw military recruits from all ethnic groups in proportion to their population. In achieving this goal, Lule hoped to authorize increased military recruitment among the Baganda, Uganda's largest ethnic group. Non-Baganda government officials opposed this policy. The National Consultative Council (NCC), which became the new legislature, and the Military Commission, which oversaw the army's operation, refused to support Lule's policies, and they voted him out of office after only sixty-eight days as president.

In late 1979, the NCC elected Godfrey Binaisa, who had served as attorney-general under Obote and Amin, to form a new government. Binaisa, an ineffective president, failed to consolidate support within the military. This allowed senior army officers to operate almost independently of the government. Rather than authorizing military recruiting among all ethnic groups, Binaisa allowed then Minister of Defense Yoweri Kaguta Museveni to enlist a disproportionate number of volunteers from his home region in the southwest. The use of regional and ethnic affiliation as a political lever prompted a power struggle with Chief of Staff David Oyite Ojok, a northerner. Binaisa tried to resolve this dispute by dismissing Ojok. The Military Commission rejected this action, ousted Binaisa and the NCC, assumed control of the government, อออออออand called for national elections in December 1980. Milton Obote, who had been ousted by Amin's 1971 military coup, returned to the presidency. Obote called on the army to restore peace, but several ethnic-based military forces emerged instead to challenge his authority.

Among the groups opposing Obote were Museveni's National Resistance Movement (NRM) and its military wing, the National Resistance Army (NRA), both of which attracted members from western Uganda. Also working to oust Obote were the Former Uganda National Army (FUNA), most of whose members had served in the army under Amin, and the Uganda National Rescue Front (UNRF), which drew members from Amin's home territory in the northwest. In addition, the Uganda Freedom Movement (UFM) and the Federal Democratic Movement of Uganda (FEDEMU), both based primarily in Buganda, opposed Obote. To suppress these groups, the Ministry of Defense spent one-fourth of the government's recurrent expenditures in 1983 and 1984 nevertheless, these groups remained active against the government.

The UNLA mounted counterinsurgency operations in numerous areas, including Arua and Moyo in the northwest, Karamoja in the northeast, and Luwero north of Kampala. The army, whose ranks were filled with poorly trained, poorly clothed, poorly fed, and irregularly paid foot soldiers, had almost no ability to sustain counterinsurgenc y op y operations. The government's inability to maintain discipline over the armed forces allowed many units to degenerate into unruly gangs. The military perpetrated numerous human rights violations and engaged in several illegal activities, including theft, looting, assault, and holding civilians for ransom.

In pursuit of remnants of Amin's army in the northwest, UNLA troops entered the area and killed thousands of civilians, many of whom were women, children, and old people. According to a 1983 United Nations (UN) report, this reign of terror forced an estimated 260,000 refugees to flee to Sudan and Zaire. In the northeast, cattle rustlers acquired an army arsenal of automatic weapons and ammunition, which they used on raids in neighboring districts as well as southern Sudan and Kenya. In response to these raids, the UNLA and Kenyan authorities mounted a pacification campaign, which resulted in the eradication or displacement of most of southern Karamoja's population by mid1984 .

Despite its many illegal activities, the UNLA's atrocities in the Luwero Triangle attracted the most international attention. In 1980 the inhabitants of this region had rejected Obote's rule and welcomed opposition guerrillas, including Museveni's NRA. Until the end of the Obote regime in 1985, the UNLA waged war against rebels and civilians in the area, and the Luwero Triangle became known for its devastation. Several local officials estimated that the UNLA killed between 100,000 and 200,000 civilians and that it detained, tortured, and assaulted several thousand others. The International Committee of the Red Cross (ICRC) reported that 150,000 people displaced from Luwero had taken refuge in its camps.

By mid-1985 the demoralized UNLA began to disintegrate. Obote's promotion of Opon Acak, a junior officer from Obote's home region of Lango, to army chief of staff alienated much of the Acholi-dominated officer corps. The UNLA's failure to defeat the NRA, which had emerged as the strongest antigovernment guerrilla group, widened the gulf between the army and the Obote regime. On July 27, 1985, Brigadier (later Lieutenant General) Basilio Olara Okello and a small group of UNLA soldiers overthrew the Obote regime. According to Okello, he launched the coup "to stop the bloodshed to create conditions for viable peace, unity, development, and the promotion of human rights."

Under the new government, which ruled through a Military Council, General Tito Lutwa Okello became head of state, and Brigadier Basilio Olara Okello served as the chief of defense forces. To establish a coalition government, Tito Okello invited all political parties and guerrilla organizations to cooperate with the new regime. In August 1985, members of FEDEMU, FUNA, UFM, and UNRF agreed to this proposal, thereby gaining representation on the Military Council. However, this alliance of former enemies proved unable to govern Uganda. The NRA took advantage of the weak coalition government, established control over rural areas of southwestern Uganda, and overran several military garrisons west of Kampala. The NRA also established an independent administration in former president Amin's home territory in the northwest.

Data as of December 1990