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Obote’s rule became increasingly brutal and autocratic, and went on until 1971 when he was ousted by Major General Idi Amin. This was during the height of the Cold War and there is evidence that US and British military agencies provided military shipments and training to Amin to support the coup. Obote was perceived as a leftist supporting pan African liberation movements supported by the Soviet Union and China and the U.S. and Britain felt they could manipulate Amin.

Like Obote, Amin engaged in divide and rule tactics, befriending Buganda and turning against Lango and Acholi. Amin purged the army of Acholi and Langi members, then had many former Acholi and Langi army members slaughtered. He moved against the Acholi and Langi civilian communities, detaining and murdering many who were prominent and the most educated. Amin installed new army members from the West Nile, appointed members from the South to key government positions and kept the animosity going between north and south. It was the slaughter of the Acholi and Langi community, in which possibly several hundred thousands were killed, which accelerated the dynamics which would later lead to the current war in Northern Uganda. Amin maintained popularity with many people, though, by ousting the Asian community, most of whom were British citizens, confiscating their land. Declaring himself president for life, Amin started claiming part of Kenya and Tanzania for Uganda, giving Tanzania the excuse to intervene and oust Amin. In 1979, a coalition force of Amin’s enemies, mostly exiled Acholi and Langi and Yoweri Mseveni’s Front for National Salvation (FRONASA) and the Tanzanian army invaded from Tanzania and overthrew Amin, who fled into exile.

New elections were organized in 1980 and Obote’s Uganda People’s Congress (UPC) won, but widespread violence and perceived voting irregularities and continued repression of the Acholi and Langi communities led to a challenge by the Democratic Party (DP) and Museveni. A coalition of forces, Museveni’s reformed National Resistance Movement/Army (NRM/A), the Uganda Freedom Movement/Army (UFM/A), and the Uganda Freedom Fighters moved against Obote’s government. They were supported by the West Nile’s Uganda National Rescue Front (UNRF) and the Former Uganda National Army (FUNA).

Fighting was countrywide but most concentrated in the Luwero Triangle. There were many atrocities during this period, especially against the Buganda population which was perceived as supporting opposition groups and for their previous support of Amin. These murders and tortures were attributed to Acholi members of the army, which the Acholi disputed. These accusations, however, would further fuel animosity between Acholi and other groups.

In 1985, conflicts between Acholi and Langi members of the military precipitated a coup and the second ouster of Obote, bringing General Tito Okello from Acholi to power. This ended the military alliance between Acholi and Langi, setting the scene for Acholi/Langi conflict. In addition to this conflict, the main conflict in Uganda was now between Okello’s government and Museveni’s National Resistance Army (NRA) which had a base in the West and increasing support in the South. Negotiations between the Okello government and the NRA took place in Nairobi in 1985, officiated by Kenya’s President Daniel Arap Moi, but the agreement never held, and NRA pressed on. It was also alleged that the Okello government perpetrated mass atrocities against civilians in order to suppress support for the NRA. NRA support grew around the country and in January, 1986, the NRA reached Kampala and overthrew the government, forcing Okello to flee north to Sudan. A new government was organized and Museveni declared president. For the first time, both political and military power was situated in the south.

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