The post-colonial regime inherited a fractured state. Milton Obote responded to this crisis of legitimacy by forming an alliance between his political party, the Uganda People's Congress (UPC) and the Buganda monarchy party (Kabaka Yekka). With this marriage of convenience, Obote became the Executive Prime Minister and Kabaka Mutesa II became the President and Head of State. However, the alliance collapsed over a conflict over land (the ‘lost counties’) between Bunyoro and Buganda. The ‘divorce’ led to widespread violence in Buganda. Obote responded by detaining five government ministers from the Bantu region, dismissing the President and Vice President and forcing President Mutesa into exile and suspending the 1962 constitution. The government also imposed a state of emergency in Buganda, occupied Buganda’s palace, following the flight of the Kabaka to England, and introduced a republican constitution. Some Bantu-speaking groups perceived this struggle for legitimacy and power as a conflict between the Bantu south and the non-Bantu (Nilotic) north.
These difficulties overlapped with the instability generated in the region by the superpowers’ quest for hegemony during the Cold War. These crises were compounded by a conflict between Obote and his army commander, General Idi Amin. In 1971, Amin seized power. Immediately after he came to power, Amin ordered Acholi and Langi soldiers, who constituted the backbone of the army, to surrender their arms. The overwhelming majority of them did so. However, many were subsequently killed. The government extended its conflict with the Acholi and Langi by arresting, detaining and killing highly educated and influential members of the ethnic groups. Over time, Amin began to target people he perceived as disloyal from other parts of the county. To protect the regime which lacked political legitimacy in the country, Amin recruited new soldiers into the national army from West Nile. In addition, he appointed prominent Bantu to important positions in his government. The regime however largely maintained the dominance of southerners in the civil service and commerce, while the northerners largely controlled the government and army.
In April 1979, the exiled rebels, who were overwhelmingly from Acholi and Langi, assisted by the Tanzanian army and Yoweri Museveni’s Front for National Salvation (FRONASA), overthrew the Amin regime. Yusuf Lule assumed power. However, ideological and ethnic conflicts within the Uganda National Liberation Front (UNLF) and the national army led to the collapse of the Lule administration within months. Godfrey Binaisa took over, but was himself deposed in May 1980 by Paulo Muwanga and his deputy Yoweri Museveni.
The new administration organised general elections in December 1980, which were won by Milton Obote and his Uganda People’s Congress. But widespread irregularities and political violence undermined the legitimacy of the elections. The main challenger, the Democratic Party (DP), rejected Obote's victory. Museveni also rejected the results. Thereafter, a number of armed groups, including Lule’s Uganda Freedom Fighters, Museveni’s Popular Resistance Army (later they were to merge to form the National Resistance Movement/Army (NRM/A), and Dr Andrew Kayira's Uganda Freedom Movement/Army (UFM/A), declared war against the Obote government. In West Nile, Brigadier Moses Ali’s Uganda National Rescue Front (UNRF) and General Lumago's Former Uganda National Army (FUNA) also engaged the army and the UPC in bitter armed opposition.
Fighting was particularly intense in the Luwero triangle, where the mostly Baganda population was targeted for their perceived support of rebel groups. Many innocent civilians were tortured and murdered by the UNLA. Although the UNLA was a national and multi-ethnic army, the NRM/A held the Acholi exclusively responsible for the atrocities committed, and this disputed perception was to shape subsequent attitudes toward the conflict.
In July 1985, conflict between some Langi and Acholi soldiers led to the overthrow of the Obote regime. The coup, which brought General Tito Okello to power, shattered the military alliance between the Acholi and Langi and escalated ethnic violence. The Okello regime invited all fighting groups and political parties to join the military government. Every armed group and political party, with the exception of the NRA, joined the administration. The NRA, however, engaged the regime in protracted peace negotiations held in Nairobi. In December 1985, the Nairobi Agreement was signed under the chairmanship of President Moi of Kenya. However, the Agreement was never implemented and Museveni seized power on the 25th January 1986.
The NRA’s seizure of power effectively meant that for the first time, socio-economic, political and military powers were all concentrated in the south. The new administration, which absorbed political and military groups from the south and Moses Ali's UNRF group, engaged in intensive anti-northern propaganda. The administration also discriminated against groups from eastern Uganda and West Nile. This severe alienation and marginalisation led to armed conflicts in Teso and West Nile. After much destruction and displacement of the population in Teso, the government negotiated an end to the conflict in the east.