From 1986 to 1994, a variety of rebel groups waged a civil war against the Ugandan government of President Yoweri Museveni. Most of the fighting took place in the country's north and east, although the western and central regions were also affected. The most important insurgent factions were the Uganda People's Democratic Army (UPDA), the Uganda People's Army (UPA), Alice Auma's Holy Spirit Movement (HSM), and Joseph Kony's army (which later became the Lord's Resistance Army). Several smaller rebel factions and splinter groups of the larger movements waged their own campaigns; the rebels often clashed with each other. All belligerents, including the government, targeted civilians and committed human rights violations. In course of fighting that involved tens of thousands of troops, the Ugandan government was able to gradually defeat or contain most rebel factions. The operations in the north and east caused great destruction and resulted in high civilian casualties.
By 1994, the HSM and UPDA had disintegrated, the UPA had been reduced to small splinter groups, and Joseph Kony and his forces were at least weakened. However, the situation in the entire region drastically shifted in that year, as outside powers intervened and began to fund insurgencies to topple Museveni. In turn, Uganda was drawn into cross-border conflicts in Zaire and Sudan. These developments resulted in a resurgence of insurgent activity in northern Uganda. Several groups which emerged during the 1986–1994 conflict, including Kony's Lord's Resistance Army, continue their insurgencies to the present day.
Background
After its independence in 1962, Uganda had fallen under a succession of authoritarian regimes, suffered from economic crises, and experienced several military conflicts. In 1979, Ugandan President Idi Amin was overthrown during the Uganda–Tanzania War, followed by the return to power by ex-President Milton Obote. Parts of Amin's Uganda Army and various anti-Obote groups consequently launched rebellions, resulting in the highly destructive Ugandan Bush War. Obote was toppled by elements of his army, the UNLA, in 1985, resulting in the formation of a regime led by Tito Okello. Although the new military leadership succeeded in convincing some rebel groups to join a coalition government, one rebel group was strongly opposed to compromise. Led by Yoweri Museveni, the National Resistance Movement (NRM) and its armed wing, the National Resistance Army (NRA), intended to achieve a full military victory and exploited the chaos after Obote's overthrow to seize large swaths of southwestern Uganda. The NRA included a large number of ethnic Tutsi who belonged to Rwandan refugee families. As a result of international pressure, the NRM signed to the "Nairobi Agreement", a peace treaty negotiated under the oversight of Kenyan President Daniel arap Moi on 17 December 1985.
The NRA quickly reneged on its promise, breaking the truce with Okello's government by launching several successful offensive operations. President Moi regarded the NRM's failure to uphold the treaty a personal insult, and consequently developed a deep resentment toward the NRM in general and Museveni in particular. After defeating the UNLA and its allies in a series of major battles, the NRA conquered Uganda's capital Kampala, in January 1986. Museveni was declared the country's new president and the NRA became the new national army. Okello's coalition government subsequently collapsed. Regardless, the UNLA continued its resistance in eastern and northern Uganda. UNLA officers appealed to civilians in the north to take up arms and join their cause, claiming that the NRA would kill everyone. If volunteers failed to emerge, civilians were simply rounded up and forcibly conscripted. The NRA had defeated the remaining UNLA units by March 1986, whereupon the latter fully disintegrated. Many UNLA fighters did not surrender, however, but hid their weaponry. A number of senior UNLA officers also retreated into Sudan, taking weaponry and recruits with them to continue the war.
In addition, many people in northern and eastern Uganda distrusted the NRA. The UNLA and allied forces, mostly ethnic Acholi and Langi from the north, had committed many war crimes in the south during the Bush War. Northerners feared that the NRA might want to take brutal revenge on the north's population. The NRM and NRA actually increased such worries through their statements, traditions, and propaganda. The NRM/NRA leadership had occasionally used racist rhetoric in regards to their northern opponents during the Bush War. Many southerners, including NRM/NRA members, regarded the northerners as primitive and even considered them non-Ugandan foreigners. Despite official condemnations by Museveni's newly formed government, the NRM takeover resulted in cases of mistreatment and murders of northerners in the south. In turn, many Acholi felt bitter about Museveni having reneged on the Nairobi Agreement and overthrowing Tito Okello who had been the country's first President of Acholi ethnicity.
History Growing unrest
In the months before and after the capture of Kampala, the NRA greatly expanded in size by recruiting thousands of new troops as well as defected troops formerly loyal to UNLA and other militant factions. In some cases, entire units were simply renamed and then integrated into the NRA, even keeping their commanders. For much of the Bush War, the NRA had maintained relatively high standards in discipline, training, and indoctrination, but the mass expansion resulted in it becoming a much more heterogeneous force. This gravely impacted the NRA as it began to secure territory captured from the UNLA in Uganda's east and north.
After UNLA had fully collapsed in March 1986, the NRA began counter-insurgency operations to eliminate groups which had refused to lay down arms. At first, the NRA encountered little opposition in former UNLA centers such as Acholiland and Teso. Many locals were surprised that the NRA soldiers behaved relatively well, and many ex-UNLA troops felt secure enough to return to their homes. The NRA also encountered little resistance in the West Nile region of northwestern Uganda. Tired of the constant war, the local elders convinced most local militants to peacefully surrender and cooperate with Museveni's government. One West Nile armed group, the UNRF (I), had even agreed to a favorable deal with the NRM, integrating its fighters into the NRA.
However, the situation began to quickly deteriorate in the north for several reasons: Acholiland and Teso had been heavily dependent on the UNLA, as the regions were poor and the soldiers' wages had supported the regions' economies. As most UNLA soldiers lost their jobs, the regions experienced economic chaos. In addition, the NRM government decided to disband many local militias which had guarded communities against cattle-raiders, mostly Karamojong groups. The NRM feared that the self-defense groups might turn into rebels. Without the militias' aid, the NRA proved unable to keep raiding in check, resulting in northern and eastern pastoral communities being devastated. Many demobilized UNLA veterans were also no longer willing to work as peasants and integrate into the civilian life, instead turning to banditry and worsening the economic unrest. The NRM attempted to co-opt local leadership in the north and east through a decentralised system of local administration, using "resistance councils" (RC). However, local elites factually lost their old power in the new NRM-dominated government. This prompted many to retreat into rural areas, where they spread their beliefs and grievances.
One of the earliest insurgencies emerged in Teso during this time. As early as January 1986, local leaders prepared for an uprising. Led by Nelson Omwero and Charles Korokoto, they organized a rebel group known as "Force Obote Back Army" or "Force Obote Back Again" (FOBA). However, FOBA quickly began to lose popular support and to splinter after beginning its uprising.
Faced with worsening security conditions due to latent militant attacks and banditry, the NRA garrisons in Gulu, Kitgum, and Teso districts became increasingly repressive. One NRA unit, the 35th Battalion, particularly tarnished the NRA's reputation through excessive behavior such as arbitrary arrests and torture of civilians. The 35th Battalion was one of the units mostly formed from non-NRA fighters, in this case ex-UFM rebels. Besides the undisciplined troops, the ethnic Tutsi troops in the NRA – who had suffered from discrimination and pogroms in the past – also proved prone to excessive violence. The increasingly brutal behavior of the NRA widened the existing rift between the NRM government and the northerners. When the government ordered all ex-UNLA soldiers to report and hand over their weapons to the NRA in May 1986, the locals consequently believed that this was a ploy to massacre all ex-UNLA forces. The tone of the radio announcement of the disarmament order was "widely" perceived as threatening, causing further unrest. The NRA then launched a gun-collection campaign in Acholiland, but many undisciplined NRA soldiers used the opportunity to harass and steal from the locals, claiming to take back everything "stolen" from southern Uganda during the Bush War. The scale of the abuses was unprecedented in the area, even compared to the situation under previous regimes. The latter had often mistreated the local elites and townspeople, but left the poor and rural mostly alone. A growing number of ex-UNLA soldiers were also arrested on suspicions of weapon ownership or anti-government activities. Most ex-combatants consequently opted to flee into the bush rather than following the order, providing recruits for emerging rebel groups. Ex-Brigadier Justine Odong Latek organized a meeting of ex-UNLA soldiers at Koch-Goma, and began to plan an uprising. In July 1986, around three-quarters of the police force were discharged, fuelling fears that the NRM government might want to punish all those who had worked for the old security forces.
Escalation in the north
In May 1986, exiled ex-UNLA members led by Brigadier Odong Latek organized a rebel group at Nimule, Sudan. It was named "Uganda People's Democratic Army" (UPDA), while its political wing was termed the "Uganda People's Democratic Movement" (UPDM). The political wing was led by Eric Otema-Allimadi, former Prime Minister in the Obote government. The group initially stayed in southern Sudan, tolerated by the Sudanese government. It is disputed whether the group received actual support from the Sudanese leadership. According to journalist Caroline Lamwaka, the UPDA was not directly supported by the Sudanese government, but was able to buy guns and bullets from Sudanese sources, including the Sudanese Armed Forces. The UPDA was organized into eight brigades, each headed by an ex-UNLA officer of Acholi ethnicity; each brigade was assigned an area in northern Uganda. The eight officers then began to collect troops inside and outside Uganda. It soon began to clash with another insurgent group, the Sudan People's Liberation Army (SPLA). This motivated the UPDA to return to Uganda.