The roots of the current war between the government of Uganda and the Lord’s Resistance Army (LRA) in Acholiland are entwined with the history of conflicts in Uganda and the rise to power of the National Resistance Movement/National Resistance Army (NRM/A). The conflict has persisted because of fragmented and divisive national politics, strategies and tactics adopted by the armed protagonists, and regional and international interests. The harrowing war has claimed many innocent civilian lives, forcefully displaced over 400,000 people and destroyed schools and health centres. In addition, the war has been characterised by widespread and systematic violations of human rights, including rapes, abductions of men, women and children, torture, increased economic decay, and national and regional insecurity.

Uganda lies along the Equator, between the great East African Rift Valleys. It is a landlocked country, bordered by Sudan in the north, Kenya in the east, Tanzania in the south, Rwanda in the southwest and the Democratic Republic of Congo in the west. With a landmass of 241,139 square kilometres, its population is about 20 million. Its territory includes Lake Victoria, Lake Albert, Lake Edward and Lake Kyoga. These lakes, together with several elaborate networks of river drainage, constitute the headwaters of the River Nile. The country’s economy is primarily agrarian, comprised mostly of smallholdings though pastoralism is dominant in Karamoja and Ankole.

Lake Kyoga forms both a physical and linguistic marker. South of Kyoga is the so-called Bantu region, with the centralised pre-colonial states of Buganda, Toro, Ankole (Nkore) and Bunyoro the dominant territories. North and east of Kyoga are the non-Bantu territories of the Acholi, Alur, Langi, Iteso and Karamojong. The Acholi inhabit present-day northern Uganda and southern Sudan, where, in the pre-colonial era, they constructed decentralised states. In the 1970s, the Acholi district of northern Uganda was divided into Gulu and Kitgum districts. In 2001, Kitgum was subdivided to create a third district of Pader. The three districts constitute an area commonly referred to as Acholiland.

Contemporary violent conflicts in the country are directly related to the profound crisis of legitimacy of the state, its institutions and their political incumbents. This crisis, in part, reflects the way the state was constructed through European expansionist violence, manipulation of pre-existing differences, administrative policies of divide and rule and economic policies that further fractured the colonial entity. These policies did not only undermine the faltering legitimacy of the state, but also impeded the emergence of a Ugandan nationalism and generated ethnic, religious and regional divisions that were to contribute in later years to instability and political violence.

One significant divide was along the lines of religious affiliation, which can be traced back to the arrival of Islam, Protestantism and Catholicism in Buganda. These religious groups engaged in a ferocious conflict for dominance, and the Protestant faction emerged victorious after the Imperial British East Africa Company intervened in their favour. Anglicans were to late dominate the top positions in the civil service, and this structural inequality was maintained after the colonial era. Consequently, religious beliefs and political party affiliations were to become entangled.

Conflicts in the colonial state were exacerbated by the partition of the country into economic zones. For example, while a large portion of the territory south of Lake Kyoga was designated as cash crop growing and industrial zones, the territory north of Lake Kyoga was designated as a labour reserve. This partition, which was not dictated by development potentials, led to economic disparities between the south and the north. The fragmentation of the society was compounded by the economic-cum-administrative policy that left the civil service largely in the hands of Baganda and the army largely in the hands of the Acholi and other northern ethnic groups. These policies also widened the gulf between the socio-political south and the socio-political north. This was further sustained by the administrative policy that relied on the Baganda as colonial agents in other parts of the country. The policy of divide and rule, which rested on so-called ‘indirect rule’, led to widespread anti-Buganda sentiment.

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.

By April 1986, the Acholi had largely come to terms with the NRA victory. The majority of former UNLA soldiers also heeded the appeal made by the government to hand over their arms and demobilise. The response by the Acholi ended the armed engagement in the territory. However, after months of relative calm, anxieties escalated when the NRA began to commit human rights abuses in the name of crushing a nascent rebellion. Over time NRA soldiers plundered the area and committed atrocities, including rape, abductions, confiscation of livestock, killing of unarmed civilians, and the destruction of granaries, schools, hospitals and bore holes escalated. These atrocities in Acholiland were justified by some as revenge for the ‘skulls of Luwero’.

Against this background of mistrust and violence, in May 1986 the government ordered all former UNLA soldiers to report to barracks. The order was met with deep suspicion, in part, because it was reminiscent of Amin's edict that led to the 1971 massacre of Acholi soldiers. Some ex-UNLA soldiers went into hiding; others fled to Sudan and some decided to take up arms. Soon, these ex-soldiers were joined by a stream of youths fleeing from NRA operations. During this period, the Sudan People's Liberation Army (SPLA), which was perceived by Acholi refugees as an ally of the Museveni government, attacked a refugee camp in southern Sudan. On August 20, 1986, some Acholi refugee combatants, led by Brigadier Odong Latek, attacked the NRA. This armed group, known as the Uganda People's Democratic Army (UPDA), was later joined by the Holy Spirit Mobile Forces / Movement (HSMF/HSM), Severino Lukoya's Lord's Army, ultimately to be followed by the Lord's Resistance Army (LRA).

The war has lasted for nearly sixteen years because of a number of interrelated factors. To begin with, the war in Acholi has become an extension of regional and international power struggles. On the regional front, Uganda provided military hardware and sanctuary to the SPLA. In retaliation, the Sudan government provided sanctuary and military hardware to the LRA. On the international front, both the Uganda government and the SPLA received military and political support from the US, in part to curtail the influence of the Islamic government in Khartoum. Another factor perpetuating the conflict has been that the war has become a lucrative source and cover for clandestine income for high-ranking military and government officials and other profiteers. In addition, the unwillingness of the government and the LRA to genuinely pursue a negotiated settlement has sustained the war. Lastly, atrocities committed by the LRA against unarmed civilians and the unwillingness of the rebel group to accept alternative political views on the conflict have prolonged the war.

The horrific and prolonged consequences of this war have devastated the society – a society that has been reduced to ‘displaced camps’, where people languish without assistance and protection. The war has also destroyed the culture and social fabric of the Acholi society. Large numbers of orphans, who fend for themselves, illustrate this tragedy. Furthermore, some children have been abducted by the LRA and forced to torture and kill. Thus, the Rt. Rev. Macleod Baker Ochola II summarised some of the effects the war on Acholiland as follows:

‘Violent deaths of our people in the hands of various armed groups; arson perpetrated on mass scale in our land; rape and defilement of our women and girls; abduction of our young people; forced recruitment of our people into rebel ranks; the prevalence of a general atmosphere of fear and disenchantment amongst our people; mass displacement of our people; creation of protected villages which have become breeding grounds for malnutrition and deaths resulting from cholera, measles, and preventable diseases amongst our people; and destruction of our infrastructures and continuous decline in socio-economic growth.’(KM, 1997)

The war has also destabilised other parts of the country and contributed to other regional conflicts in the Great Lakes. The multi-faceted and interrelated causes and consequences of the war should not, therefore, be seen as exclusively an Acholi issue. Nor should the war be treated as merely a humanitarian crisis. It has many dimensions: political, social, economic and humanitarian. As such, durable solutions will need to respond to all of these challenges.