This dyad belongs to the conflict Uganda: Government

Summary of conflict Uganda: Government

Uganda's post-independence history has been characterized by violence. The country has seen almost continuous warfare since 1978, with rebel groups in different parts of the country fighting successive regimes. A common denominator for many of the conflict phases has been political elites manipulating ethnic and regional differences in order to legitimate their claim to power. After the geographically widespread fighting of the 1980s and 1990s, only two rebel groups were active for most of the 2000s: LRA, presently not active in Uganda, but in DR Congo, South Sudan and the CAR and ADF, active in DR Congo.

Since the failure of Operation Lighting Thunder in December 2008, the LRA fighters have been dispersed over a vast territory stretching over DR Congo, CAR and South Sudan. Increasingly weakened by military pressure and defections, the group still remained a threat to the civilian population. On 4 February 2021, the International Criminal Court (ICC) convicted Dominic Ongwen, a former LRA commander with 61 counts of war crimes and crimes against humanity.

Idi Amin seizes power in 1971

After gaining independence from Britain in 1962, Uganda soon became trapped in a pattern of leadership manipulation of ethnic and religious differences. To some extent, this was a product of colonial times, which had seen the diversity of the country's people being used to divide and rule. When the country became independent, the societal cleavages were deep, and national unity absent.

Between 1962 and 1971, Milton Obote, from the northern Langi ethnic group, ruled the country. During his reign, the national armed forces were dominated by Langi soldiers as well as by fellow-northerners from the Acholi ethnic group. On 25 January 1971, Obote's government was overthrown in a coup led by Major-General Idi Amin, commander of Uganda's Army. Despite some resistance by soldiers loyal to President Obote, Amin's troops managed to seize all key installations in the capital Kampala and neighboring Entebbe. In the northeastern Karamoja region, Obote's supporters offered fiercer resistance, and it was not until 29–30 January that General Amin's forces managed to captured the last Air Force base.

To consolidate his power, Amin changed the ethnic balance of the military, recruiting heavily from the West Nile region, his home area. The army ranks were filled with Nubians in general, and Amin's own Kakwa tribe in particular. Large numbers of Acholi and Langi soldiers were massacred presumed to be supporters of the deposed Obote.

Two failed attempts to oust Amin (September 1972 and March 1974)

After having been deposed, former President Obote soon initiated both diplomatic and military efforts to ensure his return to power. Diplomacy-wise, he visited a number of African countries, searching for support or at least for continued recognition of himself as President of Uganda. On the military front, Obote went on to organize his supporters. Building on loyal officers and soldiers from the Ugandan Army – mainly from the Lango and Acholi ethnic groups – who had fled Uganda after the coup, he set up KM (Kikoosi Maalum). Only a month after Amin's coup, the training of KM commenced in Sudan.

In a parallel development, a young Yoweri Museveni was at this time en route to set up a rebel group in opposition to Amin. Exiled in Tanzania, he had approached Tanzanian president Julius Nyerere for support. However, Nyerere believed in a unified resistance under the leadership of Obote. Hence, Museveni spent 1971 trying to find common ground with the deposed president. The two differed on two crucial aspects, making this difficult. Firstly, Museveni and Obote favored different military strategies, with the former believing in fighting a guerrilla insurgency, mobilizing the population, and the latter advocating a conventional war with the backing of friendly powers such as Tanzania, Sudan and Somalia. Second, the two leaders had different views on the organization of the struggle. While Museveni sought to establish a common front with all loose opposition groupings, Obote wanted the resistance to be organized under him, as president. These fundamentally different positions made unification impossible, and instead, Museveni sought assistance from the Mozambiquan rebel group Frelimo (Frente de libertação de Moçambique: Front for the Liberation of Mozambique), which provided both training and some arms over the next few years.

Meanwhile, the KM fighters who had trained in Sudan were transferred to Tanzania in July 1972 in preparation for an invasion. Museveni, who had by then only just began setting up his group, together with some of his friends, decided to join the invasion, even though they had reservations about the plan. The initial idea had been to launch a three-pronged attack, with one group supposed to land at Entebbe Airport, using a hijacked airplane, and the other two crossing the border from Tanzania. However, the plan soon ran into trouble as the airborne group failed to take off. Despite this, a confused land invasion was launched on 17 September 1972, with over 200 fatalities reported only during the first day. It soon became apparent that the invasion would fail. The force that had launched the eastern-most invasion was driven back already on the night of the 17 September. Over the next two days, scattered groups of KM fighters made their way back to Tanzania from the western front, and by 20 September, the invasion attempt had been completely defeated.

Yet another attempt to oust Amin was made in March 1974, this time from within his own army. Dissatisfied with the president's appointment of non-Ugandans to key positions in the army and in government agencies, the Malire Reconnaissance Regiment under the leadership of Brigadier Charles Arube moved to overthrow Amin in a coup. The coup attempt got off to a good start, with key installations being captured by Arube's troops. However, Amin loyalists were eventually able to defeat the coup-makers, and the fighting resulted in hundreds of deaths. Most noteworthy about the attempted putsch was that it was organized and led by Kakwa officers, the president's fellow-tribesmen.

The ousting of Amin in 1979

After the failed invasion attempt of 1972, former president Milton Obote's rebel group KM (Kikoosi Maalum) was largely demobilized. Museveni, on the other hand, continued recruiting followers and established the rebel group Fronasa (Front for National Salvation). Having attempted and failed to initiate a guerrilla struggle within Uganda in late 1972 and early 1973, Fronasa subsequently focused its effort on military training over the next few years.

Following an interstate conflict between Tanzania and Uganda in late 1978, the situation appeared ripe for the exiled groups opposing Amin. With Tanzania on their side and with Amin's army in disarray, conditions for an invasion looked favorable. In mid-January 1979, Milton Obote broke almost six years of silence to read a statement on the situation in Uganda and to call for a nationwide rebellion to overthrow Amin's regime. The statement had been drafted together with a number of exiled groups, seeking Amin's ouster, notably FRONASA. Subsequently, KM, Fronasa, and the Tanzanian armed forces (TPDF) joined hands and invaded Uganda. In late March both KM and Fronasa joined the broad-based rebel movement UNLF (Uganda National Liberation Front), which – despite Libyan troops entering the scene on the side of Amin - succeeded in overthrowing Idi Amin on 11 April 1979.

Rebels in the West Nile (1980-83)

During President Idi Amin's years in power 1971-79, the army was fraught by ethnic manipulations and purges, leaving it largely made up by soldiers originating in Amin's own home region, the West Nile region in the north-western part of the country. Subsequently, when the victorious UNLF (Uganda National Liberation Front) together with troops from Tanzania entered Kampala (see "The ousting of Amin in 1979"), the former government army fled towards the West Nile region and was eventually forced to retreat into Sudan and Zaire. During 1980 these remnants of Idi Amin's army re-organized as FUNA (Former Ugandan National Army) and began making incursions into the West Nile region.

In October the group carried out a large-scale invasion, overrunning a number of government garrisons. However, due to internal problems, numerous rebel fighters soon began deserting while the remaining fighters were forced to withdraw in the face of a UNLA (Uganda National Liberation Army; the name of the new national armed forces) counter-attack. The relief troops sent to launch the counter-offensive were from the Gulu militia, dominated by ethnic Acholis. Acholi and Lango people had been the primary targets of Amin's atrocities, and when the Acholi troops arrived in Amin's home region, they started carrying out large-scale revenge killings on the civilian population. Thus, the last months of 1980 saw hundreds of thousands of West Nilers leaving Uganda and crossing into either Sudan or Zaire, leaving the region near depopulated.

In early 1981 the rebels were weakened by a split in the movement caused by ethnic tensions. The Aringa contingent of FUNA broke away, creating UNRF (Uganda National Rescue Front), while the Kakwas remained. In-fighting soon erupted between the two groups, with UNRF coming out on top. A majority of FUNA insurgents retreated across the border into Sudan and DR Congo (Zaire), launching occasional ambushes against the UNLA. UNRF, in contrast, remained in the West Nile and continued to engage in warfare with the UNLA throughout 1982. In December of that year, UNLA mounted the so-called Christmas Offensive, making large-scale sweeps against UNRF, again causing thousands of Ugandans to flee into southern Sudan. The offensive succeeded in substantially weakening the rebels and its activity subsequently dwindled dramatically, petering out in late 1983.

Rebels in and around Kampala: UFM's armed struggle (1982)

After having overthrown Idi Amin, the opposition coalition UNLF's (Uganda National Liberation Front) unity soon fell apart. In the subsequent struggle for power, a string of governments replaced each other. Directly after the toppling of Amin, the leader of UNLF, Yusef Lule had become the provisional president of the country. When he was dislodged from power in June the same year, one of his ministers, Dr. Andrew K. Kayiira, left the UNLF and created UFM (Uganda Freedom Movement), which came to be regarded as a Baganda (one of the largest ethnic groups in the country) army. The new group was subsequently led by Kayiira, together with B-K-Kirya and Dr. Arnold Bisase. On 9 February 1981, the group announced an armed struggle aimed at toppling the Obote regime, which had just been installed.

UFM's fighters received little if any training, and while spectacular, the group's attacks were also reckless and uncoordinated, wherefore they failed to have any greater impact on the security situation. In February 1982, a large-scale attack was launched on the Malire Barracks in the capital, but due to the lack of training and bad planning, the group ended up losing large quantities of arms and ammunition. After this setback, Kayiira attempted to build up a new structure, but the group had been infiltrated by government agents. In August, UFM camps were stormed by government forces, and many highly trained fighters were caught and killed. Several hundred of its guerrillas were subsequently captured around Mpigi in early September, after which it became clear that the movement was a spent force.

The bush war (1981-86)

After succeeding in ousting Idi Amin, Museveni's Fronasa (Front for National Salvation) became increasingly marginalized in the new national army, which was dominated by Obote's former rebel group KM (Kikoosi Maalum). Also politically, Museveni faired poorly. In June 1980, he formed a new party, UFM (Uganda Patriotic Movement), to contest the national elections that were to be held on 10 December the same year. In the atmosphere of distrust and factionalism that characterized the run-up to the elections, Museveni pledged to launch an armed struggle against any government that assumed power through a rigged election. When Obote's party UPC (Uganda People's Congress) won a majority of the votes, Museveni consequently claimed that the elections had been "rigged in advance" and vanished from sight, only to reappear in February 1981 with his newly formed rebel group, the PRA (Popular Resistance Army).

During this early stage of the conflict, most fighting took place in parts of Luwero and Mpigi districts, in the so-called Luwero triangle. Fighting-wise, the period was characterized by guerrilla warfare, with the rebels launching ambushes and quick surprise attacks on soft targets such as police posts and small army detachments, attempting to seize arms to build up their arsenal.

In a move to broaden the appeal of his group, Museveni traveled to Nairobi in mid-1981 to meet with Professor Yusufu Lule, former leader of UNLF (Uganda National Liberation Front) and president for a brief period following the ouster of Idi Amin in 1979. At the meeting, it was agreed that PRA would merge with Lule's group UFF (Uganda Freedom Fighters), thus creating the NRM (National Resistance Movement), with an armed group called NRA (National Resistance Army). Having no fighting force to speak of, Lule's contribution to the new group was largely his image. With Lule as designated chairman, NRM's political acceptance increased greatly both internationally and among the Buganda ethnic group. Since Museveni was from the Banyankole ethnic group, recruitment was difficult in the ethnicity conscious Uganda, and it was imperative for Buganda to lend their support since the conflict was fought on their territory. Museveni continued to wield most power also in the new organization, now as vice-chairman and chairman of the high command.

In mid-1982, NRA managed to withstand the large government offensive, "Operation Bonanza", which was aimed to close in and flush out NRA from the Luwero triangle. For the civilian population in the affected area, the situation became increasingly difficult during the year, as the government forces frequently turned on them after guerrilla attacks and reports about the government army's poor human rights conduct began to circulate. This would become a problematic issue for President Obote in the coming years.

In January 1983, President Obote launched his biggest offensive so far, deploying 75% of the government army's total strength in the Luwero triangle. This time NRA was unable to hold out, and the rebels were forced to retreat into Singo district in February and March. After the retreat, NRA became more mobile in its tactics, and the group's activities were carried out all over the war-zone, and at times even beyond it.

On 3 December 1983, the government army suffered a heavy setback as its Chief-of-Staff and the key man in the army, General David Oyite-Ojok was killed in a helicopter crash. This brought ethnic tensions in the army to surface. The Ugandan armed forces under Milton Obote were largely made up of two ethnic groups, Acholi and Lango. Oyite-Ojok was a Lango that had been respected by both sides, but after his death, the army became ravaged by bitter jostling for power between the two groups; something that substantially weakened the army and led to a further deterioration of morale and discipline.

NRA seized this opportunity to prepare its counter-offensive. In line with the switch to mobile warfare, NRA in February 1984 attacked the army barracks in Masindi, some 140 miles north of Kampala. This served to show both that the group could still carry out an offensive after the previous year's setbacks and that it had the capacity to do so in an area where it had not been active before. In line with this, the rebels also extended their operations to western Uganda, and in June, the group's mobile brigade attacked Hoima, a town some 180 kilometers north-west of Kampala. NRA's next move was to start to reoccupy the areas that it had left in early 1983.

In April 1985, NRA troops began making their way towards the Rwenzori Mountains in western-most Uganda and in June they were able to open a second front in the conflict. This made the already weakened government army even more war-weary. Furthermore, the following month saw a chain of events that would serve to weaken the army even further.

Two swift changes in government (July 1985 and January 1986)

Through July 1985, the Acholi–Lango tensions within the army (see the section "Bush war, 1981-86") intensified and resulted in several instances of in-fighting. On 27 July, the process culminated with the overthrow of President Milton Obote by army commander Bazilio Olara Okello and General Tito Okello Lutwa, Chief of Defense Forces, both Acholi. As a result, whole battalions of government soldiers defected, and many joined NRA (National Resistance Army), boosting the rebel group's strength.

A ruling military council was established, and some of the smaller rebel groups that had earlier fought Obote (FUNA, UNRF and UFM) were invited to join it, as was NRA. However, NRA refused, and the conflict continued. Substantially weakened, the new government initiated negotiations with the rebels. From late August and through the rest of the year, negotiations were subsequently held in Nairobi, against the backdrop of continued fighting and NRA advances in the western part of Uganda.

On 17 December 1985, the two parties signed the Nairobi Peace Agreement, but it soon became apparent that the accords would come to naught. Fighting continued in early January 1986, and both parties accused each other of not having taken the necessary measures to implement the accord. On 18 January, NRA launched its final attack on the capital. The following nine-day siege shattered the last vestige of unity in the ruling military council, and its member organizations turned on each other, thus facilitating NRA's capture of the city. On 26 January, Kampala was seized by NRA, and the so-called Bush War was over.

The conflict in the north erupts (August 1986)

When the military junta was ousted by Museveni's rebel group NRA (National Resistance Army) in January 1986, the remnants of the former government army fled towards their home region, Acholi, in northern Uganda. Pursued by the NRA, they were eventually forced to cross the border into Sudan. About 15 000 former government soldiers regrouped in Parajok in Eastern Equatoria, where they were joined by former Acholi politicians as well as Obote and Idi Amin supporters. In March 1986, they took the name UPDA (Uganda People's Defence Army), and Basilio Okello was announced to be the overall leader of the group.

When deploying throughout the north, the formerly so well-disciplined NRA's human rights record deteriorated, as newly integrated troops committed grave abuses against the civilian population. This caused large numbers of Acholi youth to flee to southern Sudan and join the newly set-up rebel group. In August UPDA launched a large-scale invasion of the north. After the initial battles, UPDA split into four brigades, two of which established bases in Kitgum district and two in Gulu. Initially, the rebels scored many successes and were able to push NRA from virtually all small towns and centers, forcing them to retreat to larger towns like Gulu. In the face of these military setbacks, NRA's abuses against the northern population increased.

At the same time as UPDA asserted itself throughout the north, a very different rebel group – which would take the armed struggle back to the vicinity of Kampala the following year – emerged in the north.

The Holy Spirit Movement and its successors (1986-88)

In 1985, an Acholi woman named Alice Auma claimed to have been possessed by a Christian spirit, known as Lakwena. In August 1986, just as the UPDA initiated their struggle, she began raising an army. This was the beginning of a very influential prophetic movement, known as HSM (Holy Spirit Movement). Speaking through Alice, the spirit Lakwena ordered a fight against evil, something that manifested itself both as an external enemy - the government - and as an internal enemy, in the form of impure soldiers and witches. The group used its own unconventional rules of warfare, called the Holy Spirit Tactics, which were intended to force the soldiers to trust God rather than their weapons and contradicted all military principles. For instance, the fighters were forbidden to take cover on the battlefield, and only a few of them were given proper arms, while the rest threw stones that were supposed to turn into grenades.

In August 1987, Alice launched an offensive towards Kampala. During the subsequent three months, the group walked a distance of over 1000 km, fighting battle after battle. It soon became apparent that HSM would have a much more difficult time once it left Acholiland, its home region. Not only did the civilian population in areas closer to Kampala not support the rebellion, they actively helped the NRA by keeping them aware of HSM 's whereabouts. The group became increasingly weakened, and in early November, the last 360 HSM fighters were pinned down in the swamps of Iganga, not far from Jinja. In the following days, the group dispersed, some giving themselves up to the NRA, while others managed to evade the government troops. Many made their way back to their home regions, whereas Alice and 118 of her supporters crossed into Kenya on 26 December.

Meanwhile, fighting continued in the north. Already prior to HSM 's march on Kampala, UPDA had become significantly weakened, both due to military setbacks leading to the loss of many of the leading figures in the movement, and to its increasingly confrontational relationship with HSM, with the latter launching successful raids on the group. The group continued to wage an armed conflict against the government through 1987, however. Aside from the weakened UPDA, Alice's cousin Joseph Kony had established a group that began launching attacks on NRA in 1987. Initially named UHSA (Uganda Holy Salvation Army), the group would eventually take the name LRA (Lord's Resistance Army). Furthermore, Alice's father Severino Lukoya declared that he would continue his daughter's struggle and established his own armed group, the Lord's Army. Relations between these three Acholi rebel groups became increasingly confrontational during 1988. Especially Kony's group launched attacks on the others, and by mid-1988, UHSA was the only rebel group still active in the region. Lukoya had been imprisoned by Kony, who claimed that he was the rightful successor of Alice, and Lord's Army subsequently fragmentized and disappeared. UPDA, for its part, opted for a negotiated settlement with the government and signed the Gulu Peace Agreement in June 1988.

Rebels in Teso (1987-1993)

Meanwhile, in the eastern region of Teso, a rebellion had erupted in 1987 with the UPA (Uganda Peoples Army) fighting the regime. The trigger for the armed opposition was the new NRM (National Resistance Movement) regimes decision to transfer a battalion of the army consisting mainly of Iteso soldiers from Teso to the Sudanese border, leaving Teso wide open for cattle raiders from neighboring Karamoja region. This was interpreted as a hostile act, and when Karamajong raiders managed to sweep almost the entire region of cattle, many Iteso called for a rebellion.

This sense of marginalization and the generally hostile attitude to the new Museveni government made Teso a fertile recruitment ground for exiled politicians, loyal to the ousted former president Milton Obote. Touring the region, they argued that Museveni was in league with the Karamojong in a plan to raid all the cattle from Teso and were subsequently able to mobilize large numbers of Iteso. The new recruits then went through training in bush camps throughout the region.

The UPA turned out to be a factious organization, and internal splits appeared already in 1988 when a faction under Commander Jesus Opirot agreed to give up the armed struggle. The following years saw both military setbacks at the hands of NRA and internal feuding, particularly between the exiled political leadership and the commanders in Uganda. By 1993 the rebellion had largely petered out.

The 1990s: regionally linked rebellions

In addition to numerous internal conditions conducive to conflict, conditions in the wider region came to play an increasingly important part in the Ugandan conflict in the 1990s. Especially the armed conflicts in neighbouring Sudan and DR Congo (Zaire) had significant implications.

Acholiland and Southern Sudan: LRA

Focusing first on the LRA (Lord's Resistance Army), formerly called UHSA (United Holy Salvation Army), it is clear that it was able to take its armed struggle to a new level in the 1990s through the support of the Sudanese government. Having suffered heavy setbacks in successive government offensives, such as the infamous "Operation North" of 1991, the rebels opted for accepting the offer of negotiations in 1993. President Museveni's Minister for the Pacification of the North, Betty Bigombe served as facilitator of the negotiations, and she, to some extent, came to enjoy the confidence of LRA. A ceasefire was in effect, and the efforts very nearly came to fruition. However, in February Museveni issued an ultimatum: if the LRA did not abandon the armed struggle in seven days, the NRA (National Resistance Army, the name of the government army) would destroy it. Predictably, the LRA did not comply with this deadline, and fighting resumed.

With the resumption of fighting, it soon became evident that the rebels had managed to secure important backing from the Sudanese government. In the regional scheme of things, this support made perfect sense, as the Ugandan regime from 1986 had supported the Sudanese rebel group SPLM/A (Sudan People's Liberation Movement/Army). Thus, in retaliation, the Khartoum regime from 1994 and until the early 2000s supported LRA, providing bases, weapons, and military training. In return, LRA fought alongside Sudanese government forces against SPLM/A.

The group's actions turned increasingly brutal, oftentimes specifically targeting the civilian Acholi population, whom Kony accused of having turned against them. With the newfound support from Sudan, there was no longer a constraint on arms, which meant that the only resource lacking was soldiers. Thus, LRA initiated the practice of carrying out mass abductions of children, who were subsequently turned into child soldiers, porters, or wives of rebel commanders. In 2003 it was reported that as many as 80% of LRA fighters were abducted children. In response to the mass abductions, the government set up "protected camps," which they subsequently forced the civilian population to move to. However, these soon proved to be counterproductive. As the army was unable to protect all camps, they instead came to serve as "pick-up centers" for the rebels.

From 2000 and onwards, the relationship between the regimes in Kampala and Khartoum improved slowly, in part due to the peace process taking place between the Sudanese government and the SPLM/A. In March 2002, the Sudanese government granted the UPDF (Uganda People's Defence Force; the name of the government army since 1996) permission to launch a major offensive against the LRA in southern Sudan, called "Operation Iron Fist." The initial plan had been to completely defeat the rebel group, but after just a few months, it became clear that this would fail. Instead, LRA crossed back to northern Uganda, and from April, the country saw attacks and brutality not witnessed since 1995 and 1996. In the following years, LRA came under even further military pressure as the Khartoum regime struck a new deal with the Ugandan government, waiving previous geographical restrictions and allowing UPDF go even further into Sudan. In 2005 this led the rebel group to split into several sub-groups, with one crossing over into Garamba National Part in eastern DR Congo (Zaire).

West Nile, Southern Sudan and Eastern Dr Congo/Zaire: WNBF & UNRF II

Following the chaotic years of the early 1980s (see the section "Rebels in the West Nile"), the West Nile region had seen relative peace prevail for over a decade until a new rebel group entered the stage in 1995. A key turning point for the region was when, in 1994, Sudanese government forces recaptured the strategic Southern Sudanese town of Kajo Keji and consolidated their control of the Sudan-Ugandan border. After this was done, the Sudanese regime assisted Idi Amin's former Foreign Minister Juma Oris in organizing a new rebel group, WNBF (West Nile Bank Front), mainly made up of Amin-era soldiers. The new rebels were subsequently infiltrated into Uganda, but could also make use of rear bases in Sudan. Claiming to fight for the introduction of multiparty democracy in Uganda, WNBF intensified its activities in 1996 and also introduced landmines into the conflict, apparently provided by Sudan.

Aside from the support stemming from the Sudanese government, the West Nile rebels also benefited from Kampala's bad relationship with neighboring Zaire (renamed DRC – Democratic Republic of Congo – in 1997). Subsequently, WNBF was allowed to have rear bases on Zairian territory as long as Mobutu Seso Seko controlled the country. However, from 1996 Mobutu was challenged by the rebel group up AFDL (Alliance des forces démocratiques pour la libération du Congo, Alliance of Democratic Forces for the Liberation of Congo), which, in turn, was supported by Uganda, Rwanda and Angola. AFDL soon gained control over eastern Zaire and could, together with Ugandan troops, flush out the WNBF rebels based in the band of Zaire adjoining the Ugandan district of Arua.

Simultaneously the rebels also faced problems in southern Sudan. Successes by SPLM/A deprived them of most of their hideouts in the neighboring country, and in March 1997, the South Sudanese rebels effectively destroyed the group in a major ambush on the road to Yei.

However, the rebellion in the West Nile region did not come to an end there. A WNBF splinter group, UNRF II (Uganda National Rescue Front II), had emerged in 1996 and launched attacks on both government troops and civilians through 1997 and into 1998, albeit with decreasing intensity. As WNBF and was allowed to set up a rear base in Kajo Keji. However – and again just as WNBF – UNRF II suffered from SPLM/A 's successes in Southern Sudan and the group was forced to retreat behind Sudanese government lines in mid-1997.

From 1998 a continuous dialogue was held between the Ugandan government and UNRF II. It finally bore fruit in December 2002, when a peace agreement was concluded between the parties. The final accord provided for the integration of around 700 rebels into the national army, while the reminders were to be given resettlement packages. All UNRF IIcommanders were to retain their ranks, and the movement was to receive ten government positions.

Rwenzori and Eastern DR Congo (Zaire): ADF

In western Uganda, primarily in the Rwenzori Mountains, a rebel group calling itself ADF (Alliance for Democratic Forces) emerged in late 1996. ADF was a conglomeration of at least three earlier groups: remnants of a separatist Rwenzori movement, NALU (National Army for the Liberation of Uganda), a small rebel group active in the area in the late 1980s and early 1990s, and extremist elements from the Tabliq Muslim community. The movement claimed to be fighting against what they perceive to be a one-party state, but most analysts agree that ADF 's struggle was really a rebellion without a political cause. Like LRA, ADF attacked indiscriminately, killing and abducting large numbers of civilians.

As with the rebel groups active in the West Nile, ADF was allowed to have rear bases in eastern DR Congo (Zaire) as long as Mobutu was in control. The rebels experienced a more problematic period after Mobutu had been toppled by the Ugandan government's allies AFDL in May 1997. However, relations between Uganda and the new Kabila regime in DR Congo (Zaire) soon soured, whereby ADF once again came to enjoy the support of the western neighbor, receiving arms and equipment.

In 1998 Uganda intervened in the conflict that had erupted in DR Congo (Zaire), ostensibly to destroy ADFs bases and to prevent the group from receiving supplies in the future. The Ugandan army's onslaught in both DR Congo (Zaire) and Uganda initially failed to marginalize the rebels, only serving to force them to move into other regions, thereby geographically spreading the conflict. However, from 2000 and on, the government managed to destroy several ADF bases in eastern DR Congo (Zaire) and the activity of the group subsequently diminished.

Negotiations with the LRA: the Juba Peace Process (2006-08)

With the exception of the brief reappearance of ADF (Alliance for Democratic Forces), LRA (Lord's Resistance Army) has been the sole rebel group active in Uganda since 2002. Thus, the post-2002 period has seen much effort put on ending this conflict, with the government's strategies oscillating between attempting to defeat the group militarily (through e.g., "Operation Iron Fist"; see the LRA section in "The 1990s: regionally linked rebellions") and trying to initiate negotiations.

After a long period of secret contacts, 2006 saw the birth of the Juba peace process, mediated by Southern Sudan's Vice President Riek Machar. One important contributing factor in bringing the rebels to the negotiation table was the International Criminal Court's indictment of the rebel group's highest leadership in 2005. However, while helping to get the process started, the arrest warrants became a major stumbling block to reaching a final deal. Despite this, some real progress was made in the negotiations in 2007 and during the first months of 2008, with several partial agreements being signed within the framework of the Juba process. In late February, the final partial agreement was signed. Preparations were subsequently made for a ceremony to be held in Ri-Kwan-Ba in Southern Sudan, at which Kony was to sign the Final Peace Agreement (FPA), which would subsequently end both the Juba process and the conflict. However, Kony failed to show up at the ceremony, something that was repeated several times throughout the year.

Despite this, the parties for a long time refrained from fighting each other. However, when Kony missed a November 2008 deadline for signing the agreement, and LRA launched attacks on civilians in southern Sudan and also initiated attacks in eastern DR Congo (Zaire), it seemed to confirm suspicions that the rebel group while engaging in negotiations, had in fact been buying time and preparing for war.

Operation Lightning Thunder and its immediate aftermath (2008-09)

On 14 December 2008 the armed forces of Uganda (UPDF), DR Congo (FARDC) and Southern Sudan (SPLA) launched Operation Lightning Thunder, beginning with a surprise air strike against Camp Swahili, LRA 's main camp in Garamba national park. Due to poor coordination, bad weather, and the dense forests in the region, the ground troops arrived late, wherefore the rebels had ample time to disperse in the jungle. For reasons that remain unknown, Kony had left the camp just before the airstrike. He was subsequently left unharmed and could organize and lead the rebels' ensuing operations. Operation Lightning Thunder continued through the rest of December and into 2009, amidst massive violence carried out by LRA against the Congolese civilian population. The worst killings took place on 24 December, and the wave of massacres was subsequently called the Christmas Massacres (for more information on this, see the section on One-sided violence).

Operation Lightning Thunder was ended on 15 March 2009, and the Ugandan troops officially left DR Congo (Zaire). The armed campaign continued through the rest of the year, however, albeit more covertly. This was mainly because it was politically difficult for Congolese President Joseph Kabila to defend the open presence on Congolese soil of Ugandan soldiers. Subsequently, somewhere between 2000 and 3000 Ugandan soldiers remained in DR Congo (Zaire) even after the end of Operation Lightning Thunder and continued pursuing the LRA rebels. Furthermore, some 1000 - 2000 UPDF troops were deployed in Southern Sudan and in CAR, (which had joined the alliance fighting the Ugandan rebels in January), operating against the rebels.

After Operation Lightning Thunder had ended, the Ugandan government hailed the offensive as a success, but many observers were skeptical. While the rebels dispersed and split into smaller groups, attacks on civilians increased dramatically. Apart from numerous attacks on villages in all three affected countries, at least one large-scale massacre was carried out by the rebels in December 2009, almost a year to the day after the Christmas massacres of 2008 (for more information, see LRA-civilians). Apart from killing more than 300 people, the rebels abducted some 250 civilians, most probably to reinforce their ranks.

Regional hunt for Kony and dispersed LRA fighters

LRA remained a regional threat through subsequent years, with its forces scattered over Central African Republic (CAR), DR Congo (Zaire) and Southern Sudan. UPDF's supply lines were badly stretched, and the force had great problems in tracking down the rebels. A guide who had worked with the Ugandan army in CAR described a situation where the soldiers were forced to wait for helicopters bringing food and water for days at a time when pursuing the rebels, which meant that they never came closer than to be four days behind them. Since LRA generally avoided direct military confrontation with the army, this meant that there were few military engagements, and the intensity of the conflict was relatively low compared to the level of fighting in the 1990s and early 2000s. Another reason for the low level of fighting was that the relationship between UPDF and especially the Congolese troops became increasingly strained. This meant that the cooperation was hampered, and UPDF denied access to certain areas and that intelligence information at times was withheld. Things came to ahead in September 2011, when the Ugandan troops were ordered to leave, as their presence became politically controversial during the presidential election.

The LRA conflict reached the international headlines in late 2011, when US President Barack Obama decided to send 100 Special Forces to the region in support of the anti-LRA effort. The troops were deployed in regional capitals as well as in the field until May 2017 when security in the southeastern Central African Republic was formally handed over to forces from the Central African Republic.

In November 2011, the African Union's (AU) Peace and Security Council authorized a Regional Co-operation Initiative for the elimination of the Lord's Resistance Army. This led to the forming of a regional task force under AU command in 2012 - the AU-RTF. The force, comprised by Ugandan, South Sudanese, Congolese and Central African troops, was tasked with tracking down and dealing with LRA. In September 2012, 360 troops of the Central African Republic's Forces Armées Centrafricaines (FACA), 2000 Ugandan troops and 500 South Sudanese troops joined AU-RTF. In February 2013, DR Congo (Zaire) deployed 500 soldiers to the effort. And in the fall of 2013, both the Congolese and the South Sudanese troops in AU-RTF appeared increasingly operational, carrying out a number of operations against LRA targets. The rebels were weakened by the military pressure and were also depleted by an increase in defection rates.

The AU-RTF remained hampered by problems, and relations between the involved governments were characterized by distrust. The Ugandan contingent was not authorized to access some areas where LRA was based. One such place was the Kafia Kingi enclave in southern Darfur, in Sudan, an area from which LRA leader Joseph Kony has rarely moved since 2011. Also, Ugandan troops were not permitted in the LRA areas of the DR Congo (Zaire).

Furthermore, the crisis that erupted in CAR and South Sudan in 2013 caused major setbacks for the alliance. When CAR 's president Francois Bozizé was ousted by the Seleka rebel alliance in late March operations against LRA ground to a halt. The new leaders perceived Uganda as the allies of the former president, and it was not until international pressure mounted that they eventually became more cooperative, allowing AU-RTF to become operational again. However, the situation in the country remained chaotic, allowing LRA to seek new safe havens and acquire vital supplies in under-patrolled areas. When the crisis in South Sudan erupted in mid-December 2013, these problems amplified. The 500 South Sudanese troops contributed to AU-RTF were withdrawn, and many of the Ugandan soldiers were drawn into the fighting on the government side. Subsequently, LRA gained a much-needed breathing room yet again.

Despite the troubled regional cooperation, most analysts agreed that the LRA was a much-diminished force. There was hardly any fighting between the group and soldiers from the allied countries, and attacks on civilians decreased substantially, defections continued to increase, the biggest success occurred in January 2015. Dominic Ongwen – one of the five LRA leaders indicted by the International Criminal Court (ICC) (see "Negotiations with the LRA: the Juba Peace Process (2006-08)) – was captured in CAR, on his way to hand himself over to the US troops. He was quickly sent to Haag, where he was charged with crimes against humanity and war crimes. While this was a success in itself, it was also a sign of the internal dissent that was growing within LRA. With the scattering of the group over a large territory, communications became problematic, and Kony increasingly lost control over many of his fighters. He subsequently became more and more violent towards the rank and file, which has caused even more dissent. Dominic Ongwen had long refused Kony's order to join him in Kafia Kingi, and when he eventually agreed, he was severely beaten. This has been taken to be one of the main things prompting his defection. Ongwen's trial began on 6 December 2016 with the closing statements from 10 to 12 March 2020, and he is still awaiting the ICC decision on conviction or acquittal. On 19 April 2017, Uganda announced the end of LRA pursuit operations in the Central African Republic since the group no longer presented a military threat. In 2018 the group only attacked police once, in Bas-Uélé DR Congo while looting Banda village, and in 2019, DR Congo Armed Forces launched an offensive in the Uele operational sector against the group in Nyangara and Dungu territories leading to 10 fatalities.

The re-emergence of ADF

Having come close to being defeated by the Ugandan army's successive offensives between 1999 and 2000, the remaining elements of ADF (Allied Democratic Forces) retreated to camps in Beni territory in eastern DR Congo (Zaire)s Nord Kivu province. After the Ugandan forces withdrew from DR Congo (Zaire) in 2003, the weak group attempted to regroup and reorganize by mobilizing mainly Congolese civilians. Slowly the group gained strength. However, in 2005 it suffered a new setback, when FARDC (Forces Armées de la République Démocratique du Congo: Armed Forces of the Democratic Republic of Congo) together with MONUC (United Nations Organization Mission in the Democratic Republic of the Congo) launched an offensive, causing the fighters to disperse into the bush around the Ruwenzori Mountains and disrupting ADF command and control for several months. Despite this, the rebel group was not dismantled but regrouped once more. In 2007 ADF rebels attempted to infiltrate back into Uganda. However, the advance group sent across the border in March, to set up bases in Bundibugyo was intercepted by the Ugandan army, and in the ensuing fighting, they were swiftly repulsed.

In November 2009, Kampala informed Kinshasa that ADF was escalating its training and recruitment in Beni region. The Ugandan government also pointed to links between the rebel group and Somali al-Shabaab, claiming that the two movements were cooperating. Some months later, in February 2010, Kampala, Kinshasa and MONUC agreed to exchange information on ADF, and the Congolese army began planning for a military operation. In June, a new meeting was held between the heads of states, and pledges were made to have a coordinated approach to address ADF. Subsequently, on 25 June, the Congolese army launched Operation Rwenzori against ADF. Fighting was fierce and caused some 100 000 civilians to be displaced in Beni territory. When the violence de-escalated in August, it was clear that the first phase of the operation had had limited success, and the Congolese army had suffered high casualties.

Nevertheless, a second phase of the operation was launched in September, and this time FARDC managed to secure control of the main ADF bases. It was debated, however, if the scattering of the rebels was due to pressure from FARDC, or if it was a strategic choice by the ADF leadership. Most analysts agree, however, that as time passed, the rebels adopted a successful proactive defense strategy, carrying out ambushes on FARDC positions and, at times, regaining control over previous strongholds. The increasingly mobile character of ADF in 2011 meant that the group appeared increasingly in Ituri province. Furthermore, in March 2012, the Ugandan army claimed that ADF had set up three new camps in North Kivu province, only 30 kilometers from the Ugandan border, near where oil exploration companies have discovered some 1.5 billion barrels of oil.

In late March 2012, FARDC launched a new offensive - Operation Radi Strike. It was fraught with problems, however, and was too short to make a real impact. When the M23 rebellion broke out (see the section on DR Congo (Zaire) in the encyclopedia), the focus of the Congolese troops shifted and fighting died down for several months. However, with FARDC largely preoccupied by M23, ADF started stepping up attacks in June 2013, causing over 60 000 people to flee across the border into Uganda. In December, in anticipation of a large-scale government offensive, the group evacuated its main bases and relocated to a number of smaller ones. They also moved troops to large towns in the area. Furthermore, on 25 December ADF fighters launched a new attack on Kamongo, which had been targeted in the July fighting as well, killing many civilians before being forced out by FARDC.

The government offensive – named Operation Sukola – was launched in January 2014 and continued through the following months. Supported by the UN troops stationed in DR Congo (Zaire), FARDC told of big successes and reports yet again said that the rebels were on the run. For several months after the offensive, the situation in the region as calm, and there was a glimmer of hope that the group had, in fact, been defeated this time. However, these hopes were dashed in October when ADF launched a new wave of attacks against the civilian population in the region. These attacks continued through 2015 and into 2016, albeit decreasing in intensity.

In April 2015, ADF suffered a substantial set back when its leader Jamil Mukulu was arrested in Tanzania. He has since then been handed over to Uganda, where he is charged with mass murder and crimes against humanity. According to ADF defectors, this had a significant impact on the scattered ADF groups, given that there was no longer a clear centralized leadership. By late 2016, the ADF groups remained dispersed, with a number of sub-factions having crystalized. Despite the limited central command and control, the various factions remained a threat to both the military and the civilian population. During 2016, the Congolese military, supported by UN troops, carried out two large-scale operations against ADF factions. Both times, they were able to evict the rebels from their Madina II bases, east of Mayi Moya in Beni territory. However, on both occasions, FARDC withdrew after the operations, and ADF fighters were able to reoccupy the camps. In October 2017 the main part of ADF transformed into IS leaving only a small faction of Mukulu loyalists led by Muzaaya refused to become part of the Islamic State. The ADF faction, led by Muzaaya, Kisokeranio and Hassan Nyanzi alias Isaac, cohabited with the Islamic State in the Rwenzori area on the border between DR Congo and Uganda. ADF and IS were both targeted in the October 2019 bombings by the Ugandan army and in 2021 an encounter between the government of Uganda and ADF was reported south-west of the Kambi Ya Yua river. After the Government of DR Congo captured one of the top ADF commanders, Benjamin Kisokeranio, in January 2022 the group disbanded, either by integrating into IS or surrendering to the government of DR Congo.