On December 17, 1985, after more than four months of negotiations, the NRA and the Military Council signed a peace accord in Nairobi. But then, on January 26, 1986, using Swedish and Libyan military assistance, the NRA abandoned the accord and seized control of the government. The new regime won some popular support by pledging it would end human rights violations, improve military discipline, and restore stability. Many UNLA personnel retreated into Sudan, regrouped, and reentered Uganda in August 1986, and Uganda was once again gripped by civil war.

From 1986 to 1990, the Museveni regime tried to end various insurgencies and to establish control over the army. Despite repeated government claims that the NRA had defeated the UNLA and other rebel groups, insurgent activity continued, especially in the northern, eastern, and western regions. In April 1988, 3,000 former Uganda People's Army (UPA) fighters and members of several other small rebel groups accepted a government amnesty by surrendering and declaring their support for Museveni's regime. In June 1988, the president concluded a peace agreement with Uganda People's Democratic Army (UPDA) commander Lieutenant Colonel John Angelo Okello. Although the NRA subsequently integrated many UPA and UPDA personnel into its ranks, thousands of others rejected the peace accord and continued to fight against the NRA.

Throughout most of the late 1980s, Museveni pursued a dual policy of offering rebels unconditional amnesties and intensifying military operations. In 1988 the government promised to pardon rebels who lacked criminal records if they surrendered those who refused would be tried as "bandits" before special courts designated to deal with insurgents.

In February 1989, Museveni declared a three-month moratorium on military operations against rebels near Gulu. Army officers sought to improve political communication with the regime's opponents as a result, a few rebels relinquished their arms. Once the moratorium expired, however, the NRA intensified assaults on rebel bases, and in mid-1989 the NRA implemented a "scorched earth" policy in the area. Troops moved several thousand civilians to government-run camps, and they burned houses, crops, and granaries in these depopulated areas. In early February 1990, the NRA tried to isolate rebel forces by rounding up some 200,000 civilians and placing them in guarded camps in eastern and western Uganda. This counterinsurgency strategy enabled the NRA to establish control over some areas, but it also eroded the government's domestic and international support, largely because of the high number of deaths resulting from inadequate food, water, shelter, and medical care in the camps. By late 1990, despite these harsh measures, a large number of rebels remained committed to the war against the NRM regime.

In the late 1980s and early 1990s, one of the most active antigovernment rebel groups was the Holy Spirit Movement (HSM) in north central Uganda. Alice Lakwena, a self-proclaimed mystic who persuaded her followers that she could turn bullets into water, led the HSM 13d6 M from its formation in April 1987 until mid-1988, when she fled to Kenya. Her successor was Joseph Kony, also a mystic who claimed to be in communication with a number of spiritual forces. The government-owned newspaper, The New Vision, reported that three HSM brigades operated around the northern town of Kitgum and that a mobile brigade of 700 soldiers operated southwest of Kitgum, near Gulu. In mid-1989, government sources reported that an NRA preemptive strike against the HSM-UPA alliance near Soroti resulted in one of the largest confrontations the NRA had encountered since 1985. More than 400 people died, about 180 were captured, and more than 500 HSM-UPA fighters surrendered the government did not report NRA losses. HSM tactics then switched from battlefield confrontations to kidnapping citizens, attacking hospitals, and ambushing vehicles to erode popular support for Museveni. By January 1990, however, the HSM, which then called itself the United Democratic Christian Movement (UDCM), had reverted to traditional insurgent tactics by launching a series of attacks in Kitgum, Lira, and Apac districts. Later in the year, the HSM mounted operations in Gulu and Soroti districts. Although it enjoyed some local battlefield successes, the NRA failed to destroy the HSM.

An NRA counterinsurgency campaign in eastern Uganda had similarly mixed results. Shortly after coming to power, Museveni disarmed and disbanded local militias that had been organized to protect the region against cattle rustlers. The NRA also absorbed militia units, such as the FUNA and former members of the UNLA, into its ranks. Museveni deployed some of these fighters in the east, and although this tactic succeeded in extending government control into some unsettled areas, in many cases it also left these groups outside government control and weakened discipline within NRA ranks. As a result of the presence of these loosely affiliated NRA troops and other groups that remained outside government control, crimes against the civilian population increased. Much of the subsequent "insurgent" activity in eastern Uganda was little more than organized banditry as many former members of the militia--nearly all of whom lacked a credible political agenda--had decided that life in the bush was preferable to joining the NRA. Continued rebel activity, largely by the UPA, and well-established patterns of cattle raiding prevented the NRA from pacifying eastern Uganda in its first five years in power.

Museveni established good relations with Buganda by offering to reinstitute the office of the kabaka. Instead of taking this step, however, he referred the question to a constitutional commission, which, by the end of 1990, had failed to rule on the matter. Meanwhile, a number of Baganda reportedly took up arms to press the regime on this issue. By mid-1989, most rebel operations in Buganda supposedly had been confined to Mpigi, the district that surrounds Kampala, and Entebbe, the site of the nation's largest airport. The government deployed only small numbers of troops to confront the Baganda rebels, confirming the view held by many Western observers that the opposition in Buganda was more political than military.

Museveni tried to consolidate support within the army by filling key NRA positions with his supporters and by punishing soldiers found guilty of committing crimes against the civilian population (see Human Rights , this ch.). Nevertheless, there have been several coup attempts against Museveni. The government has suppressed information about these incidents however, on February 17, 1989, The Guide published reports of five coup attempts since 1986. Among these was an incident in April 1988, when the NRA detained a senior army officer and more than seventy of his personnel for conspiring against the government. Other reports indicated that in September 1988 the NRA arrested and charged twenty-four people suspected of subversion and inciting soldiers to mutiny. Reports of factional opposition to Museveni within the NRA continued into the early 1990s.

Data as of December 1990