Several opposition groups claimed the elections were rigged, and united as the NRA under the leadership of Yoweri Museveni to start an armed uprising against Obote's government on 6 February 1981.

Despite the nominal end of the civil war, numerous anti-NRA rebel factions and militias remained active, and would continue to fight Museveni's government in the next decades.

Obote had been president since Uganda's independence from the United Kingdom in 1962, and his regime saw a general decline in living standards in the country, with growing corruption, factional violence, and persecution of ethnic groups.

[14][15][16] Despite initial popularity, Amin quickly turned to despotism and established a military dictatorship which accelerated the decline of Obote's regime, destroying the country's economy and political system.

[35] As the rebels knew that they could not hold the captured territory against a full UNLA counter-offensive, they mostly retreated back into Sudan after a few days[2] with a large amount of loot.

[35] The UNLA forces, considering the local population hostile, engaged in a campaign of destruction and looting across the West Nile, as Tanzanian officers tried in vain to restrain them.

[30] The West Nile rebellion was weakened by internal divisions as parts of the Uganda Army remained loyal to Idi Amin, whereas others wanted to distance themselves from the unpopular old dictator.

As the UNLA was being transformed from a loose alliance of various anti-Amin insurgent groups into a regular army, the different political factions attempted to ensure that their own loyalists would be present and dominant in the new military.

[48][49][50] In contrast to Museveni's forces and the West Nile rebels, Andrew Kayira's UFM mostly consisted of relatively well-trained ex-soldiers and was focused on high-profile urban operations.

The group hoped to destabilize Obote's government through direct attacks, a strategy which "doomed it to fail from the beginning" according to historians Tom Cooper and Adrien Fontanellaz.

The UFM was not strong enough to challenge the UNLA head-on, suffered from leadership rivalries, lacked a firm organization, and was prone to being infiltrated by pro-government spies.

To compensate, he tried to enlist further foreign aid: He hired a British private military company, and convinced the Commonwealth of Nations (including Great Britain, Canada, and Australia)[51] as well as the United States to send small teams of security advisors.

[5] The PRA also continued its hit-and-run operations with mixed successes: It overran a UNLA outpost at Kakiri on 5 April 1981, and captured important weaponry, but had to hastily retreat when a TPDF unit responded to the attack.

The Tanzanian forces consequently conducted a counter-insurgency sweep, catching a PRA column under Elly Tumwine off-guard and recapturing some of the captured guns.

So far, the PRA had mostly consisted of non-Baganda, but Lule provided the newly formed NRA with backing from the Baganda, allowing Museveni to expand his envisioned "people's war".

[60] Soon after the merger, Museveni implemented a strict code of conduct for fighters, allowing the NRA to remain highly disciplined and focused despite gradually growing in numbers and absorbing other insurgent factions[61] such as the remnants of the "Gang of Four".

[30] The Ugandan government exploited the divisions and chaos among the rebels by launching counter-attacks into Western Nile from 1981, where its regular military and "People's Militia" committed numerous atrocities.

[4] In the south, the UNLA under chief of staff Oyite-Ojok waged a counter-insurgency campaign against the NRA in the Luwero Triangle which resulted in the "genocidal killings" of thousands of Baganda civilians.

[71] On 16 June 1983, the Obote government launched Operation Bonanza, an extensive military expedition utilizing up to half of the UNLA forces, that alone claimed tens of thousands of lives and displaced a significant portion of the population.

Although the Ugandan government knew that it could not even feed its large army, let alone properly train or arm it, Obote was unwilling to demobilize troops out of fear that the soldiers could behave even worse if they were no longer employed.

Oyite-Ojok's loyal troops, most importantly the People's Militia and National Youth Army responded by carrying out revenge killings against suspected rebel supporters.

[68] Conversely, the NRA's main force in the Luwero Triangle managed to escape an encirclement operation in the Battle of Birembo in January 1985, and thus could rebuild its strength in the area.

[78][79] Meanwhile, the Ugandan government decided "to teach the Karamojong a lesson" after raiders had taken advantage of Oyite-Ojok's death to attack his farm and kill over 100 militiamen in the northeast.

In cooperation with the Kenyan government, UNLA and allied militias launched a campaign which largely destroyed or seized the Karamojong's food sources in the form of cattle and fields.

[83] After the successful coup, General Tito Okello was installed as president; this marked the first time in Uganda's history when Acholi had achieved state power.

The new Acholi leadership promptly began to use their new power to disempower and exploit other ethnic groups including Langi, resulting in the collapse of discipline and order among many military units.

[27] In addition, Okello's government suffered from a lack of respect among the country's elite, as most of its members were uneducated and considered ill-prepared to actually rule Uganda.

[83] By January 1986, the UNLA was starting to collapse as the rebels gained ground from the south and southwest,[92] with mass surrenders of government soldiers taking place in several areas.

After a few months, however, many Ugandans began to view the NRM with approval,[101] as the party actually succeeded in improving stability and restoring order throughout many parts of Uganda.

[106] The Karamojong ex-UNLA soldiers also took large quantities of weaponry to their home territories after the collapse of Okello's regime, subsequently increasing their raids in scale and numbers.