In 1985 the NRA inflicted several key defeats on the UNLF's armed wing, the UNLA, leaving the Ugandan capital, Kampala, vulnerable to attack.

The resulting peace agreement failed to end the conflict, and Okello amassed a large force of UNLA troops and allied militias to garrison Kampala in preparation for an attack, though its effectiveness was weakened by low morale, internal friction, and subterfuge.

On 26 January the NRA captured Radio Uganda, but 1,000 UNLA troops from Entebbe broke through a roadblock and began advancing towards the city.

Museveni and his chief of staff, Salim Saleh, redeployed their forces to counter the threat, in the process opening a gap in their cordon around Kampala and allowing many UNLA troops to escape.

In the evening an NRA battalion ambushed the UNLA troops advancing from Entebbe while a company moved to attack their rear, forcing them to capitulate and ending the battle.

[4][5] In February 1981 Museveni and a small band of rebels began attacking UNLA forces, signalling their entry in the Ugandan Bush War.

[7] Regardless, the group inflicted a major defeat on the UNLA in the Battle of Kembogo, causing great frustration and unrest among the security forces.

The new regime was weak and unstable, and Okello made overtures to anti-Obote rebel groups to form a coalition government and end the fighting.

[12] In August the NRA launched a series of co-ordinated attacks that resulted in the capture of significant amounts of territory in central and western Uganda.

[13] In late September, the NRA laid siege to the UNLA troops in the provincial centre of Masaka and, soon thereafter, the town of Mbarara, both key urban areas in southern Uganda.

[14] In October Museveni warned that, in the event of the failure negotiations ongoing between the NRM and the UNLF in Nairobi, "the NRA would take Kampala by force".

In contrast, the UNLA's remaining forces were increasingly suffering from defections, low morale, and internal divisions along ethnic lines.

[18] The NRA's success at Masaka and Mbarara also solidified their control of the centre and south-western sections of the country and left Kampala vulnerable to attack.

[19] To take advantage of its improving military situation, the NRA High Command decided to launch an offensive to capture the city.

[26] UNLA and FUNA troops blocked their advance by placing artillery—including anti-aircraft guns— at the Busega roundabout,[26][25] where the Masaka and Fort Portal roads entered the capital.

[26] On 23 January, the government forces' artillery bombarded the areas in and around Kampala where the NRA was present, including Rubaga, Lubigi, and Busega.

[23] On early 24 January, a UNLA Bell helicopter made several attempts at disrupting the NRA artillery in the swampy area near Busega, bombing their positions until being driven away by the rebels' anti-aircraft fire.

[23] A band of NRA soldiers led by Kasirye Gwanga reconnoitred the area, and, discovering that it had been abandoned, radioed a message to their headquarters.

[33] For the most part, the UNLA and FUNA soldiers defending the city were demotivated and poorly led; many deserted or outright defected to the NRA.

[26] Fighting at Lubiri was severe;[32] the UNLA garrison successfully blunted an attempt by NRA troops to scale the barracks wall, so the latter resorted to besieging the installation with grenades and machine guns.

[30] In the afternoon NRA artillery struck an armoury near the UNLA's headquarters, Republic House, causing a large series of explosions.

At about 21:00 a platoon of the 3rd Battalion managed to successfully climb over the wall at the Lubiri barracks, finding the location to have been abandoned by UNLA forces.

[38] The 11th Battalion only started to encounter substantial resistance in an area between a thicket dubbed "Bat Valley" and Wandegeya, as the local UNLA soldiers held well-concealed positions, set up at 14.5mm gun, and fought with determination.

[45] Early in the evening the 7th Battalion captured the Makindye barracks,[46] reportedly aided by the defection of local FEDEMU and UFM troops to the NRA.

[47] Three high-ranking UNLA commanders surrendered when the city fell to the NRA; namely chief of staff Lieutenant General Zeddy Maruru, Brigadier Fred Okecho, and Colonel Samuel Nanyumba.

[53] Unlike previous, drawn-out engagements in the Ugandan Bush War, the NRA had won the battle through overwhelming force and direct attack.

[54] The removal of the NRA roadblock on the route to Jinja allowed many UNLA troops to escape the city and reorganise to launch a new rebellion eight months later.

Saleh maintained that he had ordered the roadblock's removal in consideration of "humanitarian reasons", as there could have been "a blood bath and [UNLA troops'] families would perish in the fighting".

[61] Despite Museveni's promises, many northerners in Kampala—viewed as beneficiaries of the Obote and Okello regimes—especially Acholi and Lango people, were subject to abuse and discrimination following the NRA's takeover; some were killed in the streets or forced out of their jobs or homes.

[63] Museveni's government sent an emissary to Sudan to entreat Okello to order the remaining UNLA forces to surrender, but he stated that he no longer controlled them.