[13] Parts of Amin's Uganda Army and various anti-Obote groups consequently launched rebellions, resulting in the highly destructive Ugandan Bush War.

[17] As a result of international pressure, the NRM signed to the "Nairobi Agreement", a peace treaty negotiated under the oversight of Kenyan President Daniel arap Moi on 17 December 1985.

Despite official condemnations by Museveni's newly formed government, the NRM takeover resulted in cases of mistreatment and murders of northerners in the south.

[5] For much of the Bush War, the NRA had maintained relatively high standards in discipline, training, and indoctrination,[25] but the mass expansion resulted in it becoming a much more heterogeneous force.

[30] Without the militias' aid, the NRA proved unable to keep raiding in check, resulting in northern and eastern pastoral communities being devastated.

[24][31] Many demobilized UNLA veterans were also no longer willing to work as peasants and integrate into the civilian life, instead turning to banditry and worsening the economic unrest.

[30] Faced with worsening security conditions due to latent militant attacks and banditry, the NRA garrisons in Gulu, Kitgum, and Teso districts became increasingly repressive.

[43] Auma consequently organized the "Holy Spirit Mobile Force" (HSMF) as the HSM's armed wing with 80 ex-UNLA and ex-UPDA combatants who believed in her messianic teachings.

In addition, Auma implemented draconian discipline and a strict code of conduct, organizing a military police and logistics groups to enforce these and keep the HSM well-organized.

This operation resulted in a major defeat of the HSM on 18 January, when about 350 rebels were killed in battle,[50] including Lieutenant Colonel Eric Odwar.

[54] In the counter-insurgency operations against the HSM, the Tutsi NRA soldiers committed so many massacres that President Museveni sent special military judges to "curb his own army" in the north.

They formed the "Uganda People's Army" (UPA) and appointing Peter Otai as overall leader and Francis "Hitler" Eregu as military chief commander.

[33] The western rebels were based in Zaire (present-day DR Congo) and reportedly supported by the government of Zairean dictator Mobutu Sese Seko.

This aid allowed NALU to grow into an "irritant" to Museveni's government, although the group lacked the popular support which the old Rwenzururu movement had enjoyed.

[33] West Nile native and ex-President Idi Amin unsuccessfully attempted to organize a rebel invasion into Uganda from Zaire in 1989, but was arrested by Zairean security forces and subsequently returned to his exile in Saudi Arabia.

[68] In December of that year the UFA's leader, Captain Charles Barau, threatened that his forces would try to kill all Libyans in Uganda if they did not leave the country within 30 days.

[69] UFA was later identified as military wing of the Uganda National Democratic Alliance (UNDA),[70] although the latter was reportedly founded under the leadership of Sam Luwero in 1989.

Tablighi Jamaat militants led by Jamil Mukulu twice raided the Old Kampala Mosque in 1991, attempting to seize the offices of the Uganda Muslim Supreme Council (UMSC).

Although the situation was defused as a result of talks organized by Mengistu Haile Mariam of Ethiopia and Ali Hassan Mwinyi of Tanzania, tensions continued.

[74] In January 1988, Kony successfully attacked the UPDA's 115th Brigade, and convinced many of its troops including Captain Mark Lapyem to join his movement.

Atrocities became commonplace such as when the NRA's 106th Battalion locked 120 suspected UPA supporters into a rail wagon at Okungolo, leaving 69 to die from thirst and heat within a day.

Despite these differences, Lukoya put great importance in portraying himself as Auma's successor which included enlisting the support of the same spirit commanders, most of whom reappeared in his movement.

Lukoya also enlisted new spirits, most of whom were individuals of importance to the Acholi or HSM who had died during the last years, such as the ghost of UNLA chief commander David Oyite-Ojok.

The NRA forcibly removed about 100,000 people from Gulu and its surroundings; hundreds were executed without due process, homes were burned, and goods plundered.

[89] Kony's forces increased their attacks, operating in small groups that terrorized other rebel factions and kidnapped growing numbers of schoolchildren, students, women, and men.

[91][90] Led by Major General David Tinyefuza, the NRA closed off the districts of Apac, Gulu, Lira, and Kitgum in early April 1991.

Regardless, the combined NRA-Arrow Boys operations succeeded in greatly weakening the rebels, with the government claiming that 3,000 of Kony's fighters had been "eliminated" in Kitgum in May 1991.

Overconfident, the NRA decided to end Operation North in July 1991, and left the Arrow Boys to mop up Kony's remaining troops.

[6] In addition, the SPLA rebels were weakened from late 1991, allowing the Sudanese National Islamic Front government to partially restore its authority in the Sudanese–Ugandan border area.

[33] In that year, several Tablighi Jamaat radicals including Jamil Mukulu were released from prison, whereupon they organized the Ugandan Muslim Freedom Fighters (UMFF) and started a small-scale insurgency in Buseruka, western Uganda.