Besigye allowed an early internal FDC election for a successor president, which took place on 24 November 2012.

When the National Resistance Movement and Army (NRM/A) came to power in January 1986, he was appointed Minister of State for Internal Affairs.

In 1991, he became commanding officer of the mechanized regiment in Masaka, central Uganda, and in 1993 was appointed the army's chief of logistics and engineering.

In 1999, Besigye wrote a document critical of the government, "An Insider's View of How the NRM Lost the Broad Base".

The government accused him of being behind a shadowy rebel group, the People's Redemption Army (PRA), allegedly based in the Democratic Republic of the Congo (DRC).

Besigye's supporters said the government had fabricated the existence of the insurgents to harm his credibility among Ugandans and the international community.

In November 2005, William Lacy Swing, the United Nations special envoy to the Great Lakes region, confirmed the existence of the PRA, naming it as one of the foreign, armed groups operating in the eastern DRC.

The treason charges pertained to his alleged links to the PRA and the 20-year-old northern Ugandan Lord's Resistance Army rebellion.

Museveni was accused of trumping up charges against Besigye in an attempt to discredit him or prevent him from standing in the election.

The government reacted by banning all public rallies, demonstrations, assemblies or seminars related to Besigye's trial.

On 25 November, Uganda's high court granted Besigye bail, but he was immediately sent back to jail on military charges of terrorism and the illegal possession of weapons.

Besigye denied the charges and has argued that as a retiree from the armed forces, he should no longer be subject to an army court-martial.

[2] In the 2011 elections Besigye for the third time in a row lost to Museveni, with a sharp decline from previous polls, failing to win in a single region.

Though the election was lauded as one of the most free and fair in Ugandan history,[citation needed] Besigye claimed that Museveni used intimidation and rigging to win a fourth term in office.

[citation needed] Besigye was arrested for a fourth time on 28 April, during a "walk-to-work" protest over the high prices of food and fuel.

Besigye's support of gay rights[6] together with Youth MP Abe Moses was a contentious issue in Uganda, where homosexuality is already a crime under the Ugandan Penal Code.

Besigye was arrested on 1 October 2012 after attempting to make a speech to vendors in Kiseka market in Kampala.

[11][12][13] Besigye opted not to run for president in the 2021 elections, saying he would lead the opposition in "plan B" to cause change in the country.

[16] After the 2021 elections Besigye launched the people's front for transition, an umbrella movement with a common goal of causing change in Uganda.