[11] The conflict began on 13 February 1996, when the CPN (Maoist) initiated an insurgency with the stated purpose of overthrowing the Nepali monarchy and establishing a people's republic; it ended with the signing of the Comprehensive Peace Accord on 21 November 2006.

However, communist groups, uncomfortable with the alliance between the ULF and the Congress, formed a parallel front: the United National People's Movement (UNPM).

In November 1990, the Communist Party of Nepal (Unity Centre), or CPN(UC), was formed, and included key elements of the UNPM.

On Friday, 1 June 2001, King Birendra, and his entire family were killed in a massacre at the Narayanhiti Palace – the official residence of the Shah monarchs.

On 25 July 2001, the government of Sher Bahadur Deuba and the Maoist insurgents declared a ceasefire, and held peace talks from August to November of that year.

[13]: 335  The failure of these peace talks resulted in the return to armed conflict, beginning with the Maoist attack on an army barracks in Dang District in western Nepal, on 22 November.

[17] On 1 February 2005, in response to the inability of the relatively democratic government to restore order, King Gyanendra seized direct power and declared a state of emergency in an attempt to definitively end the insurgency.

[13]: 338  On 22 November 2005, with support from the Indian government, Maoist rebels and the SPA jointly issued a 12-point resolution, which described autocratic monarchy as the main obstacle to "democracy, peace, prosperity, social upliftment and an independent and sovereign Nepal",[20] and included a commitment to hold elections to a constituent assembly and for the Maoist rebels to renounce violence.

[13]: 339  On 9 August, the government and the Maoist rebels agreed to accept the United Nations to monitor the peace process and to manage the arms of both sides.

[13]: 340  On 21 November, the government, the SPA, and the Maoist rebels signed the Comprehensive Peace Accord, which formally ended the civil war.

[13]: 340 The Civil War forced young workers to seek work abroad, predominantly in the Persian Gulf and south-east Asia.

As a transitional justice mechanism, in July 2007, the Ministry of Peace and Reconstruction proposed legislation that would establish a Truth and Reconciliation Commission in Nepal.

[63] The parliament set up a Truth and Reconciliation Commission to investigate:"Murder, abduction and taking of hostage, causing mutilation and disability, physical or mental torture, rape and sexual violence, looting, possession, damage or arson of private or public property, forced eviction from house and land or any other kind of displacement, and any kind of inhuman acts inconsistent with the international human rights or humanitarian law or other crimes against humanity.

In 2016, commissioner Madhabi Bhatta of the TRC, a hardliner advocating that amnesty will not be given to perpetrators of serious crimes and that no one has immunity, said on national television that even Prachanda, the then-Prime Minister and former supreme commander of the guerrillas, will be questioned by the commission, reporting that she felt security threats from the former extremists.

[67] Leaked footage of Prachanda was later telecasted by Image Channel on 5 May 2009, in which Parchanda claims to have given the UNMIN an inflated number of Maoist fighters.

[67] On 17 April, the NA stated that it could not start the recruitment process of former Maoist combatants until the structure—leadership and size—of the General Directorate had been finalised at the political level.