On 11 January 1994, General Roméo Dallaire, commander of UNAMIR (United Nations Assistance Mission for Rwanda), sent his "Genocide Fax" to UN Headquarters. The fax stated that Dallaire was in contact with "a top level trainer in the cadre of Interhamwe-armed militia of MRND." The informant—now known to be Mathieu Ngirumpatse's chauffeur, Kassim Turatsinze, a.k.a. "Jean-Pierre" – claimed to have been ordered to register all Tutsi in Kigali. According to the memo, Turatsinze suspected that a genocide against the Tutsis was being planned, and he said that "in 20 minutes his personnel could kill up to 1000 Tutsis". Dallaire's request to protect the informant and his family and to raid the weapons caches he revealed was denied.
Following Habyarimana's death, on the evening of 6 April, a crisis committee was formed; it consisted of Major General Augustin Ndindiliyimana, Colonel Théoneste Bagosora, and a number of other senior army staff officers. The committee was headed by Bagosora, despite the presence of the more senior Ndindiliyimana. Prime Minister Agathe Uwilingiyimana was legally next in the line of political succession, but the committee refused to recognise her authority. Roméo Dallaire met with the committee that night and insisted that Uwilingiyimana be placed in charge, but Bagosora refused, saying Uwilingiyimana did not "enjoy the confidence of the Rwandan people" and was "incapable of governing the nation". The committee also justified its existence as being essential to avoid uncertainty following the president's death. Bagosora sought to convince UNAMIR and the RPF that the committee was acting to contain the Presidential Guard, which he described as "out of control", and that it would abide by the Arusha agreement.
The genocide was organised by members of the core Hutu political elite, many of whom occupied positions at top levels of the national government. Most historians agree that a genocide against the Tutsi had been planned for at least a year. However the assassination of Rwandan president Juvénal Habyarimana on 6 April 1994 created a power vacuum and ended peace accords. Genocidal killings began the following day when soldiers, police, and militia executed key Tutsi and moderate Hutu military and political leaders.
On 7 April, as the genocide started, RPF (the Rwandan Patriotic Front) commander Paul Kagame warned the crisis committee and UNAMIR that he would resume the civil war if the killing did not stop.
Thousands sought refuge in the Official Technical School (École Technique Officielle) in Kigali where Belgian UNAMIR soldiers were stationed. On 11 April, the Belgian soldiers withdrew, and Rwandan armed forces and militia killed all the Tutsi.
On 12 April, the Belgian government, which was one of the largest troop contributors to UNAMIR, and had lost ten soldiers protecting Prime Minister Uwilingiliyimana, announced that it was withdrawing, reducing the force's effectiveness even further.
On 17 May 1994, the UN passed Resolution 918, which imposed an arms embargo and reinforced UNAMIR, which would be known as UNAMIR II. The new soldiers did not start arriving until June, and following the end of the genocide in July, the role of UNAMIR II was largely confined to maintaining security and stability, until its termination in 1996.
By 13 June, RPF (the Rwandan Patriotic Front) had taken Gitarama itself, following an unsuccessful attempt by the Rwandan government forces to reopen the road; the interim government was forced to relocate to Gisenyi in the far north west.