However, the war radicalized the internal opposition. The more of a threat the RPF became, the more mainstream the Hutu Power ideology became. Hutu Power portrayed the RPF as an alien force intent on reinstating the Tutsi monarchy and enslaving the Hutus that had to be resisted at all costs. This political force led to the collapse of the first Habyarimana government in July 1993, when Prime Minister Dismas Nsengiyaremye criticized the president in writing for delaying a peace agreement. Habyarimana, a member of the MRND political party, dismissed Nsengiyarmye and appointed Agathe Uwilingiyimana, who was seen as less sympathetic to the RPF, in his stead. However, the main opposition parties then refused to support Madame Agathe's appointment, each splitting into two factions: one calling for the unwavering defense of Hutu Power and the other, labeled "moderate", that sought a negotiated settlement to the war. As Prime Minister Uwilingiyimana was unable to form a coalition government, ratification of the Arusha Accords was impossible. The most extreme of the Hutu parties, the Coalition for the Defence of the Republic, which openly called for ethnic cleansing, was entirely unrepresented in the Accords.
The security situation deteriorated throughout 1993. Armed Hutu militias attacked Tutsis throughout the country, while high-ranking adherents of Hutu Power began to consider how the security forces might be turned to genocide. In February 1994, Roméo Dallaire, the head of the military force attached to the United Nations Assistance Mission for Rwanda (UNAMIR), which had been sent to observe the implementation of the Arusha Accords, informed his superiors, "Time does seem to be running out for political discussions, as any spark on the security side could have catastrophic consequences."
In the United Nations Security Council, early April 1994 saw a sharp disagreement between the United States and the non-permament members of the council over UNAMIR. Despite a classified February Central Intelligence Agency (CIA) analysis predicting half a million deaths if the Arusha process failed, the U.S. was attempting to reduce its international commitments in the wake of the Somalia debacle and lobbied to end the mission. A compromise extending UNAMIR's mandate for three more months was finally reached on the evening of Tuesday, the fifth of April. Meanwhile, Habyarimana was finishing regional travel. On April 4th, he had flown to Zaire to meet with president Mobutu Sese Seko and on the sixth flew to Dar es Salaam, Tanzania for a one-day regional summit for heads of state convened by Tanzania's President. On the return trip that evening he was joined by Burundian president Cyprien Ntaryamira, and a couple of his ministers, who preferred the faster Dassault Falcon 50 that the French government had given to Habyarimana over his own presidential plane.
According to interim Prim Minister Jean Kambanda's confession to the ICTR, President Mobutu Sese Seko of neighboring Zaire, (now DRC) had warned Habyarimana not to go to Dar-es-Salaam on April 6. Mobutu said this warning had come from a very senior official in the Elysée Palace in Paris. There was a link between this warning, said Mobutu, and the subsequent suicide in the Elysée of François de Grossouvre, a senior high-ranking official working for President François Mitterrand, an official who had killed himself on April 7 after learning about the downing of the Falcon.
Shortly before 8:20 pm local time (6:20 pm UTC), the presidential jet circled once around Kigali International Airport before coming in for final approach in clear skies. A weekly flight by a Belgian C-130 Hercules carrying UNAMIR troops returning from leave had been scheduled to land before the presidential jet, but was waved off to give the presidents priority.
A surface-to-air missile struck one of the wings of the Dassault Falcon, before a second missile hit its tail. The plane erupted into flames in mid-air before crashing into the garden of the presidential palace, exploding on impact. The plane carried three French crew and nine passengers.
The attack was witnessed by numerous people. One of two Belgian officers in the garden of a house in Kanombe, the district in which the airport is located, saw and heard the first missile climb into the sky, saw a red flash in the sky and heard an aircraft engine stopping, and then another missile climb. He immediately called Major de Saint-Quentin, part of the French team attached to the Rwandan para-commando battalion Commandos de recherche et d'action en profondeur (CRAP), who advised him to organize protection for his Belgian comrades. Similarly, another Belgian officer stationed in an unused airport control tower saw the lights of an approaching aircraft, a light traveling upward from the ground and then the aircraft lights going out. This was followed by a second light rising from the same place as the first and the plane turning into a falling ball of fire. This officer immediately radioed his company commander, who confirmed with the used control tower that the plane was the presidential aircraft
A Rwandan soldier in the military camp in Kanombe recalled,
You know, its engine sound was different from other planes; that is, the president's engine's sound ... We were looking towards where the plane was coming from, and we saw a projectile and we saw a ball of flame or flash and we saw the plane go down; and I saw it. I was the leader of the bloc so I asked the soldiers to get up and I told them "Get up because Kinani [a Kinyarwanda nickname for Habyarimana meaning "famous" or "invincible"] has been shot down.' They told me, "You are lying." I said, "It's true." So I opened my wardrobe, I put on my uniform and I heard the bugle sound.
A Rwandan officer cadet at the airport who was listening to the Radio Télévision Libre des Mille Collines heard the announcer state that the presidential jet was coming in to land. The spoken broadcast then stopped suddenly in favor of a selection of classical music.
French aircraft crew:
In Camp Kanombe, the bugle call immediately after the crash was taken by soldiers to mean that the Rwandan Patriotic Front had attacked the camp. Every soldier rushed to his unit's armory to equip themselves. Soldiers of the paracommando brigade Commando de Reconnaissance et d'Action en Profondeur (CRAP) assembled on the parade ground at around 9 pm while members of other units gathered elsewhere in the camp.
At least one witness stated that about an hour after the crash there was the sound of gunfire in Kanombe. Munitions explosions at Camp Kanombe were also initially reported.
The senior officer for the Kigali operational zone called the Ministry of Defence with the news. Defence Minister Augustin Bizimana was out of the country, and the officer who took the call failed to reach Col. Théoneste Bagosora, the director of the office of the minister of defence, who was apparently at a reception given by UNAMIR's Bangladeshi officers.
The news of the crash, initially reported as an explosion of UNAMIR's ammunition dump, was quickly relayed to UNAMIR Force Commander Dallaire. He ordered UNAMIR Kigali sector commander Luc Marchal to send a patrol to the crash site. Numerous people began calling UNAMIR seeking information, including Prime Minister Agathe Uwilingiyimana and Lando Ndasingwa. Madame Agathe informed Dallaire that she was trying to gather her cabinet but many ministers were afraid to leave their families. She also reported that all of the hardline ministers had disappeared. Dallaire asked the prime minister if she could confirm that it was the president's plane that had crashed, and then called UNAMIR political head Jacques-Roger Booh-Booh to inform him of developments. Madame Agathe then called back to confirm that it was the president's jet and he was presumed to be on board. She also asked for UNAMIR help in regaining control of the political situation, as she was legally next in the line of succession, but some moderate ministers allied to her had already begun fleeing their homes in search of safety.
At 9:18 pm, Presidential Guards whom a UNAMIR report described as "nervous and dangerous" established a roadblock near the Hotel Méridien. Several other roadblocks had been set up prior to the attack as part of security preparations for Habyarimana's arrival. The patrol of UNAMIR Belgian soldiers sent to investigate the crash site was stopped at a Presidential Guards roadblock at 9:35 pm, disarmed and sent to the airport.
Soldiers in Camp Kanombe had interpreted the bugle after the crash to mean that the RPF had attacked the military camp and ran to arm themselves. Units had gathered at assembly points by around 9 pm. One such unit was a section of the para-commando brigade CRAP, which was ordered to collect bodies from the crash site. Later, two French soldiers arrived at the crash and asked to be given the flight data recorder once it was recovered.
A Rwandan colonel who called the army command about 40 minutes after the crash was told that there was no confirmation that the president was dead. About half an hour later, roughly 9:30, the situation was still confused at army command, though it appeared clear that the presidential aircraft had exploded and that it had probably been hit by a missile. News then arrived that Major-General Déogratias Nsabimana, the army chief of staff, had been on the plane. The officers present realized that they would have to appoint a new chief of staff in order to clarify the chain of command and began a meeting to decide whom to appoint. Col. Bagosora joined them soon afterward. At about 10 pm, Ephrem Rwabalinda, the government liaison officer to UNAMIR, called Dallaire to inform him that a crisis committee was about to meet. After informing his superiors in New York of the situation, Dallaire went to attend the meeting, where he found Bagosora in charge.
The Burundi Civil War continued after the death of Ntaryamira, both being sustained by and feeding into the instability in its Rwandan and Congolese neighbors. Over 300,000 people would die until a government of national unity was established in 2005.
At some point following the April 6 assassination, Juvenal Habyarimana's remains were obtained by Zairian President Mobutu Sese Soko and stored in a private mausoleum in Gbadolite, Zaire (now Democratic Republic of the Congo). Mobutu promised Habyarimana's family that his body would eventually be given a proper burial in Rwanda. On May 12, 1997, as Laurent-Désiré Kabila's ADFL rebels were advancing on Gbadolite, Mobutu had the remains flown by cargo plane to Kinshasa where they waited on the tarmac of Kinshasa International Airport for three days. On May 16, the day before Mobutu fled Zaire, Habyarimana's remains were burned under the supervision of Indian Hindu leader.
A now-declassified U.S. State Department intelligence report from 7 April reports an unidentified source telling the U.S. ambassador in Rwanda "rogue Hutu elements of the military—possibly the elite presidential guard—were responsible for shooting down the plane. This conclusion was supported by other U.S. agencies, including the CIA and Defense Intelligence Agency. Philip Gourevitch, in his bestselling 1998 book on the genocide, We Wish to Inform You That Tomorrow We Will Be Killed With Our Families, framed the thinking of the time:
Although Habyarimana's assassins have never been positively identified, suspicion has focused on the extremists in his entourage—notably the semiretired Colonel Théoneste Bagasora, an intimate of Madame Habyarimana, and a charter member of the akazu and its death squads, who said in January 1993 that he was preparing an apocalypse.
The 1997 report of the Belgian Senate stated that there was not enough information to determine specifics about the assassination. A 1998 report by the National Assembly of France posited two probable explanations. One is that the attack was carried out by groups of Hutu extremists, distressed by the advancement of negotiations with the RPF, the political and military adversary of the current regime, while the other is that it was the responsibility of the RPF, frustrated at the lack of progress in the Arusha Accords. Among the other hypotheses that were examined is one that implicates the French military, although there is no clear motive for a French attack on the Rwandan government. The 1998 French report made no determination between the two dominant theories. A 2000 report by the Organisation of African Unity does not attempt to determine responsibility.
A January 2000 article in the Canadian National Post reported that the UN war crimes prosecutor Louise Arbour had suppressed a report detailing accusations by three Tutsi informants that the RPF under Kagame had carried out the assassination with the help of a foreign government. The UN later clarified that the 'report' was actually a three page memorandum by investigator Michael Hourigan of Australia, who had been unsure of the credibility of the information and simply filed it into archives. The UN then sent the memo on to the International Criminal Tribunal for Rwanda, where defense attorneys had expressed interest in using it on behalf of their clients.
In 2004, a report by French anti-terrorist magistrate Jean-Louis Bruguière, investigating the deaths of the French aircraft crew, stated that the assassination had been carried out on the orders of Paul Kagame. The report relies heavily on the testimony of Abdul Ruzibiza, a former lieutenant in the RPF, who states that he was part of a cell that carried out the assassination with shoulder-fired SA-16 missiles. Ruzibaza later published his testimony in a press release, detailing his account and further accusing the RPF of starting the conflict, prolonging the genocide, carrying out widespread atrocities during the genocide and political repression. The former RPF officer went on to publish a 2005 book Rwanda. L’histoire secrete with his account. Bruguière reportedly claims that the CIA was involved in Habyarimana's assassination.
In November 2006, Bruguière issued another report accusing Kagame and the RPF of masterminding the assassination. In protest, Kagame broke diplomatic relations between France and Rwanda. Linda Melvern, author of Conspiracy to Murder: The Rwandan Genocide, noted
the evidence the French judge had presented alleging President Kagame's involvement in the murder of his predecessor was very sparse, and that some of it, concerning the alleged anti-aircraft missiles used to down the presidential jet, had already been rejected by a French Parliamentary enquiry.
Even the location from which the missiles were fired is disputed. Eyewitnesses have variously stated that they saw the missiles launched from Gasogi Hill, Nyandungu Valley, Rusororo Hill and Masaka Hill. Some witnesses claim to have seen used shoulder-launched missile launchers on Masaka Hill.