Many of the refugees were Hutu fleeing the predominantly Tutsi Rwandan Patriotic Front (RPF), which had gained control of the country at the end of the genocide.
While there has been much scholarship about the emergence of these separate ethnic identities, particularly through the colonial governance structures, before and after independence in 1961, people within Rwanda acted within the parameters of the Tutsi-Hutu division.
Museveni then supported a failed RPF invasion of Rwanda in 1990, as both a reward to an ally and in the hopes that the large Rwandan refugee population in Uganda would return home.
[7] The invasion, and the subsequent occupation of parts of the northern prefectures of Byumba, Umutara and Ruhengeri, internally displaced many Hutus and heightened ethnic tensions.
The assassinations of Habyarimana and Cyprien Ntaryamira on 6 April 1994 became the pretext for the start of the Rwandan genocide, which resulted in the deaths of several hundred thousand people, mostly Tutsi, over the next three months.
At the beginning of the genocide in April 1994, the Rwandan Patriotic Front began an offensive from territory in northern Rwanda that it had captured in previous fighting and made rapid progress.
Hutus fled the advancing RPF forces, with French historian Gérard Prunier asserting, "Most of the Hutu who had stayed in the country were there because they had not managed to run away in time.
[12] Contrary to refugee flows in other wars, the Rwandan exodus was not large numbers of individuals seeking safety, but a large-scale, centrally directed initiative.
On 28—29 April, 250,000 people crossed the bridge at Rusumo Falls into Ngara, Tanzania in 24 hours in what the UNHCR agency called "the largest and fastest refugee exodus in modern times".
As the RPF captured the capital of Kigali, the military of France set up a safe zone in southwest Rwanda in June 1994 in what was dubbed "Opération Turquoise".
[14] The French soon ended their intervention, leading to the flight of 300,000 people from the Zone Turquoise west towards the Zairean town of Bukavu in July and August, while a further 300,000 remained in internally displaced person camps.
[15] On 18 July 1994, RPF forces captured the northwestern town of Gisenyi and declared a new government with Pasteur Bizimungu as president and Kagame in the newly created position of vice-president.
[16] Gisenyi was the center of the provisional government and its fall caused over 800,000 Rwandans to cross into Goma, Zaire, over four days in late July.
However, by September 1994 rumors of violence by the RPF within Rwanda, combined with tightened control by the Hutu leadership of the camps, has drastically reduced the rate of return and eventually stopped it altogether by early 1995.
The refugees near Goma were located at Mugunga on a plain of volcanic rock, which was so hard that the French troops and aid workers were unable to dig graves for the bodies that began to line roads.
[22] The international media coverage of the plight of the refugees eventually led U.S. President Bill Clinton to call it the "world’s worst humanitarian crisis in a generation" and large amounts of relief was mobilized.
The American military formed an emergency logistical operation, based out of Entebbe International Airport in Uganda, to ferry supplies and relief personnel to the crisis regions.
[32] Refugees who disagreed with the structure, who tried to return to Rwanda or were too frank with aid workers in discussing the situation were subject to intimidation and murder.
[33]As the initial acute humanitarian crisis was stabilized, aid workers and others began to raise concerns about the presence of armed elements in the camps.
Humanitarian workers reported that former government officials, especially near Goma, were passing out large amount of money to the militia to control the refugees on their behalf.
The first to leave was Médecins Sans Frontières, who stated that "this humanitarian operation was a total ethical disaster" as it rewarded those responsible for the genocide rather than punishing them.
In light of their abandonment by its trusted partners and the insecurity, High Commissioner Sadako Ogata was asked why UNHCR did not simply leave as well.
The International Criminal Tribunal for Rwanda (ICTR) and community gacaca courts exist to punish those who planned and carried out the genocide, but the scale of violence forced the Rwandan people into an occasionally uneasy coexistence.
The forests of Virunga National Park, home to the endangered mountain gorilla, were badly damaged by the demands for firewood and charcoal made by the refugees.
The exception was the international humanitarian aid community and the United Nations, for whom the Great Lakes crisis was an agonizing dilemma that has been the topic of extensive analysis and ethical arguments.