Uganda has perhaps the harshest refugee laws in the region. Refugees were confined to designated refugee camps and refugee status was transferred between generations: the children born in Uganda from refugee parents were themselves considered refugees. However, as the refugee numbers grew the population overflowed the boundaries of the camps set up during the initial refugee crisis. The one benefit of refugee status was that it gave children access to United Nations aid, in particular UNHCR scholarships, which allowed most young people to escape the camps and find work in urban areas in Uganda and abroad. This and the resulting success of many Tutsi bred resentment among both Ugandan nationals, which often manifested as work-place discrimination.
During the political crisis of the late 1960s, the administration of Milton Obote passed a bill called the Control of Alien Refugees Act, which declared Rwandese to be a special class subject to arbitrary detention. In 1969, Obote ordered all "unskilled foreigners" to be removed from government jobs, affecting thousands of Banyarwanda. ("Banyarwanda" are all persons who speak the Kinyarwanda language, which includes the indigenous Banyarwanda who lived in southern border regions, the descendants of Hutus who had come as migrant laborers in the mid-1920s, and the more recent Tutsi refugees.) Obote also ordered a census of all ethnic Banyarwanda, with the intention of ensuring that they would have no influence over the political process. The census was interrupted by the 1971 coup of Idi Amin, which was greeted with relief by many Banyarwanda. While some Banyarwanda joined the security forces, other joined the anti-Amin forces gathering in Tanzania. Prominent among these was a teenage Fred Rwigema, who was recruited by Yoweri Museveni into his Front for National Salvation.
Two of the 27 people who were part of the 1981 NRA raid at Kabamba that began the war were Tutsi refugees: Fred Rwigema and Paul Kagame, who had grown up together in Kahunge refugee camp and were both active members of RANU. By the time that the victorious NRA entered Kampala in 1986, about a quarter of its 16000 combatants were Banyarwanda, while Rwigema was its deputy commander. After the Museveni government was formed, Rwigema was appointed deputy minister of defense and deputy army commander-in-chief, second only to Museveni in the military chain of command for the nation. Kagame was appointed acting chief of military intelligence. Other Tutsi refugees were highly placed: Peter Baingana was head of NRA medical services and Chris Bunyenyezi was the commander of the 306th brigade. Tutsi refugees formed a disproportionate number of NRA officers for the simple reason that they had joined the rebellion early and thus had accumulated more experience.
The contributions of the Banyarwanda in the war were immediately recognized by the new government. Six months after taking power, Museveni reversed the decades-old legal regime and declared that Banyarwanda who had resided in Uganda would be entitled to citizenship after 10 years. In December 1987, RANU held its seventh congress in Kampala and renamed itself the Rwanda Patriotic Front. The new RPF, dominated by Banyarwanda veterans of the war, was far more militaristic than the original RANU.
Nevertheless, in a 1988 conference of the political diaspora in Washington, D.C., most of the exiled community agreed that the Tutsi should become naturalized citizens of the countries in which they resided, while those who wished to return could do so through a process of peaceful negotiation with the Rwandan government.
The final change came with a 1990 debate on ranches in Mawagola County, Masaka District and the issues it raised about whether citizenship should emanate from resident or indigenous status. The ranches had been gradually taken over by 200,000 pastoralists, about 80,000 of whom were said to be refugees. The owners of the land had raised the rent for using the land and for access to water, eventually resulting in a squatter uprising and outbreak of violence. A political firestorm erupted when the government sided with the squatters, as ranchers and others accused the president of favoring the nonindigenous Banyarwanda over the 'real Ugandans'. The opposition managed to put the topic of indigeneity and its relationship to citizenship and legal rights at the center of the political debate. Thus backed into a corner and in need of maintaining his political coalition, the president backed down, agreeing that the Banyarwanda were foreigners with no rights as citizens. Within the army, refugee officers were systematically removed, with the replacement of refugees in favor of individuals with claims to indigeneity eventually extending into other government agencies.
A senior RPF commander, speaking in 1995, summed up the effect this experience had on him:
You stake your life and at the end of the day you recognize that no amount of contribution can make you what you are not. You can't buy it, even with blood.
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