The Rwandan Patriotic Front was dissatisfied with the Hutu government of Juvénal Habyarimana, who Pasteur Bizimungu was reportedly close to in the 1980s. After Habyarimana's death in a plane crash April 6, 1994 decades of complex ethnic, social and political hatreds were ignited and led to the Rwandan Genocide.
Eventually in July 1994 the Rwandan Patriotic Front gained control of the country and established a national unity government. The RPF leader, Tutsi Paul Kagame, was chosen vice-president, and Bizimungu was chosen President so that the majority Hutus would still be highly represented in the government. Bizimungu was chosen largely for his harsh criticisms of Hutu hardliners. Bizimungu frequently reported that the hardliners assassinated his close friend Juvénal Habyarimana and reportedly supplied information to the MI6 demonstrating the involvement of Hutu hardliners and French intelligence in the assassination.
During Bizimungu's administration, many believed that Kagame had true control of the government. Bizimungu, as deputy leader of the RPF, eventually came into a conflict with Kagame amid growing differences with the government over its policies and what he saw as an unwarranted crackdown on dissent. He resigned in March 2000, and Kagame became president.
In May 2001, Bizimungu founded an opposition movement, the Party for Democracy and Renewal (PDR), known as Ubuyanja in the Kinyarwanda language. It was almost immediately banned by the government, which accused it of being a radical Hutu party. Critics claim that the government is simply crushing opposition figures under the pretext of inciting racial tensions. Bizimungu was placed under house arrest for continuing the operations of the party on April 19, 2002 and charged with endangering the state. On June 7 2004 he was sentenced to 15 years in prison for attempting to form a militia, inciting violence and embezzlement. He received a five-year sentence for each of these convictions, which were to run consecutively. On 17 February 2006, represented by a team of attorneys including Peter Zaduk, Bizimungu's appeal, based on the fact that he was convicted of crimes different from those with which he was initially charged, was denied by the Supreme Court.