Under mounting international pressure, a power-sharing agreement brought Cyprien Ntaryamira, a Hutu, to power. Only weeks after his election, Ntaryamira died in a plane crash with Rwandan President Juvenal Habyarimana in April 1994, the event which marked the beginning of genocide in Rwanda. Amidst ongoing violence between government forces and Hutu-led militias, power in Burundi remained concentrated in the Tutsi-dominated military, although a Hutu, Sylvestre Ntibantuganya, held the presidency.
With Hutu increasingly targeted in Burundi's capital Bujumbura, hundreds of civilians fled to eastern Congo in 1995. On July 25, ex-President Pierre Buyoya staged a bloodless military coup, pledging to restore order to the country. Neighboring states reacted by imposing an embargo on Burundi, which remained in place until January 1999 at the cost of increasing impoverishment. Under conditions of extreme poverty, continued inter-ethnic violence, and international pressure, Buyoya began to lift restrictions on the activities of political parties.
In August 2000, the Arusha conference brokered a peace agreement between the government and the Hutu opposition. The accord called for democratic elections and an ethnically balanced military and government. In 2003, the Pretoria Agreeement was signed, which brought the National Council for the Defense of Democracy (CNDD), the militarily strongest Hutu rebel group, into the peace process and laid the foundation for the critical work of creating a new bi-ethnic military. The same year, according to new constitutional conditions, Buyoya stepped down from the presidency and an interim, multiparty government was created to manage the transition to elections.
Elections in 2005 resulted in a new Hutu president, Pierre Nkurunziza, a leader of the CNDD. The oldest Hutu rebel group, the National Liberation Force (FNL) continued fighting -- although without posing a significant threat to the transition process -- throughout this period. It was only in 2009 that serious progress was made in disarming the FNL.
Deploying the first African Union force
In February 2003, the African Union approved its very first operation, deploying soldiers from South Africa, Mozambique, and Ethiopia to Burundi to assist in the disarmament, demobilization, and reintegration process. In June 2004, the AU forces reformed into the basis of the United Nations Operation in Burundi (ONUB), a Chapter VII mission designed to facilitate the agreements between the army and rebel groups while protecting civilians. The UN withdrew its peacekeepers at the end of 2006 and opened the UN Integrated Office in Burundi (BINUB) to assist in post-conflict development.
In 2005, the UN and Burundi began discussions to establish a new mechanism for transitional justice: a hybrid institution that included a special court to prosecute war crimes and human rights violations and a truth commission to bring reconciliation. Both would be mandated to consider cases that have taken place in Burundi since independence from Belgium in 1962. Internal political unrest and disagreements between Burundi and the UN have interrupted and slowed the process to create and implement this new system of justice.