Karake was appointed deputy commander of the African Union peacekeeping force in Darfur, Sudan in August 2007, and in January 2008 became deputy of the UN mission in Darfur. He left this command in April 2009. In February 2008 a Spanish judge indicted Karake, alleging that when he was Rwanda's intelligence chief between 1994 and 1997 he was responsible for a series of political assassinations and massacres. Human Rights Watch claimed that forces under his command had killed civilians in 2000 while fighting Ugandan troops in the Congolese town of Kisangani. The United Nations was embarrassed by the allegations of earlier human rights abuses, and agreed to extend Karake's tenure beyond its expiry in October 2008 only after pressure from the United States and the United Kingdom, and when Rwandan PresidentPaul Kagame threatened to withdraw all Rwandan troops from Darfur if Karake was fired. In April 2010 President Kagame announced a shake-up of the military command, and a few days later ordered the arrests of Karake, who was accused of immoral conduct, and of former air force chiefCharles Muhire, accused of corruption. The men were said to be members of an exclusive circle of top officers in the former Rwandan Patriotic Front. The arrests followed newspaper reports that the two, reported to be popular and powerful figures in the military, had disagreements with Kagame.
2015 Arrest in London
Karake was arrested on 20 June 2015 in London, on an arrest warrant from Spain. Karake had been indicted in 2008 together with 39 other high-ranking Rwandan officials for grave crimes alleged to have been committed between 1990 and 2002, including the crime of genocide. As a result of Spanish legislation which weakened the doctrine of universal jurisdiction, the indictment was modified in 2014, and the charges were restricted to terrorism against nine Spanish nationals. Karake in particular was accused of numerous crimes, "including two massacres that claimed the lives of Spanish nationals in 1995 and 1997". The Rwandan government responded with Foreign MinisterLouise Mushikiwabo calling the arrest an outrage. Karake had a court meeting the day of his arrest and was remanded in custody. On 10 August 2015, Karenzi has been freed by the UK justice, considering that "the relevant laws on the conduct alleged in this case do not cover the acts of non-UK nationals or residents abroad.".