A prominent opponent of the Hutu Power ideology, Kavaruganda was known to be ill-regarded by some members of the MRND regime. On February 17, 1994, UNAMIR commander Roméo Dallaire received information of a plot to assassinate Kavaruganda and Lando Ndasingwa. In his book Shake Hands with the Devil, Dallaire claims that he informed them of this plot, and neither were surprised. UNAMIR dispatched five Ghanaian soldiers to protect Kavaruganda's house.
On April 7, members of the government's Presidential Guard arrived at his door, claiming they were taking him to safety. Kavaruganda's wife Annonciata Kavaruganda claims he knew this was a ruse, but went with them anyway, seeing no other option. He was killed later that day.
According to Annonciata Kavaruganda, the Ghanaian soldiers were friendly with the Rwandan militiamen who had come for Kavaruganda, laughing and drinking together while the government soldiers beat her and her children. 
- ^ Carol Off. 2000. The Lion, the Fox, and the Eagle: A story of generals and justice in Rwanda and Yugoslavia. Random House. ISBN 0-679-31138-6.
- Neuffer, Elizabeth. The key to my neighbor's house: seeking justice in Bosnia and Rwanda (MacMillan 2002), page 98.
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