 In the latter half of the 1980s and the first half of the 1990s, Prendergast worked for a variety of organizations in the U.S. and Africa, focusing primarily on peace and human rights.At the end of 1996, he joined the National Security Council as Director for African Affairs and thereafter served as a special adviser to Susan Rice at the United States Department of State.As a special adviser, Prendergast was a member of the team behind the successful two-and-a-half-year U.S. effort to broker an end to the Eritrean–Ethiopian War.