This chapter examines comparatively three instances of extreme political violence in Indonesia and Indonesian-occupied territory over more than fifty years: the mass killing of roughly half a million communists and leftists in 1965–6; the unnatural death or killing of at least 100,000 people in East Timor from 1975 to 1999; and the systematic physical and cultural decimation of the indigenous population of West Papua from 1963 to 2020. It describes the unique dimensions of each case – including key patterns and variations in the violence, the historical and political conditions that gave rise to it, the identities of the perpetrators and victims, and differences in the degree and nature of resistance. At the same time, it highlights the remarkable similarities and continuities across the three cases. It argues that, despite their differences, these three cases form part of a single broad pattern of extermination and genocide perpetrated by the Indonesian state, driven by competition over valuable resources and facilitated by the acts and omissions of powerful foreign actors.