This chapter traces the origins of the Papua conflict to two basic sources: the manner of Papua's incorporation into Indonesia during the 1960s and the mode of Jakarta's subsequent rule over the province, particularly during the New Order period. It examines the Papua conflict in terms of the complex histories of decolonisation, Cold War geopolitics and the evolution of the Indonesian state. It also outlines the evolution of Australia's policy from opposition to Indonesian rule over Papua to strong support for Suharto's New Order regime.The troubled decolonisation process that resulted in Papua's incorporation into Indonesia produced a small pan-Papuan elite which, under the politically charged atmosphere of the Cold War, opposed Indonesian rule and asserted Papua's right to self-determination. The subsequent policies adopted by Indonesia expanded existing opposition and generated significant local resistance. While these policies were intended to strengthen Papua integration, they in fact alienated many Papuans from the state.