This chapter examines the settlement of the separatist conflict fought in Aceh, Indonesia. It demonstrates that after the loss of East Timor, Indonesia toughened its approach to separatist claims and reaffirmed its acceptance of impunity and belief in the relative importance of state survival over human rights. The chapter argues that this and the UN’s absence from the peace process, meant that the inclusion of an unrestricted amnesty in the final peace agreement was unsurprising. However, the chapter also details the evolution of the separatists’ ideas about the relationship between peace and justice and the importance of ending impunity for human rights violations in Aceh. It demonstrates that although the protection of human rights and the pursuit of accountability for past violations was a key pillar of the separatists’ claim, as the conflict and negotiations wore on, the possibility of Acehnese independence faded, and a political future for its key protagonists became probable, they accepted the pragmatic view that amnesties may help end conflict, allow some measure of self-determination and, perhaps ironically, facilitate the protection of human rights.