Contrary to the rhetoric of the ‘War on Terror’, Indonesia’s counterterrorism policies are neither specific responses to transnational terror networks, nor simply a byproduct of the post-9/11 era. Rather, counterterrorism policies in Indonesia are entangled with historical state reactions to internal security challenges – ranging from social violence to terrorism and secessionism – since the country’s independence in 1945. While these different conflicts varied in nature, they are united as disputes over the basic institutions and boundaries of the state. While the state, in seeking to maintain its territorial integrity and defend its institutions, has responded in a variety of ways to these conflicts, the coercion and repression used under President Suharto contributed to the rise of Jemaah Islamiyah (JI) and its splinter groups and left a legacy of mixed responses to terror. Terrorism and counterterrorism in Indonesia are rooted within this context of the disputed postcolonial state. While states like the US and UK have committed their militaries abroad in an effort to exterminate foreign militants, Indonesia has crafted responses to various sources of domestic violence – including different secessionist movements and JI – on an ad hoc basis and has utilized different security institutions, from the military to the police.