In the early 2000s, Indonesia witnessed a proliferation of Islamist paramilitary groups and terror activity in the wake of Suharto’s downfall. Having said this, over the years since Suharto’s downfall, the dire threat predictions have largely failed to materialize at least strategically. This outcome raises some interesting questions about the ways in which Indonesian policy responded to the security threat posed by Islamist militancy. Drawing on Temby’s thesis about Darul Islam and Negara Islam Indonesia and combining this with Colombijn and Lindblad’s concept of ‘reservoirs of violence’, the following article argues that countering the conditioning factors underlying militancy and the legacy of different ‘imagined de-colonizations’ is critical for degrading militant threats (especially Islamist ones) in Indonesia. Persistent and excessive punitive action by the state is counterproductive in the long run. It runs too high a risk of antagonizing and further polarizing oppositional segments of the population. That in turn perpetuates a ‘ghettoized’ sense of enmity and alienation amongst them towards the state and wider society. By situating localized responses to the problem in historical context, the following underscores the importance of preventative persuasion measures for limiting the reproduction of militancy in Indonesia.