From small reclusive beginnings steeped in pietistic Salafism, Boko Haram has evolved into a real threat to national security in Nigeria. A factor that cannot be overlooked in the sect’s emergence and transformation is the regrettable history of ethno-religious differences that are now perhaps at an all-time high in the country. Such differences have always threatened political stability in Nigeria, but no less disturbing have been Nigeria’s lack of resolve to deal with the differences, and the perennial tendencies of the political class to exploit them for partisan advantage. This article enquires into Boko Haram’s origins and the factors that sustain its deadly campaign of terror, and how these have been helped by Nigeria’s lack of attention to the actual root causes of the kind of threat that Boko Haram represents today. It examines Nigeria’s aggressive counterterrorism efforts, and contends that it has been politicized in a way that enhances the sect’s threat. It has deepened ethno-religious rifts and provided fodder for political mudslinging. The article argues for a counterterrorism response that deemphasizes military aggression and invests political will in resolving the underlying tensions that enhanced the sect’s emergence.