I postulate that there is a divorce between the Free Exercise Clause of the Unite States Constitution and the freedom it sought to protect. Consequently, we have a polity besieged by diminishing freedoms and fear, which inadvertently manifests as intolerance. The thesis utilizes historical responses to antithetical ideologies like communism and polygamy to draw a parallel between the ugly past and terrorism; and to highlight a fundamental ideological lapse in the prosecution of the war on terror. A case Study of the Al-Qaeda Terrorist Organization revealed that it is a fully functional organization, albeit clandestine, that embodies the elements of public administration and the ability to set goals and coordinate resources for the fulfillment of specific terrorist goals. Some have viewed religion as an endless good, yet it remains a significant source of socio-cultural schism in the society. Mere toleration and the use of contemporary law are insufficient to dispel the dangers posed by radical Islamists. The violence and tension among various faiths are exacerbated by three dominant factors: first, the uncanny inclination of people toward political correctness; second, an inherent loophole in the Free exercise Clause; third and paramount is subversive religious doctrines. Also, apathy, complacency and a degree of religious naiveté in the polity all play into the rising religious disquietude. The thesis concludes that Free Exercise Clause is under attack and that terrorism and extremism are the bane of subversive religious injunctions. Suggestions are offered in the conclusion. / Department of Political Science