The popularisation of Islamic philosophy, particularly the writings of Mulla Sadra (d. 1640), following the 1979 Islamic revolution in Iran have recounted many vicissitudes and open condemnations by Qom's scholarly community. The writings of Mulla Sadra represent the fullest and grandest expression of philosophy in Islam, one that not only benefits from a millennium of Islamic thought before it but also formulates and crystallizes in an unprecedented manner, the various latent modes and dimensions of "prophetic philosophy"; consequently, following the Islamic revolution, the figure of Mulla Sadra became that of the philosopher par excellence. Khumayni seems to have encouraged the linkage of the study of philosophy and mysticism with the political theory of vilayat-i faqih rooted in a philosophical paradigm known as the 'Unity of Existence' by which man is led to God, learns to open himself up to spiritual wisdom, and then returns to the world as one who has become united with God thereby reflecting God's divine attributes, placing Khumayni in a privileged position to maintain order in the realm of worldly politics. However, following growing dissatisfactions with clerical hegemony and the popularisation of claims by Khumayni's adepts linking their right to govern the state with divine authority, significant segments of the clerical community in Iran have begun to align themselves politically with a pre-1979 school of thought, namely maktab-e tafkik, that has made it its prime concern to separate non-Shi'i elements from so-called Islamic philosophy. How this links to dissident clerical politics is the central theme of this paper. Based on my recent field research in Qom and Tehran, and drawing on the small number of extant Arabic and Persian manuscripts by proponents of the maktab-e tafkik, my paper will argue that dissident members of the clergy in Iran have mounted an intellectual (and sometimes, ad hominem) attack on Mulla Sadra in order to break the link between Khumayni's philosophical extrapolations based on Sadrian philosophy and, the establishment of the Islamic Republic of Iran, thereby challenging the foundational pillars that uphold the Islamic Republic of Iran. It will be seen that recent assaults by maktab-e tafkik thinkers and their political allies on state-linked philosophers are contributing to the polarisation of Qom's scholarly community and concomitantly challenging the very legitimacy of the system of vilayat-i faqih which, in the eyes of tafkikis, is built on un-Islamic foundations, a phenomenon rapidly catching on with elements of the anti-government movement.