Why did Christian theology supplant Greek philosophy in the time of the Roman Empire? Heidegger briefly dwells on this issue in his 1929 lecture on metaphysics. He notes that metaphysics has a twofold character—first, it represents beings as beings, or the truth of beings in their universality; second, it tries to represent the truth of the highest being (which can be regarded as God, though Heidegger has not used the word “God” in his lecture).
The first character of metaphysics (beings in their universality) is ontological, while the second character (being of the highest being) is theological. Thus, metaphysics as a whole has no choice but to be onto-theological. The Greek philosophy which was popular in the Roman Republic and the subsequent Roman Empire was primarily ontological—the theological element was missing from it. By supplying the crucial theological element, Christian theology fulfilled the vacuum in Greek metaphysics and supplanted Greek philosophy.
In light of what Heidegger has said, Aquinas’s work in the thirteenth century can be viewed as a continuation of the Christian theological project, which began in the Roman era, on Greek (chiefly Aristotelian, in the case of Aquinas) philosophy. In my opinion, this theological project ended in the eighteenth century with the rise of atheistic and utopian Enlightenment philosophy.