However, even though Hobbes maintains that his arguments are completely consonant with Christianity, his notion that God is not present in this world was a drastically sacrilegious stance to take in the seventeenth century. Hobbes frequently condemns "atheists" in Book III, seemingly as an effort to distance himself from that category. Hobbes certainly believed in God; his philosophy leads him back again and again to the conclusion that there must be a Prime Mover who does intervene in the world, albeit only through the mediation of matter. However, by deducing that God is never personally present in this world--even in the incarnation of Christ--Hobbes placed himself in a shaky position relative to contemporary religious belief.

Hobbes's technique in Book III is primarily that of literary criticism. His reconstruction of Biblical exegesis to conform to his materialist arguments of Books I and II was a daring move in the cultural climate of the seventeenth century. While scientific endeavor throughout the century was concerned with reconciling the facts of nature with religious beliefs, the tendency was either to subsume natural knowledge under theological knowledge (as in the trial and execution of Galileo) or to separate natural knowledge from theological knowledge entirely (this was the strategy of Robert Boyle and members of the Royal Society, who maintained that the study of natural facts did not have implications for religion). Contrary to these prevailing tendencies, Hobbes takes theological knowledge and reinterprets it to conform to his determination of natural facts and philosophical conclusions. Hobbes shows that the Bible confirms his scientific claims, thus subordinating theology to natural philosophy, rather than the other way around.

But such a strategy was unlikely to be widely accepted in seventeenth-century England. A natural philosophy that had fewer consequences for religious belief and was less constraining of theological knowledge was more politically acceptable to contemporaries than Hobbes's monolithic philosophy. This may be why Hobbes's version of science did not become influential, despite its capacity to generate secure knowledge, while the more separatist version of science represented in the Royal Society came to be the basis of modern experimental science.