In the years after the publication of the second edition of the Principia, Newton further elaborated his vision of the genealogy of knowledge, and his subsequent conception of the limits of ‘legitimate’ knowledge. Metaphysics now emerged for him as the unifying force that explained all the evils of intellectual life, above all pagan idolatry; the hubristic rationalism in theology that gave birth to odium theologicum and persecution; and the unwarranted search for speculative, causal explanations in natural philosophy. In a set of elaborate writings, ranging from the ecclesiastical-historical ‘Of the Church’ (in which we see the influence of Bayle’s close friend Jacques Basnage) to further polemical writings against various followers of Leibniz and Malebranche, he developed his mature vision of a Kingdom of Darkness at the centre of which lay speculative, metaphysical philosophy. The manuscript ‘Tempus et Locus’ should be dated to this period, rather than to the 1690s. Finally, it is shown that Newton’s earliest followers understood perfectly the broad methodological message which he was trying to advance, and continued to disseminate it aggressively in their writings. The earliest decades of the eighteenth century were devastating for the practice of ‘philosophy’ as it had been conducted for much of Western history.