This chapter explores the development of Newton’s methodological thought up to c.1700, as well as that of his first followers. Newton’s caution in not antagonising Huygens in particular is highlighted. It was only in this decade that Newton started to emphasise the natural-theological significance of his natural philosophy, especially in manuscripts related to the Classical Scholia. But there was no metaphysical component; rather, Newton insisted on the analogical predication of the divine. Even more important was his reconsideration of the Hypotheses of the first edition, which eventually became the Rules of Philosophising of the second. It is shown that these were not abstract methodological principles, but rather a set of dialectical arguments designed to negate the possibility of weightless matter. Nonetheless, they shaped Newton methodological agenda and language for the rest of his life. His position was understood perfectly by his earliest follows: David Gregory and John Keill, both of whom were teaching in Oxford.