With the publication of The Miraculous Conformist in 1666, Stubbe resumed a polemical career in which he speaks with his old anticlerical ‘Hobbesist’ voice, though no longer freely but in a code full of cryptic meanings. We are now in a position to examine the principal sequence in his career as an early Restoration polemicist, his famous attacks on the Royal Society, delivered and published between 1669 and 1671. In these he defended Aristotle, Galen and Scholastic learning against the new philosophy of the Royal Society, as it was put forward by Thomas Sprat and Joseph Glanvill. The standard accounts of the controversy have interpreted him as a conservative defender of church and monarchy, wedded to the old Scholastic ‘humanism’ against the new scientific ‘naturalism’ and fighting a rearguard action against science and progress. Were this view correct, Stubbe would have had to make a considerable about-face between early 1666 and 1669 when the controversy began.