The Protestant cause in Ireland apparently victorious and the Church of Ireland restored to its pre-1685 privileges, King was able to look past the immediate political consequences of his doctrinal and theoretical principles and begin to work toward positioning them in a broader universal context. Part of King's frustration throughout the Jacobite years, and his source of impatience with the Dissenters throughout his life, was that immediate day-to-day concerns interfered with what would have been more important and constructive debate about the fundamental truths upon which a civil society could be built that would, by virtue of its founding principles, be inclusive, liberal and stable as all people of reason would voluntarily seek to participate in its function. Such a set of guiding principles would be self-evident and self-proving, as precisely and logically structured as mathematics and physical sciences.

King was a philosopher, a participant in the Dublin Philosophical Society and a correspondent of the Royal Society, whose motto, ‘nullius in verba’, adapted from Horace's Epistles (I.i.14) rejects the notion of blind obedience and encourages a reliance on observable experimentation. The turmoil of William's accession would see Sir Robert Southwell elected as Royal Society president in 1690 (and re-elected annually until 1695). Southwell, scion of a Munster planter family, was William's principal secretary and accompanied the new monarch to Ireland in 1690 and would later be appointed Secretary of State for Ireland.