Wilkins was spared the pain of witnessing the end of the Commonwealth in Oxford, and of being ejected from his post like other Heads of Houses. On September 3, 1659, he resigned the Wardenship, and was succeeded on September 5th by Walter Blandford, one of the Fellows who had submitted to the Visitors in 1648, and later, in that strange time of opinions which "could be changed," had made his peace with the Royalists. During his Wardenship of six years the College flourished. He was made Bishop of Oxford in 1665, and was in 1671 promoted to the See of Worcester, another of the many Wadham Bishops.
Wilkins left Wadham to become Master of Trinity College, Cambridge. He had been invited there by the Fellows, on whose petition he was presented by Richard Cromwell. Thirty years later Cambridge, as if in exchange for value received, sent Richard Bentley to Wadham, who left it to return to Cambridge as Master of Trinity,—an interchange of which neither University can complain.
At Cambridge Wilkins' stay was brief. He was Master of Trinity only for ten months, but in that short reign he proved himself as vigorous and effective as he had been at Wadham: he stimulated and organised the College teaching, and made his Fellows work, by instituting disputations, and examinations at elections, probably fallen out of use in the troubles of the fifteen previous years; yet here as elsewhere he was able to win and rule, for "he was honoured there and heartily loved by all." At Cambridge, Burnet tells us, "he joined with those who studied to propagate better thoughts, to take men off from being in parties, or from narrow notions, from superstitious conceits, and fierceness about opinions." He must have had as his allies there Cudworth and Whichcote, men of his own age, and one younger, Stillingfleet, the Latitudinarians, from whom our Broad Churchmen are theologically descended.
The evil days came soon: despite the petition of the Fellows who wished to keep him, he was ejected from the Mastership when the King came back. "The whirligig of time brings in his revenges," and what Pitt had undergone Wilkins had to undergo.
Pope describes, surely with some exaggeration, the troubles of Wilkins during the eight years between his departure from Cambridge and his being made Bishop of Chester. He was a man whom no misfortunes could crush—elastic, resolute, resourceful master of his fate,—
"Merses profundo, pulchrior evenit."
He had many friends and a great reputation; they brought him various preferments,—the lectureship at Gray's Inn, the vicarage of St Lawrence Jewry, and the Deanery of Ripon, within a few years after his banishment from Cambridge. Preferment may not have brought him happiness, but it must have prevented his fortunes from being, as Pope says they were, "as low as they could be." He suffered indeed one calamity—a cruel one to a man of his pursuits and tastes: in the great fire of London the vicarage house of St Lawrence Jewry was burnt, and with it were destroyed his books and the collection of scientific instruments made during his residence at Oxford with the help of the members of the club.
Add to this that he was out of favour both at Whitehall and at Lambeth on account of his marriage—for that reason "Archbishop Sheldon who had the keys of the Church for a great time in his power, and could admit unto it and keep out of it whom he pleased, I mean (Pope hastens to explain) disposed of all Ecclesiastical Preferments, entertained a strong prejudice against him." This prejudice the Archbishop, when later, on the introduction of Ward, he came to know him better, acknowledged to have been unjust, a signal instance of Wilkins' power of winning men. The Latitudinarian was at first coldly received at Lambeth: the brother-in-law of Cromwell was not acceptable at Whitehall. His friend Ward did not desert him, but "followed up good words with answerable actions," and procured for him the Precentor's place at Exeter,—"the first step which Wilkins ascended to a better fortune."
In Charles II. he soon found a still more powerful friend. The King, who was himself the broadest of Latitudinarians, as far as Protestantism was concerned, was not repelled by Wilkins' theological views, and yielded readily to the attractions of a versatile and agreeable man of science. Science was the most creditable of Charles's tastes and occupations; the one in which he took a genuine and enduring interest.