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 emigrating to Carolina, and thence to have gone to London, where, along with Baillie of Jerviswood, Fletcher of Saltoun, and James Stewart of Coltness, he endeavoured to raise money for Argyll's contemplated expedition to Scotland. The necessary money, which Argyll had fixed at 30,000l., was not to be got, and it was thought expedient that Carstares should return to Utrecht. He there had many meetings with both the English and Scotch exiles; but there was a want of unanimity in their counsels, and Carstares advised delay. The discovery of the Rye House plot, which led to the execution of Lord Russell on 21 July, was followed in a few days by the capture of Carstares, who had again crossed the Channel, and was seized at Tenterden in Kent, where he was in hiding under his mother's name of Mure. On his refusal to take the corporation oath and abjure the covenant he was sent to prison, and after a fortnight's imprisonment removed to London, where he was twice examined before a committee of the council. He was thence transmitted to Scotland, as he himself thought, and the event proved, ‘because it was judged that violent tortures which the law of England, at least the custom, does not admit of, would force to anything.’ On 14 Nov. he was committed to the Tolbooth of Edinburgh. After lying there some time in the hope of a voluntary confession, Spence, one of his associates, was, under torture, forced to name Carstares as participant in Argyll's plot, and the same instrument, the thumbkins, with the threat of the boot, joined with Lord Melfort's assurance that his depositions should not be used against any person, induced him to make a deposition as to his knowledge of the plot. Contrary to the promise embodied in a minute somewhat modified in form, declaring only that Carstares was not to be brought ‘as a witness,’ the privy council published an abstract, and used it at the trial of Baillie of Jerviswood, who was found guilty and executed. Carstares expostulated, but without any effect, against the breach of faith in using his depositions, and, declining payment of his expenses during imprisonment, returned by way of England to Holland. After a tour in the Low Countries and the Rhine, he settled for a short time at Cleve, and in the winter of 1686–7 at Leyden, where he was appointed second minister of the Scottish congregation and chaplain of William of Orange. He accompanied William in his voyage to Torbay, and conducted the thanksgiving service on the beach where the troops landed. From this time Carstares was seldom long absent from William. He had apartments at court, and accompanied the king as chaplain in his campaigns. When the jealousy of others attacked him, ‘Honest William Carstares’ was the only answer the king deigned to make to these detractors. He was nicknamed by the Jacobites ‘the cardinal,’ and, especially in Scotch affairs, his advice was constantly taken. He had the courage to offer it even when not asked if he deemed it useful to his country's interest. The revolution settlement, by which the Scottish presbyterian church was established, was pre-eminently the result of his counsels. William himself was disposed to favour the episcopal form of church government, or at least some compromise between it and presbyterianism, but Carstares satisfied him that this was impossible. His ‘Hints to the King’ were founded on the argument that ‘the episcopal party were generally disaffected to the revolution … whereas the presbyterians had almost to a man declared for it, and were, moreover, the great body of the nation.’ Carstares was sent to consult with Lord Melville, the commissioner in Edinburgh, and, having rejoined the king after the victory of the Boyne at the siege of Limerick, returned with him to London. When there the draft of the proposed Scottish Act of Settlement of the church was forwarded by Melville and considered clause by clause by the king and Carstares, who suggested modifications embodied in remarks, which William dictated to him and which were adopted. One of them is a sufficient example of their tendency: ‘Whereas it is said their majesties do ratify the presbyterian church government to be “the only government of Christ's church in this kingdom,” his majesty deems it may be expressed otherwise, thus: “To be the government of the church in the kingdom established by law.”’

On the knotty point of patronage Carstares advised against its abolition, but Melville took the opposite view, and William gave a reluctant assent to the act for repealing patronage.

In 1691 Carstares accompanied William to Flanders. It was at this time that the measures which led to the massacre of Glencoe were determined on, but the only reference to them in Carstares's correspondence is an approval of Lord Breadalbane's scheme to distribute money among the chiefs, so that he appears to be free from the stain which rests on the memory of the Master of Stair and William. The next two years he was again with the king in the Flanders campaigns, and received from him a gift of the ward of Lord Kilmarnock. ‘I am apt to think it will have much to do,’ he writes