Mr. Locke and several of his Friends, London, 1708).
Immediately after the battle of the Boyne (1 July 1690) Molyneux paid a hurried visit to his old father, who had persisted in remaining in Dublin. On his return through Wales he was mistaken by the Denbighshire militia for William Molyneux, eldest son of Lord Molyneux, for whose apprehension 500l. reward had been offered ; but having proved his identity he was, after a brief detention, allowed to proceed on his journey. In December 1690 he was suddenly recalled to Dublin by the news that he had been placed on a commission for stating the accounts of the army. He was shortly afterwards rejoined by his wife and infant son, but recent events had proved too much for her delicate constitution, and on 9 May 1691 she died. A parliament, the first with the exception of Tyrconnel's convention that had met for twenty-six years, having been summoned for October 1692, Molyneux was returned as one of the representatives of Dublin University. In the discussion on the right of the commons to originate money bills Molyneux appears to have played a neutral part, for shortly before the dissolution he was nominated a commissioner of forfeited estates, with a salary of 400l. a year. But the ill reputation of the commissioners with whom he was to act induced him to decline the appointment, and his conduct, which was highly applauded, led to a reconstitution of the board. In July 1693 Trinity College conferred on him its honorary degree of LL.D., and in 1695 he was again chosen to represent the university in parliament. He was assiduous in his attention to his parliamentary duties, and during the absence of the lords justices Galway and Winchester in the winter of 1697-8 he shared the responsibility of government with the lord chancellor, John Methuen [q. v.], and the lord mayor, Mr. Van Homrigh.
From his correspondence with Locke it appears that Molyneux was at this time engaged in investigating the effect that the recent legislation of the English parliament was having on the linen and woollen industries of Ireland. His interest in the matter moved Molyneux to publish early in 1698 the work by which he is best known—viz. 'The Case of Ireland's being bound by Acts of Parliament in England stated.' It was, he admitted to Locke (Familiar Letters, p. 269), ' a nice subject,' but he thought he d treated it with discretion, and consequently had not hesitated to put his name to it and even to dedicate it to his majesty. None the less, he thought it prudent, till he saw how it was taken by the English parliament, not to cross the Channel, for though 'not apprehensive of any mischief from them, yet God only knows what resentments captious men may take on such occasions.' In substance the book is based on the treatise, 'A Declaration setting forth how and by what means the Laws and Statutes of England from time to time came to be in force in Ireland,' attributed by some to Patrick Darcy [q. v.] and by others to Sir Richard Bolton [q. v.] But Molyneux's effort has special value of its own as an attempt to prove the legislative independence of the Irish parliament. It made an immediate sensation, and two replies were at once forthcoming viz. 'A Vindication of the Parliament of England,' &c., by John Cary [q. v.], London, 1698, and 'The History and Reasons of the Dependency of Ireland,' &c., by William Atwood [q. v.], London, 1698. The Irish government was supposed to have given some encouragement to its publication, and Methuen, as if to divert responsibility from the Irish ministry, himself introduced it to the notice of the English House of Commons on 21 May 1698 (Vernon, Letters, ii. 83). The business was referred to a committee. On 22 June the committee reported, and it was unanimously resolved 'that the said book was of dangerous consequence to the crown and parliament of England' (Parl. Hist. v. 1181). An address embodying the resolution was presented to the king (Journals, House of Commons, xii. 337) ; but there appears to be no ground for Macaulay's opinion (Hist, of England, v. 60) that Molyneux himself stood in any personal danger, or for the general belief that the book was condemned to be burnt by the common hangman. About the beginning of July Molyueux went to England in fulfilment of a longstanding promise to visit Locke. ' I reckon it the happiest scene of my whole life,' he wrote (Familiar Letters, p. 272), in reference to his meeting with Locke and to the time he spent with him at Oates and in London. He reached Dublin again on 15 Sept., but shortly afterwards he was attacked with a severe fit of the stone. He died on 11 Oct. 1698, and was buried beside his wife, in the tomb of his great-grandfather, Sir William Ussher, in the north aisle of St. Audoen's ; Church, Dublin, where a monument with a long Latin inscription (cf. Gilbert, Hist. of Dublin, i. 283) was erected to his memory. The monument was removed by his grandnephew, Sir Capel Molyneux, in order to be repaired, but owing to Sir Capel's death soon ; afterwards it was never replaced. In 1869 a tablet was fixed in the church on its site
