(afterwards second Earl of Manchester) [q. v.], he became vicar of Kimbolton, Huntingdonshire, where he organised an independent church. According to Edwards, he was much in Yorkshire, spreading his independent opinions especially at Hull. At Kimbolton (apparently) on 22 July 1643 seven persons belonging to Hull formed themselves into an independent church for that town.
He was summoned (12 June 1643) to the Westminster assembly of divines, having had, according to Calamy, a considerable hand in selecting them (his father was on the list, but did not attend), and was sent to Scotland (20 July) as one of the assembly's commissioners with Stephen Marshall [q. v.] His locum tenens at Kimbolton appears to have been Robert Luddington (1586–1663), who on Nye's return became pastor of the Hull independent church. On 20 Aug. he preached in the Grey Friars Church, Edinburgh, but ‘did not please. His voice was clamorous. … He read much out of his paper book. All his sermon was on … a spiritual life … upon a knowledge of God, as God, without the scripture, without grace, without Christ’ (Baillie). He returned (30 Aug.) before Marshall. On 25 Sept. he delivered an ‘exhortation’ at St. Margaret's, Westminster, preliminary to the taking of the ‘league and covenant’ [see Henderson, Alexander, 1583?–1646], by the houses of parliament and the assembly. Nye showed that the covenant in upholding ‘the example of the best reformed churches’ did not bind to the adoption of the Scottish model. He received the rectory of Acton, Middlesex, on the sequestration (30 Sept.) of Daniel Featley [q. v.] John Vicars [q. v.] says he was offered a royal chaplaincy in December if he would abandon the covenant and agree to moderate episcopacy.
In the proceedings of the assembly, Nye took a decided part with the ‘dissenting brethren,’ of whom Dr. Thomas Goodwin [q. v.], ‘vulgo vocatus Dr. Nine Caps,’ was the leader. The rift began early, for on 20 Nov. 1643 the Scottish commissioners found the assembly in ‘sharp debate’ on a proposition, by ten or eleven independents, that every congregation should have its ‘doctor’ as well as its ‘pastor.’ This was compromised by agreeing that ‘where two ministers can be had,’ their functions should be thus distinguished. The thoroughgoing independents were four, Goodwin, Nye, William Bridge [q. v.], and Sydrach Simpson [q. v.] With them was Jeremiah Burroughes [q. v.], who, however, was content to abide by the parochial system, as against ‘gathered churches.’ These issued the ‘Apologeticall Narration’ (1643). William Carter (1605–1658) joined them in signing the ‘dissent’ (9 Dec. 1644) from the assembly's propositions on church government; the published ‘Reasons’ (1648) for dissent were signed also by William Greenhill [q. v.] That so small a party proved so serious a trouble to the assembly is inexplicable till it is remembered that the strict autonomy of ‘particular churches’ was the basis of the English presbyterianism of Thomas Cartwright (1535–1603) [q. v.] and William Bradshaw (1571–1618) [q. v.], while the ‘presbyterian government dependent,’ defended (1645) by John Bastwick, M.D. [q. v.], in opposition to the ‘presbyterian government independent,’ was an exotic novelty. No differences of doctrine or worship divided the ‘dissenting brethren’ from the presbyterians. In January 1644 attempts were made by Sir Thomas Ogle [q. v.] to attach Nye to the royalist side. He was urged to go to Oxford, and again promised a royal chaplaincy. Nye wrote the preface to the ‘Directory’ (1644), a very able document. In harmony with the freedom from ‘set forms’ which it advocated, Nye successfully opposed the exclusive authorisation of any psalm-book, and the obligation of sitting to the table at communion. He was for ‘uniformity, but only in institutions’ (Minutes, 20 Nov. 1644). His party was most at issue with the assembly on the question of the liberty to be given to ‘tender’ (religiously affected) consciences. Goodwin and Nye had a robust belief in the ultimate victory of good sense; they proposed to treat fanaticisms as follies, not as crimes, and to tolerate all peaceable preachers.
During the progress of the assembly Nye was a frequent preacher, holding, according to Edwards, besides his Acton rectory, four lectureships at Westminster and others in London. His lecture at the abbey was worth 50l. a year. He was with Marshall in 1647 as one of the chaplains to the commissioners in treaty with the king in the Isle of Wight; on the failure (28 Dec.) of the treaty he got up a London petition against further personal treaty with Charles. What view he took of the fate of Charles does not appear. He was one of the ministers who proffered their religious services to the king on the morning of his execution. In April 1649 he was sent in vain, with Marshall and others, to persuade the secluded members to resume their places in parliament.
The turn of the tide for the independents came in 1653. Cromwell appointed ‘triers’ (20 March 1654) and ‘expurgators’ (28 Aug.) for admitting and dismissing clergy; Nye was on both commissions. His examination of
