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Milton’s views are not quite as much our own as the more triumphant treatments suggest; but they bear testimony to the radicalizing effects of war, and the possibilities arising from the luxuriant political and religious debates. These were important domestic liberties, and not the ones at stake when Parliament had met in the aftermath of defeat in the second Bishops” War. Increasing freedom of worship and of expression offered opportunities which Williams and Milton felt were good in themselves. For others they were a temporary means to achieve other ends. For royalists these radical arguments, openly expressed in print, confirmed everything they had been saying since 1642, and this made it even more uncomfortable for those within the parliamentary alliance but worried by escalating radicalism.

On 4 January 1645 Parliament agreed to replace the Prayer Book with the Directory of Worship. Much of the Directory was very welcome to all parts of the parliamentary alliance – containing forms of worship free of popery, idolatry and superstition – but it was to be imposed through a national Presbyterian system. Congregational attempts to secure a different framework of church government had been derisively dismissed by the Commons (insisting that no more than 300 of their objections should be published) in December. On 6 January a proposal that voluntary congregations could exist alongside parochial ones, within a national church, was rejected by the Commons without a vote. A week later it was agreed that parochial congregations should be grouped under presbyteries, as the basis for national church government.47

Had he still had them, this would have been music to the ears of William Prynne – the former martyr to the Protestant cause. He had characterized Milton’s views on marriage as ‘divorce at pleasure’. In January 1645 he championed religious discipline in Truth Triumphing, which called for the establishment of a binding ecclesiastical discipline and the absolute suppression of all heresies and schisms, and cited tradition against novelty in favour of such discipline. This led him into conflict with John Lilburne, who had suffered alongside him in opposition to Laudianism in the 1630s. On 7 January Lilburne published his Copie of a letter… To Mr. William Prinne Esq., in which he argued that no earthly power had authority over the kingdom of God and that persecution of individual consciences was the work of the Devil.48

These principles, once stated in detail and at length, were difficult to reconcile, but in practice it continued to be possible for people who differed on these issues to co-operate in the war effort. Sir Cheney Culpeper eventually came to denounce Scottish Presbyterians and their allies as miniature popes: ‘I never shall make any difference between an imperial, national, provincial, presbyterial, parochial or congregational Pope’. In March 1648 he declared himself an ally of the Lilburnists, noting that ‘the Scottish aristocratical interest both in church and state… having… [pulled] down the power of monarchy and episcopacy, do begin to find themselves to be part also of that Babylonish rubbish which must down’. For Culpeper the conscience was God’s peculiar, a place beyond episcopal or any other jurisdiction, and all attempts to constrain conscience represented a form of bondage akin to the Babylonish captivity endured by the Israelites. But in November 1644 he admitted to having no hope ‘but in our geud brethren the Scots’.49 Many like him must have hoped that conflicts over discipline could be subordinated to the larger conflict – the form of church government was not, necessarily, one of the marks of a true church.50

It is difficult to know how many separatists there actually were in England in 1644. By then there were perhaps thirty-six Independent churches in London. They included seven congregations of Particular Baptists, who believed that the saved should undergo an adult baptism and who produced a collective confession of faith in 1644. There were also five congregations of General Baptists, who