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Disputes about strategy and tactics within the army of the Eastern Association became inflected with these larger concerns about religious order. The Earl of Manchester was thought by many to be far too reluctant to seek out action following Marston Moor. On 10 August, Manchester refused an order to go against Rupert in Chester, where a significant force seemed to be mustering, something symptomatic of his military and political caution. Not until September did Manchester agree to take cavalry to the aid of Brereton in Cheshire. On 1 September the Committee of Both Kingdoms wrote the first of fourteen letters urging the army to move south to prevent the royal army, now returning from its victory over Essex at Lostwithiel, from regaining winter quarters in Oxford. Three orders from the Commons reinforced the message, and the need for haste, but by mid-October the army was still no further west than Reading.57 Newbury and its aftermath confirmed this reluctance on Manchester’s part. This perhaps reflected revulsion at what he had seen during the siege of York, and was certainly fuelled by a growing sense of the futility of the conflict.

Cromwell, his second-in-command, on the other hand, had no such hesitations, and was becoming embroiled in partisan struggle within the army. In particular Cromwell was in open conflict with Lawrence Crawford, a Scottish major-general. Crawford accused Cromwell of packing the army with Independents, which was probably true after York but not before. Cromwell had intervened to protect Independents from hostile Presbyterian officers, but this was probably in a spirit of brotherhood that he shared with his superior, Manchester. After August 1644, though, there is evidence that he actively promoted sectarians in the army. He was motivated in this, it seems, by growing resentment of the persecuting spirit of Presbyterian officers, hostility to the increasingly obvious determination among them to impose a Presbyterian settlement on England and a feeling that victory at Marston Moor belonged to him, not them. When Cromwell became openly critical of Manchester’s generalship in the autumn of 1644 it was inevitably inflected with these religious tensions. Although Manchester remained popular in the association, his command was increasingly difficult and, to many at Westminster, increasingly ineffective.58

The military advantages of an alliance with the Covenanting Scots were therefore offset by the political and religious complications that it created: many Protestants did not see Presbyterianism as liberation; nor was it what most opponents of Charles had been seeking in 1640. Potentially at least, Covenant politics were deeply problematic even for those committed to further reformation, particularly so on the issue of church government. In the autumn of 1644 Cheney Culpeper does not seem to have found the tensions irreconcilable, and he was clearly not alone. Similarly, William Dowsing, apparently more Independent than Presbyterian on matters of church government, was very active in 1644 extirpating popery and superstition in East Anglia, acting under warrant from the Presbyterian Earl of Manchester. On the other hand, his journal finishes in October.

Formal peace negotiations reopened at the end of 1644, with the parliamentary coalition in a strong military position but increasingly publicly divided over what kind of settlement to insist upon. There had been contacts between the two sides throughout 1644, with Essex a key figure on the parliamentarian side. The Oxford parliament had written to him in February, hoping that he could be an instrument of peace, and shortly before the surrender at Lostwithiel he had been contacted directly by Charles. On both occasions he said, as he always did, that he did not have the power to treat on his own behalf. Among the royalists there were significant divisions, and considerable personal hostility to Rupert. He secured a kind of agreement