The expansion of the Royal Navy under Charles I increased demand for experienced captains and despite being in his sixties, William Rainsborough was among those selected by the Earl of Northumberland, then Lord High Admiral.

The absence of a significant Royalist navy meant the fleet was largely employed supporting coastal operations or cutting supply lines, and accompanied by his brother William, who had returned from North America,[7] Rainsborough spent most of the first year of the war on patrol duty in the Irish Sea.

Promoted colonel in the Army of the Eastern Association, in 1644 he was given command of a new infantry regiment, whose members included several volunteers from New England, among them his brother-in-law, Stephen Winthrop, and former Wapping neighbour, Nehemiah Bourne.

[8] In April 1645, Rainsborough was made colonel of an infantry regiment in the recently formed New Model Army, although his appointment was initially opposed by the moderate Presbyterians who dominated Parliament.

[9] They were concerned at the religious views of various officers nominated by Cromwell and his associates, while Rainsborough was known to be sympathetic not only to the group later known as Fifth Monarchists, but also the Anabaptists, a sect persecuted by mainstream Protestants throughout Europe.

After taking Berkeley Castle in December 1645, he moved onto the Siege of Oxford, which surrendered in June 1646, ending significant Royalist resistance in the First English Civil War.

[12] By early 1647, the New Model Army was owed more than £300,000 in wages, an enormous sum for the period, while Parliament was struggling with a shattered economy, an outbreak of the bubonic plague, and Charles' refusal to agree a peace settlement.

This mattered because moderate MPs like Denzil Holles took up arms in 1642 to ensure the king ruled in partnership with Parliament, not to remove him, and viewed radicals like Rainsborough as a greater threat than the Royalists.

Along with others including Colonel William Goffe, a Fifth Monarchist and later regicide, Rainsborough became convinced further negotiations with the king were pointless, and accused Cromwell of "base servility" in seeking to continue them.

Like the "Heads of Proposals", its terms included freedom of worship for non-Catholics, but went further by demanding equality before the law regardless of social standing, [b] and Universal suffrage for all men over 21 years of age.

[20] As the political situation deteriorated amid rumours of an imminent Royalist rising, the Council of Officers needed a reliable man in charge of the navy, currently headed by William Batten, a Presbyterian supporter of the Parliamentary opposition to Cromwell.

Led by William Batten, on 27 May six ships declared their support for the king, including the Constant Reformation, whose crew put Rainsborough into a small boat heading for London.

In March 1649, the Leveller John Lilburne published a tract titled The Second Part of England's New Chaines Discovered, which among other things accused the Council of Officers of involvement in Rainsborough's death.