Cromwell left London in May to suppress the royalists in Wales, and took Pembroke Castle on the 11th of July. Meanwhile behind his back the royalists had risen all over England, the fleet in the Downs had declared for Charles, and the Scottish army under Hamilton had invaded the north. Immediately on the fall of Pembroke Cromwell set out to relieve Lambert, who was slowly retreating before Hamilton's superior forces; he joined him near Knaresborough on the 12th of August, and started next day in pursuit of Hamilton in Lancashire, placing himself at Stonyhurst near Preston, cutting off Hamilton from the north and his allies, and defeating him in detail on the 17th, 18th and 19th at Preston and at Warrington. He then marched north into Scotland, following the forces of Monro, and established a new government of the Argyle faction at Edinburgh; replying to the Independents who disapproved of his mild treatment of the Presbyterians, that he desired "union and right understanding between the godly people, Scots, English, Jews, Gentiles, Presbyterians, Anabaptists and all; ... a more glorious work in our eyes than if we had gotten the sacking and plunder of Edinburgh ... and made a conquest from the Tweed to the Orcades."
The incident of the Second Civil War and the treaty with the Scots exasperated Cromwell against the king. On his return to London he found the parliament again negotiating with Charles, and on the eve of making a treaty which Charles himself had no intention of keeping and regarded merely as a means of regaining his power, and which would have thrown away in one moment all the advantages gained during years of bloodshed and struggle. Cromwell therefore did not hesitate to join the army in its opposition to the parliament, and supported the Remonstrance of the troops (20th of November 1648), which included the demand for the king's punishment as "the grand author of all our troubles," and justified the use of force by the army if other means failed. The parliament, however, continued to negotiate, and accordingly Charles was removed by the army to Hurst Castle on the 1st of December, the troops occupied London on the 2nd; while on the 6th and 7th Colonel Pride "purged" the House of Commons of the Presbyterians. Cromwell was not the originator of this act, but showed his approval of it by taking his seat among the fifty or sixty Independent members who remained.