During the nine years of the English military occupation of Scotland everything was merely provisional; nothing decisive could occur. In the first place (October 1651), eight English Commissioners, including three soldiers, Monk, Lambert, and Deane, undertook the administration of the conquered country. They announced tolerance in religion (except for Catholicism and Anglicanism, of course), and during their occupation the English never wavered on a point so odious to the Kirk. The English rulers also, as much as they could, protected the women and men whom the lairds and preachers smelled out and tortured and burned for witchcraft. By way of compensation for the expenses of war all the estates of men who had sided with Charles were confiscated. Taxation also was heavy. On four several occasions attempts were made to establish the Union of the two countries; Scotland, finally, was to return thirty members to sit in the English Parliament. But as that Parliament, under Cromwell, was subject to strange and sudden changes, and as the Scottish representatives were usually men sold to the English side, the experiment was not promising. In its first stage it collapsed with Cromwell's dismissal of the Long Parliament on April 20, 1653. Argyll meanwhile had submitted, retaining his estates (August 1652); but of five garrisons in his country three were recaptured, not without his goodwill, by the Highlanders; and in these events began Monk's aversion, finally fatal, to the Marquis as a man whom none could trust, and in whom finally nobody trusted.

An English Commission of Justice, established in May 1652, was confessedly more fair and impartial than any Scotland had known, which was explained by the fact that the English judges “were kinless loons.” Northern cavaliers were relieved by Monk's forbidding civil magistrates to outlaw and plunder persons lying under Presbyterian excommunication, and sanitary measures did something to remove from Edinburgh the ancient reproach of filth, for the time. While the Protesters and Resolutioners kept up their quarrel, the Protesters claiming to be the only genuine representatives of Kirk and Covenant, the General Assembly of the Resolutioners was broken up (July 21, 1653) by Lilburne, with a few soldiers, and henceforth the Kirk, having no General Assembly, was less capable of promoting civil broils. Lilburne suspected that the Assembly was in touch with new stirrings towards a rising in the Highlands, to lead which Charles had, in 1652, promised to send Middleton, who had escaped from an English prison, as general. It was always hard to find any one under whom the great chiefs would serve, and Glencairn, with Kenmure, was unable to check their jealousies.

Charles heard that Argyll would appear in arms for the Crown, when he deemed the occasion good; meanwhile his heir, Lord Lorne, would join the rising. He did so in July 1653, under the curse of Argyll, who, by letters to Lilburne and Monk, and by giving useful information to the English, fatally committed himself as treasonable to the Royal cause. Examples of his conduct were known to Glencairn, who communicated them to Charles.

At the end of February 1654 Middleton arrived in Sutherland to head the insurrection: but Monk chased the small and disunited force from county to county, and in July Morgan defeated and scattered its remnants at Loch Garry, just south of Dalnaspidal. The Armstrongs and other Border clans, who had been moss-trooping in their ancient way, were also reduced, and new fortresses and garrisons bridled the fighting clans of the west. With Cromwell as protector in 1654, Free Trade with England was offered to the Scots with reduced taxation: an attempt to legislate for the Union failed. In 1655-1656 a Council of State and a Commission of Justice included two or three Scottish members, and burghs were allowed to elect magistrates who would swear loyalty to Cromwell. Cromwell died on the day of his fortunate star (September 3, 1658), and twenty-one members for Scotland sat in Richard Cromwell's Parliament. When that was dissolved, and when the Rump was reinstated, a new Bill of Union was introduced, and, by reason of the provisions for religious toleration (a thing absolutely impious in Presbyterian eyes), was delayed till (October 1659) the Rump was sent to its account. Conventions of Burghs and Shires were now held by Monk, who, leading his army of occupation south in January 1660, left the Resolutioners and Protesters standing at gaze, as hostile as ever, awaiting what thing should befall. Both parties still cherished the Covenants, and so long as these documents were held to be for ever binding on all generations, so long as the king's authority was to be resisted in defence of these treaties with Omnipotence, it was plain that in Scotland there could neither be content nor peace. For twenty-eight years, during a generation of profligacy and turmoil, cruelty and corruption, the Kirk and country were to reap what they had sown in 1638.