When war broke out between King Charles and the English Parliament in 1642, the sympathies of Presbyterian Scots lay naturally with the Puritan-dominated Parliament. They also saw that if the king defeated Parliament, he would be able to turn the full resources of England against them and their Presbyterian church would be doomed. Therefore, in January 1644, the Covenanters allied with the English Parliament against the king. In the process, they probably wrecked any chance that the Highlands could be peacefully incorporated fully into the Scottish state. Although Lowlanders overwhelmingly supported the Covenant, there was considerable sympathy for the king in the Catholic Highlands. For over 18 months an army of Royalist Highlanders, reinforced by Irish Catholics, under the brilliant leadership of James Graham, marquis of Montrose, ran rings around Covenanter forces until it was defeated at Philiphaugh in the Borders in September 1645. This armed intervention greatly increased the animosity of Lowlanders towards Highlanders. In future Highlanders would not only be thought of as barbarian cattle thieves but as rebels and supporters of Popery.
The alliance between the Covenanters and the English Parliament broke down in 1648. After the English Parliament parted Charles I from his head in 1649, the Scots proclaimed his son Charles II king. This presented a clear danger to the new English republic and in 1650 Oliver Cromwell, fresh from his victory in Ireland, invaded and conquered Scotland. For the first time, all of Britain and Ireland was under the control of a single government. Scotland was given back its independence by Charles II at the Restoration in 1663 but Cromwell had shown that the balance of power in the British Isles had swung decisively in favour of England. Developments in tactics, weapons and logistics meant that even remote inhospitable regions like the Highlands could be brought under the control of a central government, providing it had the will and the money to pay for it. But Scotland after the Restoration was wracked by religious conflicts as the government began a persecution of the Covenanters, known as the ‘Killing Times’, in which Highland levies played a prominent part. The Highlands were allowed to go their own way until after the so-called Glorious Revolution in England in 1688 which saw the Catholic King James VII and II deposed and replaced by the joint rule of his Protestant sister Mary and her Dutch husband William of Orange. James’s supporters, known as Jacobites (from the Latin lacobus, James’), actively sought his restoration to the throne.