On 1 February 1644, he was appointed Lieutenant-General to Prince Maurice, newly appointed Captain-General of the King's forces in Scotland. However, this appointment did not come with many troops. The earl of Newcastle was able to spare him 100 badly mounted men, 2 small cannons, and the militia of Cumberland and Westmorland. His only advantage was that the main Scottish army, 21,000 men under Lord Leven, had by this point crossed over into England. On 13 April he entered Scotland at the head of a force of 1,300 men, but the bulk of them were militia, who rapidly deserted once they left England, and by the start of May, Montrose was forced back into England, where for some time he campaigned, capturing Morpeth on 29 May, although he failed to capture Sunderland. Prince Rupert, on his way to relieve York, summoned Montrose to his aid, but luckily for Montrose he did not arrive in time to be involved at Marston Moor, meeting with Rupert two days after the battle.
It was soon after this that his brief but dramatic string of successes began. While at Carlisle, he heard that a force of 1,000 Irishmen under Alaster MacDonald had landed in Scotland, and with two friends entered Scotland. In a lucky moment, he intercepted a messenger from MacDonald, actually address to him, and was thus able to find MacDonald's small force. His arrival, with his royal appointment, instantly transformed their position. A force of Atholl clansmen, sent to deal with the Irish, instead joined them, as did a force of Grahams, Montrose's own clansmen, giving Montrose a reasonably army. However, he was still faced by larger and better equipped Covenanting armys, one at Perth, one at Aberdeen and a third coming from the west of Scotland. On 1 September 1644, he defeated the first of these forces at Tippermuir, just outside Perth, capturing a good supply of arms and powder. However, the highlander element of his army promptly returned home with their booty, leaving Montrose once again with just the Irish. After two weeks of rapid movement, he then defeated the Aberdeen army under Lord Burleigh (battle of Aberdeen, 13 September 1644), leaving just Argyll's force to deal with. This force was determinedly chasing Montrose, and had now twice come across the wreck of defeated armies. They reached Aberdeen one week after the battle, to find Montrose gone into the mountains, where Argyll was too wise to follow. Montrose came out in October, inflicting a minor defeat on Argyll at Fyvie Castle before once again retreating to the mountains. This time he marched west, emerging to ravage Argyll's own Campbell lands. Once again he found himself faced by a much larger Covenant army, but after a quite stunning march through the mountains gave him the advantage of surprise, he was able to defeat Argyll at Inverlochy (2 February 1645). Montrose still faced serious opposition. Leven's army was now concentrated in the Borders, and he was under pressure to return to Scotland, while Baillie had yet another army with which he now pursued Montrose, coming very close to catching him at a great disadvantage at Dundee in early April. Baillie now split his force, allowing Montrose to defeat one part under Colonel Urry at Auldearn (9 May 1645), in what many consider to be the most skilfully conducted battle of the entire civil war. Finally, he defeated Baillie at Alford (2 July 1645), and again at Kilsyth (15 August 1645). This series of victories set both Charles I and David Leslie on a path to Scotland, although Charles was soon forced back. Sadly for Charles, Montrose's fortunes were about to suffer a total reverse. On 17 August, he entered Glasgow at the head of his army, but his attempts to win over former enemies soon lost him large parts of his army, especially the Highlanders, denied their plunder. When the Town Council of Glasgow convinced Montrose to excuse them from paying a £500 fine that was to have gone to the troops, the Highlander element of his army dissolved, returning home in droves. Montrose marched south into the borders, hoping to recruit a new force, but instead he was surprised by Leslie, with 6,000 men, and at the battle of Philiphaugh (13 September 1645) his remaining force, largely composed of his loyal Irishmen, was wiped out. Even this defeat did not entirely end Montrose's efforts. He retreated to the highlands, and attempted to raise another army. However, by now Charles's cause was doomed. After his surrender to the Scots, Charles sent Montrose an order to lay down his arms. Montrose received this order on 31 May 1646, and after making sure it was genuine, negotiated generous terms - a free pardon for all but three - including Montrose - and those three were to leave the country before 1 September. True to form the Committee of Estates in Edinburgh made efforts to stop Montrose leaving, hoping to be able to execute him without appearing to have broken the terms of surrender, and Montrose was forced to leave Scotland hiding on a Norwegian ship.
Having served Charles I so well, Montrose was sacrificed by Charles II. The Scots had crowned Charles II as King of Scotland in 1649, but only as long as he agreed to the Covenant. While he negotiated with the representatives of the Covenant, Charles sent Montrose back to Scotland with a totally inadequate army, hoping to overthrow the Covenanters by force. Montrose landed at Kirkwall on the Orkneys on 23 March 1650, but failed to raise the support he had expected, and was quickly defeated. He was captured, taken to Edinburgh, and on 21 May 1650 hanged. Only a month later, having thus lost his most able supporter, Charles agreed to sign the Covenant.