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When the Scots finally joined the English Civil War, Baillie came south in Leven's army. At Marston Moor (2 July 1644) he commanded the two Scottish brigades at the right of the Parliamentary armies front line, where he helped steady the line. By the end of 1644 he found himself back in Scotland, now threatened by the victories of Montrose, at the head of a force of infantry detached from the main Covenanting army in England. On his arrival in the Highlands, he was sent to garrison Perth, while Montrose continued his career of conquest, soon leaving Baillie with the only significant Covenanting army in the Highlands. He had his first chance against Montrose at Dundee, which fell to Montrose on 4 April. Baillie had been shadowing Montrose, and was only one mile away when his presence was discovered. and Montrose and his army escaped him. In the campaign that followed, Baillie did poorly. First, he was tricked by Montrose, who initially marched along the coast towards Arbroath. Baillie cut cross country on a shorter route, and reached Arbroath well before Montrose could have, only to find that Montrose had doubled back as soon as it was clear Baillie had taken the bait, crossed just behind Baillies army, and reached safety in the hills. Worse was to follow. Baillie now decided to split his force, and attempt to catch Montrose between his own force, and a detachment commanded by Sir John Urry. This would have been dangerous against a normal opponent and in easy country, but against Montrose, considered to be the best general of the Civil War, and in rough hill country it was doomed. Sure enough, Urry was defeated at Auldearn (9 May 1645), losing all but 100 of his men. Baillie had been advancing to aid Urry at the time of the battle, but rather than a fight, all he got was a chase, and after a series of forced marches his army was in desperate need of some rest, which he got at Inverness. By June he was able to move again, and advanced into Gordon country, from where Montrose was getting much of his cavalry. Montrose was forced to move north to deal with Baillie, but at a first encounter at Keith refused battle. Baillie was suffering from political interference, in the shape of a travelling Committee of Estates, headed by the duke of Argyll, who understood little of the military situation and were always ready to attack. Baillie was finally forced into battle at Alford (2 July 1645), where his army was destroyed. In the aftermath of Alford, Baillie, furious with the interference of Argyll and the Committee, attempted to resign, but was instead ordered to take command of a new army, once again, to his great annoyance, to be accompanied by Argyll and his Committee. This new army was almost immediately threatened by Montrose, who briefly appeared outside Perth, only to be chased away by Baillie, who then found himself faced by a suddenly reinforced foe, and retreated back to Perth, determined not to risk battle with his new and inexperienced troops until he had the advantage of numbers. However, a chance arose to cut Montrose off from his Highland stronghold, and the committee insisted that Baillie took it. Once again, he was defeated by Montrose, this time at Kilsyth (15 August 1645) - his final involvement against Montrose who was defeated at Philiphaugh on 13 September.
Like many Scots, Baillie found himself fighting against their former allies in the second civil war. Baillie commanded the infantry in the duke of Hamilton's doomed invasion of England. The expedition came to grief at the battle of Preston (17-19 August 1648). Baillie and his infantry were at the front of the army, and avoided almost all of the fighting, before on 19 August Hamilton decided to make a break for safety with his cavalry, and ordered Baillie to surrender with the infantry, something he only did under protest, surrendering to Cromwell, with whom he had once fought.
The English Civil War , Richard Holmes & Peter Young, an early work by one of the country's best known military historians, this is a superb single volume history of the war, from its causes to the last campaigns of the war and on to the end of the protectorate.
