The English Civil War in a phrase used to cover the period of unrest from 1638 -1660 and simply put is generalist and wrong as all the countries of the British Isles were involved.
Conflict began in Scotland when in 1638 a National Covenant was signed to resist a number of the King's innovations, especially the Prayer Book. This in turn led to armed revolt and two wars known as the Bishops' Wars which resulted in a defeat of Charles by the Scots.
The English Parliament, using the King's need for money to raise an army, effectively caused the outbreak of armed conflict in England and so in 1642 the English part of the Civil War broke out. Initially, apart from sending an army to Ulster the Covenanters stayed aloof from the wars, but in 1644 following the signing of a treaty with the English Parliament, a large Covenanter army crossed the Tweed on New Years day and advanced into England.
However, some in Scotland continued to side with the King. These were most prominent in the Islands Highlands and north-east of Scotland. There were several factors that inclined people towards Royalism. Among them were religion, culture, clan politics and political allegiance. The man who would emerge as their leader was James Graham Marquis of Montrose.
Montrose had already tried and failed to lead an uprising but later in 1644 he was presented with a ready made Royalist army. The Irish agreed in that year to send an expedition to Scotland. From their point of view, this would tie up Scottish Covenanter troops who would otherwise be used in Ireland or England. The Irish sent 2000 men organised into a three regiment brigade under the command of Alasdair MacColla Macdonald to Scotland. Shortly after landing, the Irish linked up with Montrose at Blair Atholl and proceeded to raise forces from the MacDonalds and other anti-Campbell Highland clans - the rising was now a reality.
The new Royalist army led by Montrose and MacColla was in some respects very formidable. Its Irish and Highland troops were extremely mobile, marching quickly over long distances - even over the rugged Highland terrain - and were capable of enduring very harsh conditions and poor rations. Although armed in the conventional form of Pike and Musket used by most armies at the time, they added more traditionally armed Highland troops to their ranks who were capable of launching rapid charges, firing their muskets at close range before closing with swords, pikes and other ironmongery.
However, the clans from the west of Scotland could not be persuaded to fight for long away from their homes, seeing their principal enemy as the Campbells rather than the Covenanters. The mainstay of the rebellion would always be the less colorful but steady regular Irish and Scottish infantry. This enabled the Royalists to win a string of victories, although they were unable to hold territory after they had taken it, retreating again and again to the safety of the Highlands.
Victory followed victory and eventually in February 1645 the Campbells met the Royalist and Highland force at Inverlochy near Ben Nevis and the Campbells were crushed, taking heavy casualties.
Their victory at Inverlochy gave the Royalists control over the western Highlands and attracted other clans and noblemen to their cause. The most important of these were the Gordons who for the first time provided the Royalists with an effective cavalry force.
Another Covenanter army under John Hurry was hastily assembled and sent against the Royalists but was defeated in a close run fight at Auldearn near Nairn. Another Covenanter army was crushed by Montrose's men at Alford, and another at Kilsyth when it tried to block the victorious Royalists advance into the Lowlands. This string of battles both destroyed existing well trained Veteran units and showed the dangers of sending half-trained, or even untrained, troops into battle and resulted in giving Montrose temporary control over almost all of Scotland.
However, whereas Montrose wanted to further Royalist objectives by raising troops in the south east of Scotland and marching on England, MacColla showed that his priorities lay with the war of the MacDonalds against the Campbells, and occupied Argyll. The Gordons also returned home, to defend their own lands in the north-east. Montrose, his forces having split up, was routed by the Covenanters at Philiphaugh. The Royalist victories in Scotland therefore evaporated almost overnight owing to the disunited nature of their forces.
[Based on text from Wikipedia distributed under the Creative Commons license.]