The Covenanters then found themselves at odds with the English Parliament, so they crowned Charles II at Scone and thus stated their intention to place him on the thrones of England and Ireland as well.

An important factor in the political contest with Charles was the Covenanter belief they were preserving an established and divinely ordained form of religion which he was seeking to alter.

The Covenant also expressed wider dissatisfaction with the sidelining of Scotland since the Stuart kings became monarchs of England in 1603, while the Kirk was viewed as a symbol of Scottish independence.

Widespread opposition to Crown policies meant the Parliament of England refused to fund war against the Scots, leading Charles to consider raising an army of Irish Catholics in return for abolishing the penal laws against them.

This prospect alarmed his enemies in both England and Scotland; when the Covenanters threatened to provide military support for their co-religionists in Ulster, it sparked the Irish Rebellion of 1641, which quickly degenerated into massacres of Protestant settlers in Ireland.

[2] The Covenanters responded in April 1642 by sending an army to Ulster led by Robert Monro, which engaged in equally bloody reprisals against Catholics.

By 1640, less than 2% of Scots were Catholics, concentrated in places like South Uist, controlled by Clanranald, but despite its minority status, fear of popery remained widespread.

Where Covenanters and Scottish Royalists disagreed was the nature and extent of Royal authority versus that of the people, including through the popularly governed Presbyterian church; the relative narrowness of this distinction meant Montrose was not unusual in fighting on both sides.

[6] Royalism was most prominent in the Scottish Highlands and Aberdeenshire, due to a mix of religious, cultural and political reasons; Montrose switched sides because he distrusted Argyll's ambition, fearing he would eventually dominate Scotland and possibly depose the King.

It should be said some of these factors overlap that spanned the Irish Sea: for instance, the MacDonalds were Catholics, were sworn enemies of the Campbells, and had a strong Gaelic identity.

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.

Unwisely, Montrose let his men pillage Perth and Aberdeen after taking them, leading to hostility to his forces in an area where Royalist sympathies had been strong.

[12] In April Montrose was surprised by General William Baillie after a raid on Dundee, but eluded capture by having his troops double back on the coast road and fleeing inland in a corkscrew retreat.

As the royally commissioned lieutenant-governor and captain-general of Scotland, Montrose used his powers to summon parliament to meet in Glasgow, but the limitations of his triumph soon became clear.

Approximately 100 Irish prisoners, having surrendered upon promise of quarter, were executed, and 300 of the Royalist army's camp followers – mostly women and children – were killed in cold blood.

The Covenanters could not get their erstwhile allies to agree on a political and religious settlement to the wars, failing to get Presbyterianism established as the official religion in the Three Kingdoms and fearing that the Parliamentarians would threaten Scottish independence.

Despite their conflict with the Scottish Royalists, the Covenanters then committed themselves to the cause of Charles II, signing the Treaty of Breda (1650) with him in the hope of securing an independent Presbyterian Scotland free of Parliamentarian interference.

Charles landed in Scotland at Garmouth in Moray on 23 June 1650 and signed the 1638 Covenant and the 1643 Solemn League immediately after coming ashore.

The threat posed by King Charles II with his new Covenanter allies was considered to be the greatest facing the new English Republic, and Oliver Cromwell left some of his subordinates in Ireland to continue their conquest of the island and returned to England in May.

By the end of August, his army was reduced by disease and running out of supplies, so he was forced to order a retreat towards his base at the port of Dunbar.

Seeing some of Cromwell's sick troops being taken on board the waiting ships, Leslie made ready to attack what he believed was a weakened remnant (though some historians report that he was ordered to fight against his better judgment by the Covenanter General Assembly).

Leslie's army, which had strong ideological ties to the radical Kirk Party, was destroyed, losing over 14,000 men killed, wounded and taken prisoner.

Although this was the largest force put into the field by the Scots during the Wars, it was badly trained and its morale was low as many of its constituent Royalist and Covenanter parts had until recently been fighting each other.

In July 1651, under the command of General John Lambert, part of Cromwell's force crossed the Firth of Forth into Fife and defeated the Scots at the Battle of Inverkeithing.

In danger of being outflanked, Charles ordered his army south into England in a desperate last-ditch attempt to evade Cromwell and spark a Royalist uprising there.

Meanwhile, Monck took Stirling on 14 August and Dundee on 1 September, reportedly killing up to 2,000 of its 12,000 population and destroying every ship in the city's harbour, 60 in total.

Under the terms of the Tender of Union, the Scots were given 30 seats in a united Parliament in London, with General Monck appointed as the military governor of Scotland.

Monck garrisoned forts all over the Highlands – for example at Inverness, and finally put an end to Royalist resistance when he began deporting prisoners to the West Indies as indentured labourers.

Monck, who had served Cromwell and the English Parliament throughout the civil wars, judged that his best interests and those of his country lay in the Restoration of Charles II.

More soldiers usually died of disease than in action at this time (the ratio was often 3–1), so it is reasonable to speculate that the true military death toll is higher than this figure.