Updated: Nov 19
The wars that took place across the British Isles in the mid-17th century ('Wars of the Three Kingdoms': England, Scotland and Ireland) are some of the most complex and confusing events in British/Irish history. Much of the reason for this was the fact that Ireland was an English colony and the King of Scotland (James VI) was offered the English throne in 1603 when their queen (Elizabeth I) left no heirs. For anyone interested in Scotland or Britain generally in this time period, I hope to clarify some of the reasons as to why there was some switching of sides and how they were rooted in fundamental differences between English and Scottish societies.
Later Covenanters held services outdoors in protest of the king's interference in the Church of Scotland, which will be explained at a later point
Probably the most important difference between England and Scotland was religion, because though both countries were mostly Protestant, their own varieties came about in very different ways. In England, the Reformation was initiatied by King Henry VIII, who wanted to divorce his then wife, Catherine of Aragon, so he could marry Anne Boleyn instead. The Catholic Church forbade divorce, so breaking from the papacy allowed him to to do so. He began the process in 1529 and it was completed by about 1536.
Henry VIII was a man who liked to get his way, he even beheaded Anne Boleyn, the woman he broke England from the Catholic Church for so he could marry!
In contrast, the Scottish Reformation happened later (in 1560) and was opposed by the monarch, Mary Queen of Scots (and her regent mother, Mary of Guise, before the queen came of age to rule). Scottish Protestantism mainly took hold among merchants and other burgesses and the predominant form of Protestant thought became Calvinism, which teaches that it is predestined who will be saved on Judgement Day. Much of this was due to the charisma of the Calvinist preacher John Knox. There was also a political dimension, with Scottish Protestants wishing to draw Scotland closer to England, while Catholics favored keeping the 'Auld Alliance' with France.
Mary Queen of Scots was raised in France and remained Catholic until her death in 1587. She was consistently attacked by John Knox, who saw rulership of a woman as unnatural.
To put it simply, the difference was one of who initiated the Reformation: in England, it was a top-down imposition by the monarch that confiscated property from the monasteries, but otherwise left much of church structures and services intact (to the point where the Church of England is technically both Catholic and Protestant). In Scotland, it was a bottom-up movement among commoners (mainly the middle classes), who struggled against the monarch to try and bring about a Presbyterian Church of Scotland (a Church run by elders chosen from among the congregations, rather than bishops appointed by the monarch).
Even then, there was a constant conflict between Presbyterians and Episcopalians in Scotland; Episcopalians acknowledge the Scottish monarch as the head of the Kirk (Scots for 'Church'), while Presbyterians believe that Christ is the head of the Kirk. Essentially, the issue was one of authority, because under a Presbyterian system the monarch is technically just like every other parishoner, and therefore subject to the ordinances of the Kirk elders. King James VI was, unsurprisingly, an Episcopalian.
The Kirk in the early 17th century was therefore caught in a tug-of-war between the General Assembly (the Kirk's governing body) and the monarch (initially James VI, then followed by his son, Charles I, from 1625). The Scottish parliament was dominated by Presbyterians, but there were also English Presbyterians who thought their own Reformation hadn't gone far enough and they wanted a Church more like the Scottish one. Because they wanted to 'purify' the Church of England of its remaining Catholicism, they became known as 'Puritans'.
However, all of these religious issues were also bundled up with political ones, as James and Charles I believed in the 'divine right of kings' to rule and that he could and should rule England and Ireland without the English parliament if he so wished (the Presbyterian-dominated Scottish parliament was too strong by that point, so dissolving it was simply a pipe-dream for these kings).
The problem for Charles was that he couldn't have his way in England and Scotland at the same time; his attempts to force Episcopalian church liturgy on the Scots ended in humiliating defeats for him in the 'Bishops Wars' of 1639 and 1640, because he needed the financial support of the English parliament to fight the Covenanters (Scottish Presbyterians who resisted his impositions). But the English parliament would only help him if he agreed to share more power with them, which he refused to do.
Charles I believed wholeheartedly in his 'divine right' as his father did, but also lacked his father's political skill (since James had experience being King of Scotland before rulling England too)
The tension between Charles and the English parliament led to civil war in England in 1642; supporters of the king were nicknamed 'Cavaliers' and those of the parliament 'Roundheads'. The Scots initially sat on the sidelines, before the Covenanter-dominated Scottish parliament decided to support their English counterparts in 1643 and sent an army into England. By 1645, the English parliament had decided to reform their army, creating the 'New Model Army', which was defined by its professionalism and its ability to send troops to fight outside their home county. The NMA became a hotbed of religious and political radicalism, no doubt fostered by the camraderie between the soldiers who fought in it.
This may also have been a result of the fact that both the Church and monarchy of England were more hegemonic than their Scottish counterparts; by this I mean that since the Reformation had been imposed by an English monarch, it meant that England's institutions were inherently more elitist and there was less representation for commoners. In Scotland the Kirk was dominated by Presbyterians, who were much more populist, so since commoners had much more say in the Scottish Kirk and parliament than their English counterparts, they were overall less tolerant of radicalism.
Within the NMA, groups such as 'the Levellers' emerged after Charles' defeat in 1646, who demanded extended suffrage, religious tolerance (though not for Catholics, of course) and equal rights (for all Protestant men). An even more radical splinter group from the Levellers were known as 'the Diggers', because they advocated (and in some cases attempted) to farm land in common, so they were basically early socialists.
However, perhaps the most important radicals were the religious ones known as 'Independents' or 'Separatists', who were early secularists that believed in separation of church and state; their movement gave rise to groups such as the Baptists. Undoubtedly the most influential Independent was Oliver Cromwell, cavalry lieutenant and second-in-command of the NMA. Most of the Covenanters saw the English Independents as a threat to their goal of reforming the Church of England on Presbyterian lines, so the Scottish parliament actually decided to side with Charles and invade England in 1648.
Cromwell was an astounding cavalry commander and like so many dictators since him, he maintained his support through the army
An early indication that this would happen comes from the fact that Charles initially surrendered to a Covenanter army in England rather than the NMA, because he thought the Scottish parliament's terms were more acceptable than those of the English one. This was probably because England's parliament was initially in a weaker position than the Scottish one, so their demands on Charles were overall harsher.
The combination of the English parliament's exasperation trying to reign Charles in, coupled with the radicalism (particularly religious) within the NMA meant that, once they defeated the Scots and English royalists, it was decided that Charles would be tried for high treason. He was found guilty and beheaded on Tuesday 30th January 1649. This act horrified the Scots (along with pretty much all other Europeans), which led to the Scots agreeing to crown Charles' son in exile, Charles II.
However, the Scots made his coronation conditional upon not only proclaiming Presbyterianism the official religion across the Three Kingdoms, but also becoming Presbyterian himself. They also wanted him to disavow his and his father's most loyal Scottish supporter, James Graham, 1st Marquess of Montrose; which he did (Montrose led a failed invasion of Scotland and was executed on 21st May 1650).
To give an example of how important religion was to the Scots, around 3,000 soldiers and 80 officers were expelled from the Scottish army by the more radical Covenanters for failing to pass their tests for what they considered to be 'acceptable' religious and political beliefs, depriving the Scots of many experienced troops1. They were defeated by Cromwell at the Battle of Dunbar and the more radical Covenanters (the 'Kirk Party') were ousted from power and replaced by a faction headed by the royalist James Hamilton, 1st Duke of Hamilton, who decided to invade England with Charles.
However, Charles and the Scots were defeated at Worcester in 1651 and so he fled into exile once again. Thereafter, Cromwell completed the only successful English conquest of Scotland by 1654 and abolished the Scottish parliament, incorporating Scotland into the Commonwealth (not to be confused with the modern-day 'Commonwealth of Nations', which is a British monarchic institution). The Commonwealth was headed by Cromwell as Britain and Ireland's first and (so far) only dictator.
Cromwell's iron grip lasted until his death in 1658 (during which time Christmas was banned), but his son, Richard, had no military experience and wasn't able to hold together the country with charisma as his father had. He was deposed less than a year after his father's death, but problems then emerged between the army and the parliament, who couldn't agree on how to balance power between themselves.
Charles II during his coronation at Westminster, no doubt a much grander ceremony than his Presbyterian-dominated coronation at Scone in 1650
Thus, Charles was invited back in 1661 and crowned as king once again (this time at Westminster rather than Scone). The former leader of the Covenanters, Archibald Campbell, 1st Marquess of Argyll, attempted to be reconciled with Charles, but Charles had him arrested, tried for treason and beheaded for collaborating with Cromwell (not that Argyll had much of a choice when Cromwell conquered Scotland).
This was not the end of the Covenanter movement though, as a group from Galloway rose up in 1666 in response to Charles' attempts to impose Episcopalianism on the Scots as his father had done. They were defeated at Rullion Green in Midlothian though, so it was clear that the Covenanters no longer had the popular support they once enjoyed in the decade before Scotland's defeat by Cromwell.
The government responded by doubling down on persecuting Protestant dissenters, but also made the concession to allow Presbyterian ministers to retain control of their churches. The persecution was mainly directed at those similar to the Independents of the NMA, who refused to attend church services and organized their own 'conventicles' of worship (outdoors and in their own homes).
This culminated in the assassination of the Archbishop of St Andrews, James Sharp, in 1679 by radical Covenanters, so John Graham of Claverhouse, 1st Viscount of Dundee, was dispatched to root out the conventicles. The Covenanters responded by defeating Claverhouse at the Battle of Drumclog in Lanarkshire. They were eventually defeated by Claverhouse at Bothwell Brig (also in Lanarkshire) and what resulted was one of the most tragic events of Scottish history: the imprisonment of 1,200 Covenanters in Greyfriars Kirkyard, Edinburgh, by Sir George Mackenzie of Rosehaugh, 'Bluidy Mackenzie'.
The Covenanters' Prison in Greyfriars Kirkyard, Edinburgh
The Covenanters were basically left open to the elements in cages and only given the minimum amount of food to keep them alive. Even then, many died of maltreatment and those that didn't agree to sign a 'bond of good behavior' were shipped off to 'work off their offenses' as indentured servants on Barbados. Two-hundred died in a shipwreck destined for the Caribbean.
This foul treatment led to the emergence of an extreme Covenanter faction known as the 'Cameronians' (after their founder, Richard Cameron) that renounced allegiance to the Stuart monarchy and advocated Charles' removal (an especially radical move considering the Stuarts were a Scottish dynasty). Government oppression had given rise to radicals in Scotland akin to those earlier found within the English NMA, though the problem for these Scottish radicals was that they didn't have the same level influence within the army (especially a victorious one as the NMA once was).
The Cameronians signed the 'Sanquhar Declaration' in the Ayrshire village of the same name in 1680, but this only resulted in a defeat (and Cameron's death) at Airds Moss (also in Ayrshire), once again by Claverhouse. The government responded with the 'Test Act of 1681', which required every office-holder to swear an oath to the king and to acknowledge royal supremacy in all matters temporal and spiritual and refraining from advocating religious or political reform.
Margaret Wilson was executed by being tied to a stake in the Solway Firth to be drowned by the rising tide in 1685, simply for refusing to take an oath against the Cameronians
The Cameronians responded by publishing a manifesto at the Mercat Cross in Lanark in 1682 and effectively formed an underground resistance network. Once again, Claverhouse was on the hunt for dissenters, for which he earned the nickname 'Bluidy Clavers'. 'Clavers' would later become a bogeyman that Ulster Scots and their American descendants would use to scare their children, such was his reputation among the Scots that emigrated to Ulster (who mainly came from the south-west, where the Covenanters drew the most support).
The Cameronians carried out guerilla raids and assassinations, so the scale of government suppression increased to the point where you could be shot on the spot for stammering when confronted with taking an oath denouncing the Cameronians2. The 'Killing Time' only ended with Charles' death from a stroke on 12th February 1685.
He was succeeded by his brother, James VII (II of England), who was much less tolerant of Protestant dissenters than Catholics (because he was Catholic himself). Despite his later attempts to roll back some of the restrictions on Presbyterians, the Scots made no attempt to stop the English from forcing him to abdicate in 1688 when they invited William of Orange from the Netherlands to take his place (once again, because he was trying to govern without the English parliament like his father).
The Stuarts had finally alienated most of the Lowlanders through decades of opposition to Presbyterianism, to the point where they didn't rise up in support of James as they had done with the two Charles'. What was different this time was that England wasn't dominated by militant religious radicals as in 1648, so the Presbyterians had come to see both James' absolutism and his toleration of Catholics as a greater threat than those who opposed him.
James VII was an interesting throwback to the time before the Reformation as a Catholic convert, but he also unfortunately retained his father and grandfather's belief in his 'divine right', which put him at odds with the Englishmen who had fought his father to achieve more representation in government
Therefore, the subsequent Jacobite Risings tended to draw their support from the Highlands and Aberdeenshire, whose inhabitants always tended to be loyal to the monarchy. Much of the reason for this was the fact that the Stuarts' governance affected little of the Highlanders' way of life, in contrast to the Presbyterians who were much more interfering in moral matters and who were constantly trying to spread their sect into the Highlands (most Highlanders were Protestant by 1678,3 but they tended to prefer Episcopalianism4).
This precedent was already set when the Marquess of Montrose had recruited Highlanders for his failed royalist uprising from 1644-1646; though part of that was simply taking advantage of the feud between the MacDonalds and the Campbells, whose chief, Archibald Campbell, was the aforementioned leader of the radical Covenanter 'Kirk Party'.
One can't help but notice that initiative to actually depose the Stuart monarchs seems to have consistently lay with the English, to the point that they executed one (Charles I) and forced another to abdicate (James II). While there was no lack of tension between the Stuarts and the Scottish parliament (especially over the authority of the Kirk), the Scots overall ended up supporting the Stuarts more often than not. Radical elements akin to those earlier found in England only appeared after consistent interference with the Kirk, but also never posed such a threat to the monarchy as the English radicals did.
This is not to say that the English were necessarily 'allergic' to a Scottish dynasty, but more that England's society and institutions had developed in a way that it could be argued they were actually more prone to revolution than the Scots were. Presbyterianism offered more outlet for commoners within their Church, in contrast to Anglicanism which was more hierarchical and rooted in Catholic organization and this was reflected on the political level in both countries.
This also probably reflects the fact that England was conquered by the Normans, who introduced feudalism and class divisions were initially strengthened by ethnic ones (French vs Anglo-Saxon), whereas in Scotland both the clan system and the creation of the burghs in the 12th century meant that commoners were more influential in religion and government. The result seems to have been that by the mid 17th century, Scottish commoners were probably more used to having political representation compared to the English ones (though Magna Carta is rightfully hailed as a step towards democracy, it was put together by barons, not commoners).
The difference in political representation also played into the fact that the Covenanters defeated Charles I and his supporters with ease in the Bishops' Wars, whereas the First English Civil War was much more evenly matched (because England had a stronger upper class than Scotland) and so it dragged on for four years. This allowed much more time for resentment against the king and radicalism to take over the NMA, as war tends to encourage extreme feelings.
2Magnusson, 2000, Scoland:The Story of a Nation, 492-496