When the Royalists were defeated for the second time the English government, exasperated by the duplicity of Charles I during negotiations, set up a High Court of Justice which found the King guilty of treason and executed him on 30 January 1649.

The leaders of the English Commonwealth government felt threatened and on 22 July the New Model Army under Oliver Cromwell invaded Scotland.

After a month of manoeuvring, Cromwell unexpectedly led the English army out of Dunbar in a night attack on 3 September and heavily defeated the Scots.

Cromwell brought the badly outnumbered Scots to battle at Worcester on 3 September and completely defeated them, marking the end of the Wars of the Three Kingdoms.

These had arisen from the Scots' refusal to accept the attempts of Charles I to reform the Scottish Kirk to bring it into line with English religious practices.

Presbyterian English Parliamentarians and the Scots wanted him to accept a modified version of the Newcastle Propositions, but in June 1647, Cornet George Joyce of the New Model Army seized Charles I,[10] and the army council pressed him to accept the Heads of Proposals, a less demanding set of terms which, crucially, did not require a Presbyterian reformation of the church.

[13] After a protracted political struggle, the Engagers gained a majority in the Scottish Parliament, by which time war had again broken out in England between Royalists and Parliamentarians.

The Scots sent an army under the command of the Duke of Hamilton into England to fight on behalf of the King in July, but it was heavily defeated at Preston and then Winwick in August 1648 by a force led by Oliver Cromwell.

[18][2] Before they would permit him to return from exile in the Dutch Republic to take up his crown, they demanded he sign both Covenants: recognising the authority of the Kirk in religious matters, and that of Parliament in civil affairs.

[24] Fairfax accepted the commission to lead the army north to defend against the possibility of a Scottish invasion, but was unwilling to strike the first blow against his former allies, believing England and Scotland were still bound by the Solemn League and Covenant.

[24] A parliamentary committee which included Cromwell, his close friend, attempted to dissuade him, pleading with him over the course of a whole night to change his mind, but Fairfax remained resolute, and retired from public life.

[27][28] Once the Treaty of Breda had been signed, the Scottish Parliament started levying men to form a new army, under the command of the experienced general David Leslie.

Members of the Covenanter government, concerned that their godly war would be corrupted by feelings of personal loyalty to the King, asked Charles II to leave.

[55] When the news of the defeat reached Edinburgh, many people fled the city in panic, but Leslie sought to rally what remained of his army, and established a new defensive line at the strategic choke point of Stirling.

[56] Major-general John Lambert was sent to capture Edinburgh, which fell on 7 September, while Cromwell marched on the port of Leith, which offered much better facilities for landing supplies and reinforcements than Dunbar.

[56] Cromwell took pains to persuade the citizens of Edinburgh that his war was not with them; he promised their property would be respected, and allowed them to come and go freely, hold markets, and observe their usual religious services, although the latter were restricted as most of the clergy had removed to Stirling.

[57] Edinburgh Castle held out until December,[58] but since it was cut off from reinforcement and supplies and offered no threat, Cromwell did not assault it, and treated its commander with courtesy.

[60] These more radical elements issued the divisive Western Remonstrance, which castigated the government for its failure to properly purge the army, and further widened the rifts between the Scots.

[58][62] During December 1650 Charles II and the Scottish government reconciled with the Engagers and those Highland chiefs who had been excluded due to their refusal to sign the Covenant.

[66] Early on 17 July, an English force of 1,600 men under Colonel Robert Overton crossed the Firth of Forth at its narrowest point in 50 specially constructed flat-bottomed boats, landing at North Queensferry on the isthmus leading from the port to the mainland.

The previously unengaged Scottish infantry attempted to retreat, but suffered heavy casualties in the running battle that ensued, losing many men killed or captured.

[71] Charles II and Leslie, seeing no hope of victory if they stayed to face Cromwell, marched south on 31 July in a desperate bid to raise Royalist support in England.

[72] Cromwell and Lambert followed, shadowing the Scottish army while leaving Lieutenant-general George Monck with 5,000 men in Scotland to mop up what resistance remained.

[75] Shortly afterwards Aberdeen, whose council saw no benefit in resisting an inevitable and costly defeat, surrendered promptly when a party of Monck's cavalry arrived.

The exhausted Scots paused in Worcester and hoped Royalist recruits would join them from Wales, the Welsh Marches and the West Country, but few did.

[73][79] Charles II had hopes of a major Royalist uprising, but very few Englishmen joined the army, partly because they found the prospect of a renewed monarchy bound by the Covenant unedifying.

A force of 1,500 from the Isle of Man gathered in Lancashire under the Earl of Derby and attempted to join the Royalist army, but they were intercepted at Wigan on 25 August by Parliamentarian troops and defeated.

[76][note 4] The conquest of Scotland, and that of Ireland, won the Commonwealth respect among its continental neighbours: by early 1652 its legitimacy had been recognised by the French, Spanish, Dutch and Danes, and its navy had been able to assert its control over the Channel and Scilly Isles, as well as England's possessions in Barbados and North America.

[93][91] Negotiations between commissioners of the English Parliament and the deputies of Scotland's shires and burghs began to formalise the incorporation of Scottish legal and political structures into the new British state.

[98] General George Monck, by then commander-in-chief of the English forces in Scotland,[99] marched south with his army, crossing the Tweed on 2 January 1660 and entering London on 3 February, where he called new parliamentary elections.