Evidently the King hoped, when he surrendered to the Scots on 5 May 1646, to place himself in a position to negotiate with them with a view to forming an alliance against Parliament, The Scots were disgruntled both at their treatment from their erstwhile allies, and by Parliament's failure to implement Presbyterianism in England. Nevertheless, the price of Scottish help for the King would involve his acceptance of the Solemn League and Covenant, a price Charles was unwilling to pay, and negotiations failed. The Parliament, itself torn by disagreement between Presbyterians and Independents, secured the King's person from the Scots by paying over to them substantial subsidies in return for their help during the war. The King passed into parliamentary hands on 30 January 1647 and was taken to Holdenby House in Northamptonshire. There, the
King continued to try to play off one side against the other, believing that he could utilise the growing dissatisfaction of the New Model with the politicians at Westminster, for his own advantage.
The divisions within Parliament after the end of the civil war in 1646 had resolved themselves into a political and religious clash between 'presbyterians' and 'independents'. The unrest within the New Model Army over arrears of back pay grew during March 1647 into political discontent. This unrest within the New Model, whose extensive military operations had won the war for Parliament, is often presented as the political radicalisation of the rank and file. It eventually led to the purge of Parliament and to the King's execution. However, the spread of radical ideas was facilitated by material grievances, especially over arrears of pay and fear of disbanding. Desperately in need of money, Parliament clearly hoped to disband most of the New Model without settling back pay. Taking upon themselves the mantle of defenders of liberty and justice, the New Model's commanders tried to coerce the civilian government into abandoning Presbyterianism. After March 1647, agitators—or spokesmen—appeared in each regiment to voice complaints, and Sir Thomas Fairfax, unable to disband such a mutinous force, ordered the army to converge on Newmarket early in June.
On 4 June the King was seized at Holdenby House by a detachment of cavalry under Cornet Joyce and taken to the army camp at Kentford Heath, near Newmarket. Joyce initially acted in concert with radical elements within the army, but appears to have informed Cromwell of his plans shortly before seizing the King. Cromwell acquiesced. In so doing, he put himself in some danger of retributive action from Westminster. Intending to channel the anger of the rank and file and to formulate a coherent policy to present to Parliament, Cromwell and Fairfax, between them, created a General Council of the Army. The Council, composed of the general officers, the regimental agitators and two officers of each regiment, was visited by commissioners from Westminster who reported back that the army was implacable. Parliament endeavoured to raise forces within the City to resist a proposed march on London, leading to severe unrest and the flight of the Speakers and radical members to the army on 26 July. Fairfax, now appearing as protector of the privileges of Parliament, marched to Hounslow Heath and entered London on 6 August without encountering any resistance. Parliament was then shown the 'heads of the Proposals' demanding biennial parliaments and religious toleration (except for Catholics). The Putney debates of the Army Council, held during October and November 1647, terminated inconclusively. Although virtually all the speakers were aware of the signal opportunity at their hands radically to improve government, the Levellers showed themselves suspicious of Cromwell and the grandees; and Cromwell, although he shared their theological position, mistrusted their social radicalism.
The Council broke up on 8 November, and on the same day the King, who had been transferred from Newmarket to Hampton Court on 24 August, escaped and reached the Isle of Wight two days later. His action meant that all further dealings between him and the army were at an end: the King had abandoned the path of negotiation. The Governor of Carisbrooke Castle on the Isle of Wight allowed the King every consideration, and negotiations with the Scots developed. On 26 December he agreed to the Engagement, whereby, abandoning his earlier reluctance, he accepted Presbyterianism in England for a three year period. The Scots promised to use their military power to restore him to authority. It was essentially a military alliance. On the 28th Charles broke off formal talks with the Parliament, which in its turn voted to have no further dealings with him. The King's confinement now became more close, but he had hopes of some military revival of his cause, and in April 1648 the second civil war broke out in a disordered fashion in England and Wales. The civil war of 1648, in which royalists and ex-parliamentarians combined with the Scots, deepened the rift within Parliament and between Parliament and the army, and the suppression of the risings by the New Model made the army stronger than ever.
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