Francis Ashley, had a suit against Cooper in the court of wards, and very probably opposed him in this matter.
Cooper does not appear to have taken either side in the contest of king and parliament. He was, however, at Nottingham on a visit to his brother-in-law, William Savile, when the king set up his standard on 25 Aug. 1642, and witnessed the scene; and he was also with the king at Derby. By the spring of 1643 he was a declared adherent of the royal cause, and attended Charles at Oxford with Falkland's introduction on a deputation from the gentry of Dorsetshire, with offers of help if the Marquis of Hertford were sent with a small force into the western counties. By Hertford he was commissioned, with three others, to treat for the surrender of Weymouth and Dorchester, and was made colonel of a regiment of horse and captain of a troop of foot, both raised at his own expense. Hertford also appointed him governor of Weymouth and Portland Isle when they should be taken. These places surrendered in August 1643, but Prince Maurice, who had succeeded Hertford, did not confirm the appointment. Cooper at once applied to Hertford, who pressed the matter upon Charles through Hyde, but in vain. Hyde then went in person to the king, and by urgency obtained the commission for the governorship of Weymouth. This is Clarendon's own account, but Cooper himself does not mention any difficulty or dispute in the matter. Charles, however, expressed to Hertford his hope that Cooper and the person appointed by the latter to Portland would, in view of the importance of the places and of his own inexperience in military matters, shortly resign their offices (Shaftesbury Papers). Cooper was at the same time made sheriff and president of the king's council of war for Dorsetshire.
It is difficult to explain the sudden change which now came over Cooper's action. He himself declares that it was through conviction that Charles's aim was destructive to religion and to the state that he gave up, in the beginning of January 1644, all his commissions under the king, and went over to the parliament. Clarendon states that it was from anger at his removal from the government of Weymouth; but there is no evidence that he was removed, and he himself asserts that only a few days before leaving the king's side he received the promise of a peerage and a letter of thanks written by Charles's own hand. It is of course very possible that the knowledge that he was expected shortly to resign his governorship at Weymouth had a good deal to do with his decisions. Clarendon has, too, a long account of Cooper's intention to raise another force called the ‘Clubmen,’ who were to put down both parties, and to insist on a general amnesty and a fresh parliament. An account by a royalist, Trevor, to Ormonde, however (Christie, Life of first Earl of Shaftesbury, i. 52), does not suggest any bad motive; and it must be remembered that the royal cause was at the time uppermost in Dorsetshire, and that Cooper left a large part of his property at the king's mercy (cf. Traill, Shaftesbury, English Worthies Series, pp. 20–2). It is worth noticing, in conclusion, that he had shortly before written to Clarendon, then Sir E. Hyde, asking for a license to leave his country, and complaining that the king's forces were weak and ill-paid there, and that his affairs were generally in bad condition (Clarendon Papers, 1734, Bodleian Library). On 24 Feb. Cooper presented himself at the parliament's quarters at Hurst Castle, and then went to London, where, on 6 March 1644, he appeared before the committee of both kingdoms, and expressed his conviction of the justice of the parliamentary cause, and his willingness to take the covenant.
On 3 Aug. 1644 Cooper received a commission from the Dorset committee to command a brigade of horse and foot in Dorsetshire with the title of field-marshal. His first service was in the taking of Wareham, the garrison of which capitulated on 10 Aug. On the 14th he was added to the committee for governing the army in Dorsetshire, and upon the recommendation of the committee of sequestration he was allowed to compound for his sequestrated estates by a fine of 500l., which, however, was never paid, and which was discharged by Cromwell in 1657. On 25 Oct. Cooper was appointed by the standing committee at Poole commander-in-chief of the parliamentary forces of fifteen hundred men in Dorsetshire; and in the beginning of November he took by storm, after a desperate action of six hours, in which he showed great courage, the house of Sir John Strangways at Abbotsbury. A vivid illustration of the ferocity of the fighting, and of an unexpected strain of cruelty in Cooper's character, is afforded by his own statement that he not only wished to refuse quarter to the garrison, but did his best to burn them alive in the house (Autob. Sketch). He then took Sturminster and Shaftesbury without resistance. In December he assisted, under orders from Major-general Holborne, in relieving Blake at Taunton, then besieged by the royalists. In his ‘Autobiographical Sketch’ he asserts that he had a commission from Essex to command in chief during this expedition. This, however,
