Cromwell (4 Feb. 1658) immediately dissolved the parliament.
In the election to Richard Cromwell's parliament, which met on 27 Jan. 1659, the ancient constitution was restored. Cooper was returned for Wiltshire and for Poole, a double election at the latter place being decided in his favour, and he once more elected to sit for Wiltshire. He was again a constant and leading speaker in opposition. In the discussion on the bill for the recognition of Richard Cromwell's title he strongly supported a resolution saving the rights of the parliament. He defended a certain member, Henry Nevil, who was charged with being disqualified by blasphemy and atheism, on the ground that no hearsay charge could be admitted; and he favoured the release of the Duke of Buckingham in February. He was, however, unsuccessful in trying to induce the house to begin by debating the limits of the Protector's power. He then vigorously opposed the recognition of the other house, and used his utmost efforts to prolong the discussion regarding the right of the Scotch and Irish members to vote, speaking on 9, 18, and 22 March. On the main question he made a vehement and bitterly personal speech on 28 March 1659, regarded at the time by Burton (if indeed this is the speech to which he refers, Christie, vol. i. app. iv. n.) as sheer obstruction, attacking Oliver Cromwell and the government and ridiculing the so-called ‘peers.’ The question of transacting business was at length carried on 28 March. Cooper, however, continued his opposition on the bill for settling taxes for the life of Richard and for a certain time after his death, and carried a resolution that after the end of the parliament no tax of any sort should be levied under any previous law or ordinance, unless it had been expressly sanctioned by the house. On the meeting of the Rump, on 7 May 1659, Cooper endeavoured to gain admission on his undecided petition for Downton; but for some reason not clear the petition was not allowed. He was, however, one of the ten elected non-parliamentary members of the council of state, and the only presbyterian in the council. From Ludlow's account, great jealousy was expressed of him as being in Charles Stuart's interest (ib. app. iii. p. lx). He took the oath of fidelity to the Commonwealth, and there is no evidence for the charge of intriguing for or corresponding with Charles with which on 18 May 1659 both he and Whitelocke were accused by the republican, Thomas Scott. The charge was indignantly denied by both of them before the council. The matter came before the Rump parliament in September, and he was there acquitted. Eighteen years later, appealing to Charles from the Tower, Cooper solemnly denied the correspondence, when it would have given him a claim upon the king's gratitude. In May 1659 Hyde was informed by Brodrick that Cooper had engaged to raise forces for the king; but his evidence is not of weight, and there is no other. On 4 June he was in correspondence, as one of the council of state, with Monck (Shaftesbury Papers, Public Record Office). As late as February 1660 he is mentioned by royalist agents as holding presbyterian views, and as working independently of the royalists; while the correspondence between Hyde and Mordaunt (Christie, i. 182) goes far in the same direction.
Shortly after the unsuccessful rising of Booth, in August 1659, Cooper was arrested in Dorsetshire, upon the evidence of a boy, who stated that he had carried a letter from him to Booth. Cooper was summoned before the council, and a committee was appointed to inquire into the matter. On 12 Sept., after hearing the committee's report, the council unanimously acquitted Cooper.
In October Cooper stood as usual for the parliamentary cause against Lambert. When the council of state was superseded by the committee of safety, on 25 Oct., he was indefatigable in his efforts to overthrow this committee and restore the power of the Rump. Upon the arrival of Monck's commissioners in London, he and Haselrig obtained a meeting with them at the Fleece Tavern, in Covent Garden, on 16 Nov., and endeavoured unsuccessfully to dissuade them from their arrangement with the committee of safety. On 19 Nov. Cooper, with eight other members of the late council, wrote to assure Monck of their co-operation, and a few days later gave him a commission to command in chief all the forces in England and Scotland. Haselrig and Morley went to Portsmouth, and Cooper was left with a commission to command the forces in London, which it was hoped would revolt. Some suspicion arising, he was taken before Fleetwood and questioned. When asked to give his word that he would not act to their prejudice, he refused, and declared his determination to do all in his power to restore the Rump. He was released, but next night an unsuccessful attempt was again made to seize him.
On 16 Dec. he, with three others, wrote to Fleetwood owning an abortive attempt on the Tower (Christie, vol. i. app. v.). Only eight days later they actually did secure it. A still more important service was that he and two others induced Lawson, with the fleet, to declare for the parliament (Clarendon,
