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Much of Batten's time was spent helping the fighting on land. When the Royalists in the south-west captured Weymouth, and besieged Melcombe, just over the bay, Batten was on his ship at the Downs, and sailed to Melcombe, landing 150 of his sailors in the town. Thus reinforced, the garrison were able to throw back a Royalist attack. By this point, Warwick's position was threatened by the Self Denying Ordinance, and on 22 May 1645 Batten was appointed as commander in chief of the fleet, although he was not promoted from Vice-Admiral, and the appointment was at least initially seen as temporary. Soon after, Batten was involved in his most impressive victory. At the battle of Colby Moor (1 August 1645), Batten helped Sir Rowland Laugharne defeat a Royalist army under Sir Edward Stradling, by landing a force of sailors behind the royalist position, in one of the few amphibious operations of the war. Likewise, he was present at the siege of Dartmouth, providing 200 sailors for the final assault (18 January 1645). He was also present for one of the last actions of the war, the siege of Pendennis Castle, which only ended on 16 August 1646.
Despite his war record, by the end of 1646 the remaining Royalists were convinced that Batten was discontented with the nature of Parliament's victory. Whatever the truth at that point, by the middle of 1647 they were proved correct. In mid-1647 the Independents gained power in London. Batten, as a Presbyterian disliked the new regime, which quickly moved to attack it's enemies. By August, with several of their colleagues under arrest, six Presbyterian MP's, including Denzil Holles and William Waller, decided to flee to Holland. Their ship had nearly reached safety when it was overhauled by a Parliamentary ship and returned to the Downs. However, Batten released them, and returned them to Holland. As a result, in September he was forced to resign, and was replaced by Colonel Rainsborough, an Independent with some experience at sea, who was loathed by the mostly Presbyterian navy.
The tension in the navy surfaced on 27 May 1648 (2nd Civil War). The Fleet refused to allow Rainsborough onboard his flagship, and arrested those officers known to be Independents. In response, Parliament re-appointed the earl of Warwick as Lord High Admiral, but even he was initially unable to regain control of the fleet in the Downs. Meanwhile, in June Batten was summoned before the Derby House Committee under suspicion of spreading disaffection in the fleet. Instead of attending, he boarded the Constant Warwick at Portsmouth, and persuaded the crew to join him in sailing to Holland to join the Prince of Wales. Prince Charles welcomed him, knighted him, and made him Rear-Admiral of what for a brief period was an impressive Royalist navy. However, after a failed attempt to bring the earl of Warwick to battle in the Thames (August 1648), the Royalist fleet was blockaded in Dutch Waters, and rapidly fell apart. Warwick offered an indemnity for those who wished to return, and Batten took advantage of it. He survived the Commonwealth, and on the Restoration was reinstated at surveyor of the navy (1660), ending his life as master of Trinity House (from 1663).