During the years immediately following, the action of the navy was for the most part purely national: as between the king and the parliament, it remained, to a great extent, neutral; but it resolutely prevented foreign interference, and readily obeyed the orders of parliament ‘to prevent the bringing over soldiers, money, ordnance, and other ammunition from beyond the seas to assist the king against the parliament of England’ (29 Nov. 1642, Penn, i. 71). About the middle of February 1642–3 Batten, in command of four ships at Newcastle, learned that a vessel had sailed from Holland with a quantity of arms and ammunition, which she intended to land at Bridlington quay. He at once went there, and finding the boats engaged in landing these stores, he opened fire on them; with what success does not appear. Queen Henrietta Maria had taken a passage from Holland in this same vessel, and was in the village at the time. According to Clarendon: ‘Finding that her majesty was landed, and that she lodged upon the quay, Batten, bringing his ships to the nearest distance, being very early in the morning, discharged above a hundred cannon (whereof many were laden with cross-bar shot) for the space of two hours upon the house where her majesty was lodged; whereupon she was forced out of her bed, some of the shot making way through her own chamber, and to shelter herself under a bank in the open fields.’ In point of fact, it does not appear that Batten knew of the queen's presence, or could in any case have acted otherwise than he did (Penn, i. 71–6, where the story is discussed in some detail). During the rest of the civil war Batten continued in active command of the fleet under the lord admiral ‘in the service of the king and parliament;’ and in May 1647 brought into Portsmouth a fleet of fifteen Swedish ships, men-of-war and merchantmen, for refusing to pay the accustomed homage to the English flag in the narrow seas; on which the admiralty committee reported to both houses of parliament that it was of opinion ‘that the vice-admiral's (Batten's) and rear-admiral's (Richard Owen's) proceedings in order to the maintenance of this kingdom's sovereignty at sea be approved of by both houses’ (Penn, i. 242–4).
It was, however, already known that the indignities recently offered to the king's person, and the authority now assumed by the army, were contrary to the spirit and feeling of the navy; and Batten was specially warned (12 June 1647) to ‘observe the tempers of the mariners and improve all means to continue them in a condition of obedience and service to the parliament.’ Three months later Batten himself was ordered by the admiralty committee to attend before them on 17 Sept. He did so, and rendered up his commission, declaring ‘that it was not out of any discontent, that if the state should be pleased to employ him again he was willing to serve them; if they should please otherwise to dispose of that command, he would be content to stay at home’ (Penn, i. 251). His resignation was accepted, and on 19 Oct. Colonel Rainborow, one of the committee, was appointed vice-admiral and commander-in-chief of the fleet. This proceeding roused the utmost indignation in the fleet, and many of the officers refused to serve under Rainborow (A Declaration of the Officers and Company of Seamen aboard His Majesty's Ships, lately reserved for His Majesty's Service, Amsterdam and London, 1648; reprinted in Penn, i. 270–2). They turned Rainborow ashore 28 May, demanded that Batten should be reappointed, and sent him a personal invitation to resume the command. This he did, when eleven ships sailed out of the fleet then in the Downs and went over to Holland, where the Prince of Wales then was; ‘not,’ wrote Batten, ‘as if I were now turned an enemy to parliaments, for I profess I shall, with the hazard of my life and fortunes, endeavour the welfare and being of free parliaments, provided it be with the just rights of the king and his subjects’ (A Declaration of Sir William Batten, late Vice-Admiral for the Parliament, concerning his Departure from London, to his Royal Highness the Prince of Wales, for satisfaction of all honest Seamen, and others whom it may concern (London, 1648; reprinted in Penn, i. 266–70). The prince conferred the honour of knighthood on Batten, and was anxious that he should continue in command of the fleet. This, however, Batten refused to do. He accompanied the prince to the Downs, and was with him when he summoned Warwick to return to his allegiance (29 Aug.); but he seems to have been shocked at the idea of fighting against his old admiral, and obtained permission to return to England.
With him also returned Captain Jordan and others, who made their peace with the parliament and served with distinction in the Dutch war. Batten seems to have been undisturbed, and indeed ignored; he took no further service under the parliament or Cromwell. There is no mention of him during the next twelve years; and though it is possible that the Robert Batten, captain of the Garland, who was slain in the fight off Dungeness 29 Nov. 1652, was his son, there is no direct evidence to that effect. On the
