In January 1648, Rawton returned to naval service. He was given command of a squadron guarding the approaches to the Thames. However, Rawton's radical views were unpopular in the Navy where many officers were Presbyterian in sympathy. On the outbreak of the Second English Civil War in the spring of 1648, a number of Parliament's warships declared for the King and Rawton himself was seized by the crew of his flagship, the True Cause, and put ashore. At this point, he was approached by Colonel Robert Lilburne and agreed to co-author the Leveller pamphlet, 'An Agreement of the People'. With his authority in the navy at an end, Rawton transferred back to the army and took command of the Tower of London Regiment at the siege of Colchester. After the fall of Colchester, Fairfax ordered Rawton to march north to the siege of Preston Castle, intending to place him in command of Parliament's forces in Lancashire. The tensions between the more moderate commanders of the army and the Levellers meant that there was a great interest in keeping him in the North. Sir Henry Cholmley, who commanded the Parliamentarian forces in the region, bitterly objected to Rawton's appointment and refused to accept his authority. Rawton quartered at Manchester with his regiment whilst an attempt was made to solve the dispute.