He is said by some, especially William Sanderson, to have persuaded the Earl of Essex to make his ill-fated march into Cornwall in 1644; he escaped with the earl from Fowey after the defeat of the parliamentary army in the first days of September 1644. Having reached Plymouth safely he became its Governor and defended the city from the besieging Royalists. With the Self-Denying Ordinance of April 1645 he lost his command in Plymouth and was obliged like his brother-in-law, the Earl of Manchester, to watch the successes of Cromwell's New Model Army from the sidelines. He, like other Lords who had sided with Parliament, was marginalised by the so-called Independents who saw no future in continuing negotiations with King Charles. The execution of the King would have appalled him.