The grant finally came into the possession of Thomas, Lord Fairfax, and in 1746 a stone was erected at the source of the north branch of the Potomac to mark the western limit of the grant.
The lords and the Scots vehemently took Manchester's part; but the Commons eventually sided with Cromwell, appointed Sir Thomas Fairfax general of the New Model Army, and passed two self-denying ordinances, the second of which, ordering all members of both houses to lay down their commissions within forty days, was accepted by the lords on the 3rd of April 1645.
He took Devizes and Laycock House, Winchester and Basing House, and rejoined Fairfax in October at Exeter, and accompanied him to Cornwall, where he assisted in the defeat of Hopton's forces and in the suppression of the royalists in the west.
On the 9th of January 1646 he surprised Lord Wentworth's brigade at Bovey Tracey, and was present with Fairfax at the fall of Exeter on the 9th of April.
He was present again with Fairfax at the capitulation of Oxford on the 24th of June, which practically terminated the Civil War, when he used his influence in favour of granting lenient terms. He then removed with his family from Ely to Drury Lane, London, and about a year later to King Street, Westminster.