His troubles began as soon as Wentworth landed in Ireland, when he immediately dismissed, without any pay, forty of the newly enrolled troopers, to make room for the gentlemen and servants he had brought with him; difficulties about payments followed, then refusals to promote Fortescue and his sons, then scandals about his lordship's visits to a 'noble lady,’ then a personal quarrel.
The business ended in a letter from Lord Strafford, after he had left Ireland, during his imprisonment in the Tower of London, ordering his steward to discharge Fortescue from the command of his troop.
Shortly after his departure Sir Henry Tichborne was appointed by the lords justices governor of the place, and brought to its relief a force of a thousand-foot and a hundred horse.
The commissioners of parliament appointed to raise a force for the suppression of the Irish rebellion selected Fortescue in June 1642 for the command of the third troop of horse intended to serve under Lord Wharton, as lord-general of Ireland.
In addition to this body of cavalry, Fortescue also raised for service in Ireland a company of infantry, which was attached to the Earl of Peterborough's regiment, and was then compelled to serve with the parliamentary army in England during the civil war.
On the eve of the battle of Edgehill, Fortescue, who was acting as major in Lord Wharton's regiment of horse, tried negotiations with Prince Rupert, and promised to desert.
On the next day, when Prince Rupert charged the left wing of the parliamentary army, Fortescue with his troop drew off from the rest of Lord Wharton's regiment and rode over to the royal horse.
Many of Fortescue's troopers forgot to throw away orange scarfs worn as the Earl of Essex's colours, and eighteen out of the sixty men of the troop were killed or wounded by the cavalry whom they had joined.
Soon after the battle, Fortescue was appointed to the command of the 10th regiment of the royal infantry, and served with the army whose headquarters was at Oxford during the remainder of the civil war.
By royal warrant of 21 August 1660 he was restored to the post of Constable of Carrickfergus Castle, an office which he was permitted to transfer a few months later to his eldest surviving son, Sir Thomas Fortescue, and was created a Gentleman of the Privy Chamber.