Under the treaty of 1649—which conceded full civil and religious equality to the Roman Catholics—Ormond was once more placed at the head of the government and in command of the royal troops. A few days after the signing of that treaty, news of the execution of Charles I. having reached Ireland, the Viceroy proclaimed the Prince of Wales by the title of Charles II., at Cork and Youghal. Prince Rupert, whose fleet had entered Kinsale, caused the same ceremony to be gone through in that ancient borough. With Ormond were now cordially united Preston, Inchiquin, Clanrickarde, and Muskerry, on whom the lead of the Supreme Council devolved, in consequence of the advanced age of Lord Mountgarrett, and the remainder of the twelve Commissioners of Trust. The cause of the young Prince, an exile, the son of that Catholic queen from whom they had expected so much, was far from unpopular in the southern half of the island. The Anglican interest was strong and widely diffused through both Leinster and Munster; and, except a resolute prelate, like Dr. French, Bishop of Ferns, or a brave band of townsmen like those of Waterford, Limerick, and Galway, or some remnant of mountain tribes, in Wicklow and Tipperary, the national, or "old Irish policy," had decidedly lost ground from the hour of the Nuncio's departure.
Owen O'Neil and the Bishops still adhered to that national policy. The former made a three-months' truce with General Monck, who had succeeded Monroe in the command of all the Parliamentary troops in his province. The singular spectacle was even exhibited of Monck forwarding supplies to O'Neil, to be used against Inchiquin and Ormond, and O'Neil coining to the rescue of Coote, and raising for him the siege of Londonderry. Inchiquin, in rapid succession, took Drogheda, Trim, Dundalk, Newry, and then rapidly countermarched to join Ormond in besieging Dublin. At Rathmines, near the city, both generals were surprised and defeated by the Parliamentarians under Michael Jones. Between desertions, and killed and wounded, they lost, by their own account, nearly 3,000, and by the Puritan accounts, above 5,000 men. This action was the virtual close of Ormond's military career; he never after made head against the Parliamentary forces in open field. The Catholic cities of Limerick and Galway refused to admit his garrisons; a synod of the Bishops, assembled at Jamestown (in Roscommon), strongly recommended his withdrawal from the kingdom; and Cromwell had arrived, resolved to finish the war in a single campaign. Ormond sailed again for France, before the end of 1649, to return no more until the restoration of the monarchy, on the death of the great Protector.