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During the closing months of 1649 the situation in Ireland seemed hopeless. Though as an unscrupulous diplomatist Ormond had few equals, he was utterly worthless as a soldier, and to make matters worse he was still distrusted by the great mass of the Irish people. In the hope of restoring unity and of encouraging the people to continue the struggle a synod of the bishops and clergy assembled at Clonmacnoise (Dec. 1649). They issued a declaration warning the people that they could expect no mercy from the English Parliament, that the wholesale extirpation of Catholicism was intended, as was evidenced by the actions of Cromwell, and that the lands of the Irish Catholics were to be handed over to English adventurers. They called upon them to forget past differences, to sink racial and personal jealousies, and to unite against the common enemy.[62] But the country distrusted Ormond, and refused to rally to his standard. Another meeting consisting of the bishops and of the Commissioners of Trust was held at Loughrea, in which it was agreed that there should be a general levy of all men fit to bear arms, and the monastery of Kilbegan was fixed as the place of rendezvous. Several of the cities and leading men refused, however, to take any part in a movement controlled by Ormond, and as a last desperate resort, at the meeting of the bishops held at Jamestown (12Aug. 1650) the bishops declared that there could be no hope of unity unless Ormond surrendered his trust to some person in whom the entire country had confidence.[63] Very reluctantly Ormond agreed to this request and left Ireland in December, having appointed the Earl of Clanrickard as his successor. The latter was a Catholic who had played a very ignoble part throughout the war. Had he displayed years before but half the energy he displayed in its later stages things might never have come to such a pass.

As it was, Cromwell made great progress in the South, though he was forced to raise the siege of Waterford, and suffered a bad defeat at Clonmel from the nephew of O'Neill. He left Ireland in May 1650, and entrusted the command to Ireton. Owing to the state of disunion Ireton was enabled to take city after city. Limerick was taken in 1651, and Terence O'Brien, Bishop of Emly, was put to death. Bishop MacMahon of Clogher, who had assumed the leadership of the army of Owen Row O'Neill after the latter's death was defeated at Scarrifhollis (1650).

Later on he was captured, and put to death, his head being impaled on the gates of Enniskillen as a warning to his co-religionists. The submission of Clanrickard in 1652 practically put an end to the war, and before another year had elapsed all effective resistance had ceased.

During the Kilkenny Confederation the Catholic Church was restored to its original position. In the districts controlled by the Confederates the bishops and clergy were allowed to occupy once more their houses and churches wherever these had not been destroyed, and religious communities of both men and women were set up again close to their former monasteries and convents, though at the same time the Catholic Lords of the Pale were alert lest they should be asked to return any of the ecclesiastical or monastic lands that had been granted to them by royal patent. In Dublin and wherever Ormond and the Royalists had authority, both clergy and people enjoyed complete toleration, but in certain portions of the North, and wherever the Puritans and Parliamentarians held sway, persecution was still the order of the day. When Dublin was surrendered to the Parliamentarians (1647) the priests, and later on, all Catholics, were expelled from the city. In the South of Ireland Lord Inchiquin acted in the most savage manner in Cashel and generally in the cities which he conquered, while the Parliamentarian party in the North showed no mercy to the Catholics who fell into their hands. After the arrival of Cromwell the prospect became even more gloomy. Though he announced that he would interfere with no man's religion, he declared that on no account could he tolerate the celebration of Mass.[64] The clergy were put to the sword in Drogheda and Wexford. The Archbishop of Tuam was killed during the war (1645); Boetius Egan, Bishop of Ross, fell into the hands of Lord Broghill and was put to a cruel death because, instead of advising the garrison of Carrigdrohid to surrender, he encouraged them to continue the struggle (1650); Terence Albert O'Brien, Bishop of Emly, was captured by Ireton after the siege of Limerick, and was hanged; Heber MacMahon, Bishop of Clogher, was put to death by the orders of Coote (1650); Bishop Rothe of Ossory died as a result of the sufferings he endured, and Bishop French of Ferns, after undergoing terrible trials in Ireland, was obliged to make his escape to the Continent.