Ormond was invited to Kilkenny, where he received a royal reception from his friends. But O'Neill marched south and compelled Ormond to beat a hasty retreat towards Dublin. Rinucinni returned to Kilkenny, and some of the prominent adherents of Ormond were arrested. A new Supreme Council was chosen, and O'Neill and Preston were commissioned to march on Dublin, but, though they brought their armies close to the city, yet, owing to underhand communications carried on between Ormond's agent, the Earl of Clanrickard, and Preston, and the jealousy between the generals, the attack was not made.
A new General Assembly had been elected and met at Kilkenny (10 Jan.
1647). After a long discussion the Ormond Peace was condemned, and a new form of oath was drawn up to be taken by all the Confederates.
Ormond, who could have done so much for his master had he obeyed his instructions and made some satisfactory offers to the Irish Catholics, surrendered Dublin into the hands of the Parliamentarians, and fled to France. To make matters worse Preston was defeated by the Parliamentarians at Summerhill (Aug. 1647), and Lord Inchiquin was carrying all before him in the South. Everywhere he went he had acted with great savagery, and was especially violent in his opposition to the Catholic religion. But early in 1648 he changed his politics, and declared for the king against the Parliament. Immediately the former friends of Ormond on the Supreme Council insisted on ****** terms with Lord Inchiquin. Rinuccini opposed such a step as a betrayal, and his action was approved by a majority of the bishops. The nuncio left the city and went towards Maryborough, where O'Neill was encamped. In May 1648 the truce with Lord Inchiquin was proclaimed, and in a few days Rinuccini issued a sentence of excommunication against all who would receive it, and of interdict against the towns which recognised it.
The Supreme Council replied by appealing to the Pope. The only result was that the division and confusion became more general. Several of the bishops and clergy were to be found on both sides. The Supreme Council dismissed O'Neill from his office, and afterwards declared him a traitor. The nuncio went to Galway, from which port he sailed in 1649. Though it is difficult to entertain anything but the greatest contempt for the Ormond faction on the Supreme Council, and though Rinuccini was an honest man who did his best to carry out his instructions, still he did not understand perfectly the situation. He allowed himself to show too openly his preference for O'Neill, and displayed too great an inclination to have recourse to high-handed methods. His arrest of the Ormondist faction on the Supreme Council and the censures which he levelled against his opponents, however justifiable these things might have been in themselves, were not calculated to restore unity and confidence.[58]
Ormond returned to Ireland in 1648 and received a great welcome from those of the Supreme Council who were opposed to Rinuccini and O'Neill. In January 1649 he concluded a peace with them by which he guaranteed that in the next Parliament to be held in Ireland the free exercise of the Catholic religion should be conceded; that the Act of Uniformity and the Act of Royal Supremacy should be abolished; that all offices, civil and military, should be thrown open to Catholics provided they were willing to take a ****** oath of allegiance; that all plans for any further plantations in Munster, Leinster, and Connaught should be abandoned, that all Acts of Attainder, etc., passed against Irish Catholics since October 1641 should be treated as null and void; that the clergy should not be molested in regard to the churches, church-livings, etc., until his Majesty upon full consideration of the desires of the Catholics, formulated in a free Parliament, should express his further pleasure; and that the regular clergy who would accept this peace should be allowed to continue to hold their houses and possessions. Further concessions were to be dependent on the king's wishes.[59] The Catholic Confederation as such was dissolved, and Ormond was installed as Lord Lieutenant to govern the country in conjunction with twelve Commissioners of Trust appointed by the Confederates. But O'Neill and his army still held out against any terms with Ormond, and a large number of the cities refused to hold any communications with him. Still he hoped to capture Dublin from the Parliamentarians before help could arrive from England, but he suffered a terrible defeat at Rathmines (2 Aug. 1649).
Less than a fortnight later Oliver Cromwell[60] arrived in Dublin with a large force to crush both the Royalists and the Catholics.
Cromwell, having taken a little time for his troops to recruit, marched on Drogheda, then held for the king by Sir Arthur Aston, and so earnestly did he push forward the siege that in a short time he carried the city by assault, and put most of the garrison and a large number of the citizens to death. Over a thousand were slaughtered in St. Peter's Church to which they had fled for refuge, and special vengeance was meted out to the clergy, none of them who were recognised being spared. Similar scenes of wholesale butchery took place at Wexford, into which his army gained admission by treachery.[61] Ormond was unable to make headway against such a commander, and frightened at last by the prospect that opened out before him, he made overtures to O'Neill for a reconciliation. O'Neill agreed to lend his aid against Cromwell. He sent a portion of his army south, and he himself, though ill, was already on the march when he died at Cloughoughter (6 Nov. 1649). His death at such a time was an irreparable loss both to the Catholic religion and to Ireland. Had he lived, and had Ormond and his faction co-operated with him, the campaign of Cromwell might have had a very different termination.