The relative success of the Ulster insurrection and the increasing disregard for Catholics by the government in Dublin, which identified with those in the English parliament seeking to weaken the position of the monarch, drew the Old English Catholics into alliance with the Gaelic Catholics. Both wings of Catholicism continued to profess their loyalty to the king, although there were popular rumors about continental kings extending recognition to Phelim O'Neill as king of Ireland. Those rumors strengthened English determination to suppress the Irish insurrection. But the loyalty of the Catholics in Ireland to Charles I also intensified parliamentary hostility to both the Catholics and the king, who were invalidly suspected of being allies. The English agreed to finance the sending of a Scottish army of 10,000 men to Ireland under Major General Robert Munro to repress the rebellion. Charles also gave his assent in March 1642 to an Adventurers' Act passed by the English parliament, which called for the confiscation of two and a half million acres in Ireland from anyone disloyal. The confiscated land would compensate those who advanced money to finance the war effort against the Irish (and also against the monarch). It would serve a decade later as the basis on which Oliver Cromwell implemented his plantation of Ireland. The Irish Catholics consequently found themselves opposed by the supporters of both monarch and parliament, a situation that would persist even after outright civil war had broken out in England in August 1642 between king and parliament.
In March 1642 the Catholic hierarchy of Ireland gave their sanction to the formation of a confederation of Catholics, which became in October the Confederation of Kilkenny. In this government, which was a substitute for the Irish parliament from which they had been excluded, the united Gaelic and Old English Catholics committed themselves to restore the rights of the church, to defend the liberties of the nation, and to maintain the prerogatives of the Crown, with the motto of “Pro Deo, pro rege, pro patria Hibernia unanimis" on their seal. However, despite the proclaimed unity, differences in temperament and strategy persisted between the Gaelic and the Old English. The former had already lost much more in terms of their holdings and were accordingly less inclined toward compromise, while the later persisted in a confidence that they might come to some kind of alliance with the English monarch against the parliamentary forces. These differences carried even to the rivalry between the two leaders who had returned from serving the Spanish king on the Continent to lead the "Catholic Confederates." One was Thomas Preston, the brother of Lord Gormanstown, an Old English peer, and the other was Owen Roe O'Neill, the nephew of Hugh, the earl who had fled Ireland in 1607.
There were also divisions on the other side between royalists and parliamentary supporters. Munro and his forces identified with the parliamentary (and low church) cause, as did many New English commanders, like Lord Broghill (son of Robert Boyle, earl of Cork), and the Gaelic leader (but also committed Protestant), Murrough O'Brien (Lord Inchiquin). The earl of Ormond, a loyal monarchist, served as commander of the army and Lord Lieutenant of Ireland. He had to contend with the parliamentary sympathies of many in the government. To add to his difficulties, the king directed him in early 1643 to deal with the Confederates in the hope of bringing them over to the royalist side.
At that stage the Confederates were strongest in Connacht. O'Neill had formed a strong army among the Gaelic in Ulster, but Preston had suffered a serious defeat at royalist hands in Wexford and the Old English had not much success in Munster. The Confederates feared that the king and parliament might ultimately come to terms, which would be to the detriment of the Catholic position. Some argued that their best strategy was to play for time with expectations of continental support. That view was more characteristic of the Gaelic leaders, whereas the Old English believed the Catholics had a better chance with a royalist success and that any reasonable arrangement with the monarchy would be wise. A papal envoy, Pietro Scarampi, who brought some money and supplies, had urged the continuance of the struggle. However, the Old English prevailed and agreed to a cessation of violence for a year in September 1643. However, the parliamentary side did not accept the cessation signed by the royal side, and Munro continued the war in Ulster, as did Lord Inchiquin a few months later.
However, negotiations between the Confederates and Ormond continued with the goal to secure a permanent settlement, although Ormond was reluctant to surrender anything that was vital to the interests of Protestantism. The king, anxious to draw upon the Confederate military forces to support his campaign in England, called upon an English Catholic, the earl of Glamorgan, to negotiate for him. Unknown to Ormond, he obtained a treaty in August 1645, which gave complete freedom to the Catholic Church in Ireland, including restoration of all churches and church property not actually being used by Protestants, in return for the supply of 10,000 men for the king in England. When it became publicly known, the king had to repudiate the treaty. Negotiations between the Confederates and Ormond continued, however, with the former hoping to win generous terms and the king, suffering from a severe defeat in July 1645 at Naseby, anxious for additional troops. In the following year, the Confederates accepted a deal less favorable, but still substantial. Similar to the earlier "Graces," it abolished the Court of Wards whereby the king had been able to assert authority over the minor offspring of a deceased Catholic lord and raise them as Protestants (as had happened to Ormond), substituted an oath of allegiance for the Oath of Supremacy, admitted Catholics to public office, and ended restrictions on Catholic education. But nothing was agreed on relating to church property.
Before the treaty had been negotiated, another papal emissary, the papal nuncio, Bishop Giovanni Battista Rinuccini, had come to Ireland. When the
Treaty was published he condemned it as a betrayal of the original terms of the Confederation of Kilkenny in that it did not secure the full rights of the church. He preached against it and threatened its proponents with excommunication. The clergy and the rank and file tended to support him, as did Owen Roe O'Neill. The latter had triumphed a few months before over Munro in the Battle of Benburb near Armagh, destroying half the forces that he had hoped to employ in the south against the Confederacy. But instead of mopping up the remainder of Munro's forces, O'Neill's army marched south relishing their triumph. On the basis of the Benburb victory, even Preston acceded to Rinuccini's wishes and rejected the treaty.
With the peace efforts having failed, the Confederates hoped to take Dublin, but further disagreements among their leaders inhibited their chances. But the Confederacy itself remained committed to Rinuccini's insistence on full restoration of the position of the Catholic Church in Ireland. Therefore, Ormond turned to the parliamentary side and agreed to surrender Dublin and the forces under his command to the parliamentary forces and withdrew from Ireland himself in mid-1647. From then on matters soured for the Confederate cause. Colonel Michael Jones, who had arrived from England with his Roundhead army of 8,000, overwhelmingly defeated Preston, who lost 5,000 men. In addition, Inchiquin swept all before him in Munster. The Confederates began to dispute among themselves. They dismissed O'Neill, appealed over Rinuccini to Rome, and came near to battle against each other. Ormond returned to Ireland and signed a new treaty with the Confederates, but by then all had changed as the king had been tried and executed by the English parliament.
O'Neill, now independent from the other Confederates and Ormond, entered into a temporary truce with the parliamentary forces. But on the other side, the Ulster Scots and Inchiquin turned against the parliamentary forces. Now a loyal monarchist, Inchiquin had captured Drogheda and Dundalk, but Ormond was unsuccessful in his assault on Dublin where the forces of Michael Jones triumphed on August 2. Two weeks later Oliver Cromwell, "Lord Lieutenant and General for the Parliament of England," arrived in Dublin with 20,000 men. The way was clear for a complete conquest of the island.