Factionalism and Disillusionment
In March 1646 a treaty was signed between Ormonde and the Catholics, which would have committed the Catholics to sending troops to aid the Royalist cause in the English Civil War. The peace terms however, were rejected by a majority of the Irish Catholic military leaders and the Catholic clergy including the Nuncio, Rinuccini. O'Neill led his Ulster army, along with Thomas Preston's Leinster army, in a failed attempt to take Dublin from Ormonde. However, the Irish Confederates suffered heavy military defeats the following year at the hands of Parliamentarian forces in Ireland at Dungans Hill and Knocknanauss, leading to a moderation of their demands and a new peace deal with the Royalists. This time O'Neill was alone among the Irish generals in rejecting the peace deal and found himself isolated by the departure of the papal nuncio from Ireland in February 1649.
So alienated was O'Neill by the terms of the peace the Confederates had made with Ormonde that he refused to join the Catholic/Royalist coalition and in 1648 his Ulster army fought with other Irish Catholic armies. He made overtures for alliance to Monck, who was in command of the parliamentarians in the north, to obtain supplies for his forces, and at one stage even tried to make a separate treaty with the English Parliament against the Royalists in Ireland. Failing to obtain any better terms from them, he turned once more to Ormonde and the Catholic confederates, with whom he prepared to co-operate more earnestly when Cromwell's arrival in Ireland in August 1649 brought the Catholic party face to face with serious danger.
Read more about this topic: Owen Roe O'Neill