Duncannon was besieged by rebel forces from January to March of 1645 and eventually captured, preventing Parliament from using it as a base of operations. Castlehaven campaigned from April to August in Munster against Inchiquin in an effort to eliminate the territory under his control, reducing his garrisons to Cork, Kinsale, Bandon and Youghal. In May of 1645 Sir Charles Coote, son and namesake of the late Mayor of Dublin, arrived in Ireland with a Parliamentary commission for the Presidency of Connaught. With the assistance of the Laggan army he conducted an expedition through Galway and besieged Sligo which fell to him in July. August found Monro attempting to besiege Charlemont but unable to maintain the siege due to lack of supply.
November of 1645 saw the arrival of the Papal Nuncio Rinuccini with arms, ammunition and Papal financial support for the Confederation as well as instructions to expel all Protestants from Ireland and establish the primacy of the Catholic Church. This view of the conflict made cooperation and negotiation with Royalist, Commonwealth and Covenanters nearly impossible. With his arrival there emerged three factions within the Confederation, with one under the influence of Rinuccini. The other two factions were the Supreme Council of the Confederation led by Ormond’s brother in law, Lord Muskerry and Nicholas Plunkett’s faction, both of whom were more inclined to negotiate a less “zero-sum” arrangement. Ormond was in negotiations with the Confederation and at the same time another Royalist negotiator, the Earl of Glamorgan, was attempting at the time to negotiate a secret treaty, both with the goal of securing forces for Charles I in England but with differing degrees of religious concession in mind for the agreement.
In March of 1646 Ormond signed a secret peace agreement with the rebels while at the same time being urged by a desperate Charles I to negotiate with the Army of Ulster as well. By May, Royalist resistance in England had been crushed and Charles I had joined the Scottish army at Newark.
As a result of Rinuccini’s contribution to the Confederation war effort, Owen O’Neil was able to assemble a force he moved towards Ulster in March. His route took him down the Blackwater towards Charlemont. Monro was on the move as well in May and planning to join forces with his nephew, George Monro, and a force from Coleraine. The Laggan Army was on the move into Connaught. There is some controversy about the reason for Monro’s movement, as to whether it was another of his now familiar sweeps through Ulster or a precursor to a major offensive operation outside Ulster.
Monro became aware of O’ Neil’s force on the 4 th of June as he crossed the Bann. This apparently came as a complete surprise and occurred as he was attempting to link up with the Coleraine force. O’Neil was found to be between the two forces and once he became aware of this O’Neil established a position at Benburb, a river crossing site on the Blackwater. Monro positioned himself to the south of O’Neil’s force along the rebel’s line of communications and could have not engaged him, but Monro was under pressure from his subordinates to engage the rebels and was also concerned about the Coleraine force that was as yet unaware of O’ Neil’s force. As Monro moved up the same side of the river as Benburb, O’Neil’s skirmishers contributed to the exhaustion already plaguing Monro’s force. Monro attacked O’Neil’s left flank along the Blackwater late in the day but the attack stalled. His force was also unnerved by the arrival of rebel forces from the direction of the expected Coleraine force which O’Neil had scattered prior to their arrival. A standoff of at least two hours occurred until the Irish counter attacked, eventually breaking and pursuing Monro’s force. Monro lost his siege train and baggage train to the rebels and perhaps as many as one in three of his men. Monro was forced to withdraw to Carrickfergus, his field army having been rendered combat ineffective. From this point on, the Army of Ulster was reduced to a force only able to garrison Carrickfergus and Coleraine lacking an offensive capability.
Owen O’Neil failed to follow up his victory, perhaps due to a lack of supplies which was a constant problem for armies in Ireland, but also perhaps knowing that he had only scattered a part of the forces available in Ulster that would oppose him.
In July the peace agreement between Ormond and the Confederation Supreme Council was denounced by Rinuccini, who arrested those associated with the Peace treaty and replaced the Supreme Council, assuming its leadership. Owen O’Neil moved his force to Kilkenny in support of Rinuccini. O’Neil and Preston, under orders from the new Supreme Council, marched on Dublin but were unable to achieve much due to logistical challenges and mutual distrust.
The failure of the Ormond peace and difficulty in holding Dublin in the face of Confederation forces, led the Earl of Ormond to open negotiations with Monro for turn over of Dublin to the Army of Ulster. These negotiations failed, but the negotiations with Parliament were successful, setting the stage for the arrival of Parliamentary forces.