During these three years of intrigue and negotiation, the position of General O'Neil was hazardous and difficult in the extreme. One campaign he had served under a stranger, as second on his own soil. In the other two he was fettered by the terms of "cessation" to his own quarters; and to add to his embarrassments, his impetuous kinsman Sir Phelim, brave, rash, and ambitious, recently married to a daughter of his ungenerous rival, General Preston, was incited to thwart and obstruct him amongst their mutual clansmen and connections. The only recompense which seems to have been awarded to him, was the confidence of the Nuncio, who, either from that knowledge of character in which the Italians excel, or from bias received from some other source, at once singled him out as the man of his people. What portion of the Nuncio's supplies reached the Northern General we know not, but in the beginning of June, he felt himself in a position to bring on an engagement with Monroe, who, lately reinforced by both Parliaments, had marched out of Carrickfergus into Tyrone, with a view of penetrating as far south as Kilkenny. On the 4th day of June, the two armies encountered at Benburb, on the little river Blackwater, about six miles north of Armagh, and the most signal victory of the war came to recompense the long-enduring patience of O'Neil.
The battle of Benburb has been often and well described. In a naturally strong position—with this leader the choice of ground seems to have been a first consideration—the Irish, for four hours, received and repulsed the various charges of the Puritan horse. Then as the sun began to descend, pouring its rays upon the opposing force, O'Neil led his whole force—five thousand men against eight—to the attack. One terrible onset swept away every trace of resistance. There were counted on the field, 3,243 of the Covenanters, and of the Catholics, but 70 killed and 100 wounded. Lord Ardes, and 21 Scottish officers, 32 standards, 1,500 draught horses, and all the guns and tents, were captured. Monroe fled in panic to Lisburn, and thence to Carrickfergus, where he shut himself up, till he could obtain reinforcements. O'Neil forwarded the captured colours to the Nuncio, at Limerick, by whom they were solemnly placed in the choir of St. Mary's Cathedral, and afterwards, at the request of Pope Innocent, sent to Rome. _Te Deum_ was chanted in the Confederate Capital; penitential psalms were sung in the Northern fortress. "The Lord of Hosts," wrote Monroe, "had rubbed shame on our faces, till once we are humbled;" O'Neil emblazoned the cross and keys on his banner with the Red Hand of Ulster, and openly resumed the title originally chosen by his adherents at Clones, "the Catholic Army."