The commander of the fort, Thomas Roche, informed Ormonde that there was no way he could hold the fort against Cromwell and that he would have to obey the summons. Ormonde promptly sent Colonel Edward Wogan, a defector from Ireton’s ranks, along with 120 cavalry, to replace Roche. They arrived just in time to save the fort. They sent a defiant answer to Cromwell, and he abandoned the siege rather than pursue it in the winter.

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Although Duncannon had a reprieve, the Confederates lost a more important place; the garrison at Cork revolted in favor of the Parliamentarians about the same time Cromwell was at Ross. The seeds of the revolt were sown before Cromwell’s coming as Protestants sought to break the dominance of Catholics, especially the Confederates.

Cromwell sent agents to widen the differences. One of them was Roger Boyle, Lord Broghill, a former royalist who joined Cromwell out of financial need. Another Cromwell agent was Colonel Richard Townsend, who pretended to be angered at the execution of the king but who was trying to corrupt the Munster forces. Their activities quickly bore fruit. The Munster Protestants had nothing to hope for and everything to fear from the Confederates. Cromwell remarked that if there had been a man like Boyle in every province, it would have been impossible for the Irish to raise a rebellion.

The result was that Broghill raised 1,500 infantry and a troop of cavalry from his family estates. Townsend led the English troops and citizens of Cork in driving out the Irish and declared the city for Parliament. The rising saved Townsend from being executed for hatching a plot to capture Inchiquin.

The revolt was a greater disaster for Ormonde than the mere loss of Cork. The Irish complained that Ormonde showed favoritism to the English, and he was thus compelled to restore Roche at Duncannon. The rest of Inchiquin’s English troops deserted, making the campaign a tribal war between Celts and English. Inchiquin was even accused of being a traitor. The accusation was false, but the damage was done, and he lost much of his already scant credibility.

With the capture of Drogheda and Wexford, the major strongholds on the east coast, and the possession of Cork, the first stage of Cromwell’s Irish campaign was over. His task was clear: reduce the garrisons that still held out in Munster and bring that province under Parliament. The rising in Cork made that task simpler by widening the gap between the Irish and the Old English. Cromwell spent as much time on diplomatic maneuvering as he did on field operations.

As matters stood in mid-November 1649, the Parliament held the east coast from Belfast down to Wexford, plus Cork in the west. Only a few towns in the north remained in Irish hands. Cromwell was still ill, so he sent Jones and Ireton to the county of Kilkenny to secure the garrisons there, cut Ormonde off from Waterford and draw him into an open engagement.

The plan was not successful. The Confederates first retired to Thomastown, then to the fortified city of Kilkenny. Ireton sent Colonel Daniel Abbott to take the town, but Abbott found that the River Nore was flooded and the bridge at Thomastown was destroyed. Ireton and Jones had to be content with sending Colonel John Reynolds to take Carriek and returning to Ross with the main army. Weather had joined disease and famine in the fight against Cromwell.

Carrick soon fell, and Cromwell, now recovered from his illness, led his army across the River Suir to Waterford

Ormonde lay with 10,000 men on the Kilkenny side of the Suir opposite Waterford and the Parliamentarians. He sent Inchiquin to try to recapture Carrick, but he failed. Cromwell had 7,000 at the beginning of the siege, but wet weather and plague reduced the number to 3,000. At that point, Ormonde could have stopped him. Again, Ormonde’s army did not come into play, because of the same disunity that plagued the Irish at Drogheda and Wexford. His army was seen by most Irish as an alien force, just as offensive as Cromwell’s. Cromwell sought to exploit this feeling in his summons to Waterford on November 21, 1649. His warning was similar to those given to Drogheda and Wexford, but the result was different. Hunger and disease had taken such a toll on Cromwell’s force that eventually he was compelled to retreat.

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