Cromwell came out of winter quarters at the end of January 1650 and began the conquest of southern Ireland. He offered terms of surrender at the city of Fethard on February 2. Officers, soldiers and priests would be allowed to march away, and the townspeople would be protected from looting. The town of Cashel surrendered without a fight, and Cromwell turned his army on Callan, a city defended by a strong wall and three castles. He attacked with cannons, took two of the castles, put their defenders to the sword and accepted the surrender of the third.

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Next Cromwell turned to Cahir, commanded by Ormonde’s half-brother, Captain George Mathews. When Mathews refused the first demand to surrender, the Parliamentarians tried to scale the walls. A force of Ulstermen repulsed the attack, but Cromwell brought up his cannons. Mathews realized he could not hold out and surrendered under terms Cromwell agreed to–that the officers, soldiers and clergymen be allowed to march out.

Cromwell pushed on, taking the towns of Kiltenan, Dundrum, Ballynakill and Kildare. He and other Parliamentarians next converged on Kilkenny, headquarters of the Confederacy. He summoned Kilkenny on March 22, 1650:

My coming hither is to endeavour, if God so please to bless me, the reduction of the city of Kilkenny to their obedience to the state of England, from which, by an unheard of massacre of the innocent English, you have endeavored to rend yourselves.

Sir Walter Butler, governor of Kilkenny and a cousin of Ormonde, responded that he would maintain the town for the king. The city was not in good shape, however. Hundreds of the garrison died of plague, and reinforcements deserted. Nearby Cantwell Castle surrendered to Cromwell. Ormonde and the Supreme Council had long since fled.

Nevertheless, Cromwell found it not so easy to take the town. The city was divided by the River Nore into two parts, Kilkenny proper and Irishtown. A plot to betray the city was discovered, and a Captain Tickell was executed. Butler refused to surrender, and an attack beginning on the 24th at Irishtown was first repulsed, but ultimately succeeded. Butler again refused to surrender, and and the Parliamentary attack continued on the 25th. Hours of bombardment caused a breach in the wall of the town proper. Two attacks by the Parliamentarians were repulsed, and a third order to attack was not obeyed, but Butler soon decided that he’d done all he could do and surrendered.

Upon payment of 2,000 pounds sterling, the citizens of Kilkenny were protected from looting, and the officers and soldiers were allowed to march out disarmed for two miles. The clergymen also were allowed to march out.

For some weeks after Kilkenny, Cromwell did not take an active role in operations; instead he directed them, first from Carrick, then from Fethard. He realized that Ormonde was at the end of his resources. On the east coast, only Waterford was not in English hands, and on the west coast the plague-devastated city of Galway. Limerick refused to admit any forces not dominated by the Catholic clergy. Furthermore, the bishop of Derry was making arrangements with foreign princes to transport several thousand men out of Ireland.

On the combat side, Inchiquin tried to invade Limerick, but was routed by Broghill. Broghill then joined Cromwell at Clonmel after beating back an invasion of County Cork by David Roche.

By the end of March 1650, there was little to do except to take Clonmel, Waterford and Limerick and reduce the scattered Irish remnants, since the last major Confederate commander besides Ormonde, Inchiquin, was negotiating with Cromwell.

Cromwell’s next objective, Clonmel, was commanded by General Hugh Duffy O’Neill, Black Hugh, who, like his uncle, Owen Roe O’Neill, had previously served in the Spanish army. At his command were 12,000 troops, mostly Ulstermen and all but 50 of whom were infantry. Ormonde promised to send aid but did not. It was in Black Hugh that Cromwell met his greatest adversary in Ireland.

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