The unexpected death of the Ulster general favoured still farther Cromwell's southern movements. The gallant, but impetuous Bishop of Clogher, Heber McMahon, was the only northern leader who could command confidence enough to keep O'Neil's force together, and on him, therefore, the command devolved. O'Ferrall, one of Owen's favourite officers, was despatched to Waterford, and mainly contributed to Cromwell's repulse before that city; Hugh O'Neil covered himself with glory at Clonmel and Limerick; Daniel O'Neil, another nephew of Owen, remained attached to Ormond, and accompanied him to France; but within six months from the loss of their Fabian chief, who knew as well when to strike as to delay, the brave Bishop of Clogher sacrificed the remnant of "the Catholic Army" at the pass of Scariffhollis, in Donegal, and, two days after, his own life by a martyr's death, at Omagh. At the date of Cromwell's departure—when Ireton took command of the southern army—there remained to the Confederates only some remote glens and highlands of the North and West, the cities of Limerick and Galway, with the county of Clare, and some detached districts of the province of Connaught.
The last act of Cromwell's proper campaign was the siege of Clonmel, where he met the stoutest resistance he had anywhere encountered. The Puritans, after effecting a breach, made an attempt to enter, chanting one of their scriptural battle-songs. They were, by their own account, "obliged to give back a while," and finally night settled down upon the scene. The following day, finding the place no longer tenable, the garrison silently withdrew to Waterford, and subsequently to Limerick. The inhabitants demanded a parley, which was granted; and Cromwell takes credit, and deserves it, when we consider the men he had to humour, for having kept conditions with them.
From before Clonmel he returned at once to England, where he was received with royal honours. All London turned out to meet the Conqueror who had wiped out the humiliation of Benburb, and humbled the pride of the detested Papists. He was lodged in the palace of the king, and chosen "Captain-general of all the forces raised, or to be raised, by the authority of the Parliament of England."