Oliver Cromwell was the Commonwealth’s best general and when the Irish Confederates signed a treaty with the remnants of the English Royalist forces of the beheaded Charles I, it was a threat that the ruling Parliament felt it had to deal it swiftly. The Confederates had controlled most of Ireland since 1641 and the treaty with the Royalist was a direct threat to the new Commonwealth.
The Battle of Rathmines prevented Dublin from falling to the Royalist and Confederate forces and gave Cromwell and his army an easy landing in August 1649. Another force under Henry Ireton landed on the 17th and combined to make a force of some 30,000 well armed and well trained New Model Army troops. Cromwell made the strategic decision that he had to take the port cities on the east coast of Ireland to secure his supply lines back to England.
Drogheda, about 30 miles north of Dublin was Cromwell’s first target. He marched north with about 12,000 troops and eleven 48 pounder siege guns, while his remaining forces secured Dublin and his lines of communications. Drogheda was garrisoned by 3,100 Royalist and Irish soldiers. Cromwell summoned the garrison to surrender which he refused to do. The New Model Army artillery quickly battered two breeches in the city walls and after two unsuccessful attacks, the third assault entered the city. There is much dispute over what happened next. Some sources say that many of the town’s people were slaughter, as was most of the garrison. Other sources say that there was no massacre of civilians. Also according to the rules of war at that time the garrison was libel to be killed because they failed to surrender before the wall was breeched.
Next Cromwell dispatched 5,000 men north under Robert Venables to defeat a Scots Covenanter army. Venables destroyed the Scots at Lisnagrvey. While Venables marched north Cromwell went south of Dublin and besieged Wexford. The town was assaulted and taken in the midst of negotiations and another massacre is alleged, the town was also burned, but is also under dispute as to what Cromwell’s part in it was. The town was so wreaked that it couldn’t be used for winter quarters for Cromwell troops. The New Model Army moved to take Waterford and Duncannon but failed and had to retire to winter quarters where it lost many soldiers to typhoid fever and dysentery.
In the spring of 1650, Waterford and Duncannon surrendered and Cromwell moved to mop up the remaining Royalist and Confederate walled strong holds, including the Confederate capitol of Kilkenny and the city of Clonmel. Even though these towns put up fierce resistant their garrisons surrendered under terms and there were no more massacres of either civilians or soldiers.
In 1650, a mutiny by Royalist troops handed Cork and most of Munster to the New Model Army. Also the Royalist-Confederate alliance fell apart as Prince Charles favored a Scots Covenanter alliance rather than the alliance with the Catholic Confederates. With these moves Cromwell left Ireland in May 1650 to lead the Commonwealth forces in the fight against the Royalist-Covenanter forces in the Third Civil War. He left Henry Ireton in command in Ireland.