After the execution of King Charles I, Oliver Cromwell was the undisputed leader of Parliament. A Council of State was created in the House of Commons in 1649, with Cromwell as its first chairman. In that capacity, he endorsed the executions of four Royalist leaders who had resisted the new regime in 1648: the Duke of Hamilton, the Earl of Holland, Lord Capel, and Colonel Poyer. The Parliament of 1649–1653 was known as the Rump Parliament, and was plagued by the conflicting views of its members, some of whom favored a purely republican form of government, while others hoped for the restoration of a monarchic power. Cromwell's primary goal in 1649 was to foster unity among his fellows, and he negotiated with the more conservative members by taking a hard line against radical republican groups like the Levellers.
In the spring of 1649, the Levellers became restless, and mutiny broke out among the regiments stationed near Oxford. Cromwell responded swiftly. In May, he rode out before the Army and promised the soldiers that they would have the new regime's full support, and asked them to stand firm against the Levellers. Together with General Fairfax, Cromwell rode out to Oxford to subdue the Levellers. The mutiny was put down, and one of its ringleaders shot.
In addition to the threats posed by a fractured government, Cromwell feared the possibility of a royalist invasion from Scotland or Ireland. Charles I's son, Charles Stuart, the future King Charles II, was in exile, and there were great numbers of people in Ireland and Scotland who still viewed him as their rightful King. In order to preempt a royalist uprising, the English decided on sending an expedition into Ireland to crush the possibility of a royalist upsurge in that country, and 1649, Cromwell was named commander of the expedition. He departed for Ireland with his army in August of that year.
Oliver Cromwell hated the Irish, largely because their loyalty to the Roman Catholic Church. He also desired to exact revenge on the Irish for a massacre of English Protestants that had occurred there in 1641. Cromwell's January 1650 Declaration to the Irish Catholic Clergy provides a good indicator of the sort of mission Cromwell had in mind: "You are part of Antichrist, whose Kingdom the Scriptures so expressly speaks should be laid in blood and ere it be long, you must all of you have blood to drink; even the dregs of the cup of the fury and wrath of God, which will be poured out unto you."
The two great battles of Cromwell's war in Ireland were the siege of Drogheda in September 1649 and the siege of Wexford in October. In both battles, Cromwell's forces behaved brutally, slaughtering civilians as well as Irish soldiers. Cromwell condoned and even encouraged this violence, which he viewed as just punishment for 1641. At Wexford, over 2000 inhabitants were killed inside the city after resisting the English for nine bloody days. The siege at Drogheda was equally brutal. The town resisted for eight days before English cannons brought down the steeple of Saint Mary's Catholic Church on September 11. The first attempt through the breach failed, and Cromwell himself joined in the second assault, which was successful. The English army swept through the town, massacring its citizens. Among those whom Cromwell specifically ordered to be killed were the members of Catholic religious orders, priests, monks, and nuns.
Cromwell's victories in Ireland, brought the entire northeast coast of the country back under the rule of the Dublin Parliament, which was united with England against the royalists. On his return to England, Cromwell was hailed as a hero. This situation further bolstered Cromwell's increasing political power. His warring on foreign soil was not over, however. The young Charles Stuart had arrived in Scotland in June 1650, and he and his royalist supporters threatened to invade England. In response, Cromwell led another preemptive strike against Charles's Scottish allies. Cromwell's strategy in Scotland was very different than it had been in Ireland, however. He was much less willing to shed Scottish blood, and attempted to win support among the Scots through written propaganda. Overall, the war in Scotland was much less successful than the one in Ireland had been, partly because Cromwell did not proceed with the same vengeful zeal. The war dragged on for a year until the Royalists were defeated at Worcester in 1651, effectively ending the struggle for the time being.