The marquess of Ormond's revitalised royalist army failed to take Dublin early in 1649, being defeated at the battle of Baggot-rath by Michael Jones. Cromwell, with 20,000 men, entered the capital on 15 August with the set purpose of punishing the Irish confederates and of restoring Ireland to order. He struck first at Drogheda where, after storming the defences, he allowed a general massacre to take place, leading to 3,000 or more deaths including those of royalist fugitives from England. Essentially, he was at first fighting against royalist forces, a combination of Ormond's, O'Neill's and Inchiquin's troops, but the royalists' best general, Owen Roe O'Neill, died in November 1649, and there was no general capable of standing against Cromwell and his powerful army. From Drogheda, Cromwell went on to storm and massacre at Wexford on 11 October, whilst other forces began to reduce Ulster and Munster. Cromwell's march led him to Ross, Carrick, Clonmel and Kilkenny, all of which surrendered to him after attack and considerable bloodshed. Only at Clonmel was Cromwell given a temporary repulse, by Hugh O 'Neill, nephew of Owen Roe, on 9 May 1650. By this time, loyal troops from Ulster were operating in southern Ireland, and on 26 May Cromwell left for England.
His successor as Lord Lieutenant and commander of the army was his son-in-law, Henry Ireton. Ormond, Inchiquin and Thomas Preston had all fled overseas, but the royalist forces were still numerous. In June, the last Ulster army of the O'Neills was defeated at Scarrifhollis, and Owen Roe's son Henry was murdered after being taken prisoner by the English commander, Coote. Hugh O'Neill surrendered Limerick to Ireton in October 1651, Galway collapsed in 1652, and the 30,000 or so men of the royalist field armies now remained to be dealt with. The government made it easy for them to take ship into Europe to pursue their military careers at a distance, but the anti-Irish propaganda based on atrocity stories of the 1641 rising led to many thousands more being trans ported into the colonies as slave labour. A High Court of Justice was established in Dublin which sent more than 50 to their deaths, although Owen Roe O'Neill and Rory O'More had already died, so avoiding public execution. In August 1652 the English Parliament passed the Act of Settlement as a means of dealing with the problem of the Catholic Irish for good and all. Nine Irish counties were seized to settle the arrears of pay of the government army and to satisfy the investors who had financed the war against the rebels in 1641/2. In 1653 Ireland was divided into two parts, with Connacht and Clare set aside as a reservation for the native Irish provided they did not settle within four miles of the sea coast. The landowners of Catholic or royalist sympathy were vigorously transplanted beyond the Shannon, the town corporations purged, and the Laudian church disestablished.
Cromwell ruled as Lord Protector of England and Ireland from December 1653 to his death in 1658, and was represented in Ireland firstly by Charles Fleetwood and then by Cromwell's son Henry, under both of whom the operation of the Act of Settlement was furthered. The objective seems to have been to install on Irish land a resident government army almost 20,000 strong, occupying over 10,000,000 acres; although some soldiers sold up and returned to England, the infusion of Protestant, sectarian men and their families
into Ireland created a permanent balance in favour of English authority. MPs were sent from Ireland to the Parliament at Westminster from 1653 and only the death of Cromwell in September 1658 brought the process to an end. Charles II was proclaimed King in Dublin in May 1660 without resistance, the army leaders choosing to follow the example of Monck in England. Charles II acknowledged their active aid or acquiescence by allowing the old rulers to remain in power and sanctioning their positions with titles. The old Irish royalists gained virtually nothing for their loyalty or their endurance.
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