The appointment of Thomas Wentworth (later earl of Strafford) in 1632 as Lord Deputy in Ireland initiated a period of government, the primary objective of which was to turn Ireland into a major revenue source for the English crown, by reducing the power of the magnates, imposing a Laudian church discipline and boosting Irish industries. At the outbreak of the King's war against the Scots in 1639, Wentworth mustered an army of 9,000 men to use in Scotland, but his downfall in the same year led to the disbandment of his army by the Long Parliament. Rule from Dublin by Lords Justices Parsons and Borlase exacerbated Irish feelings, and on 23 October 1641 it was planned to seize Dublin Castle as the signal for general revolt. The Irish leaders, Rory O'More and Conor Maguire, failed in their attempt, but in Ulster and Leinster the Irish rose against the Anglo-Scottish colonists with considerable slaughter. The Long Parliament proposed the extensive sale of rebel lands to raise money to finance a war against the rebels, but the process was slow, and the government troops were on the defensive. Rory O'More won a victory at Julianstown in November 1641, effected an alliance with the Anglo-Irish landowners of the Pale (that is the area around Dublin where there had been extensive English colonisation) and widespread revolt followed. Ulster fell almost entirely into Irish hands; Connacht and Munster were in arms. In April 1642 a Scottish army landed at Carrickfergus under Munroe to suppress the rising, the Scottish planter elements rallied to him, and the collapse of monarchical government in England by August 1642 followed by civil war, meant that Ireland was left very much to itself. In consequence, Munroe's army acted on behalf of King and parliament, whilst the earl of Ormond, Charles's Lieutenant in the country, mustered a royalist army. The Roman Catholic rebels in October 1642 established the Catholic Confederacy of Kilkenny under Rory O'More, avowing principles both Catholic and royalist, determined to restore the Catholic Church, but fearful of the results of a parliamentarian victory in the struggle against the King. The Confederacy was more or less split between outright royalists and outright Gaelic nationalists, led respectively by Thomas Preston Viscount Tara and Owen Roe O'Neill. The earl of Ormond routed Preston at New Ross in March 1643, and the real Confederate struggle was carried on by O'Neill in Ulster.
The gradual triumph of the Parliament in England led the King to entertain hopes of Irish aid quite apart from the regiments ferried over to assist him late in 1643 from Ormond's army. In August 1645 the earl of Glamorgan arrived in Ireland to treat with the Confederates for a cessation of arms and the despatch of 10, 000 fighting men into England, but the talks came to nothing. On 5 June 1646 O'Neill's army won a major victory at Benburb in County Tyrone over Munroe and the Laggan Army of the north-east, killing 3,000 men. In August, in desperation, Ormond was empowered by the King to offer peace to the Confederates but O'Neill, stiffened by Rinuccini the Papal Nuncio, turned down the terms in February 1647. On 28 July, the marquess of Ormond surrendered his authority and Dublin to Michael Jones who came from the Parliament in London with 8,000 men. Thomas Preston tried to drive Jones out of the capital, but was routed at Dangan Hill with heavy losses. On 13 November the Lord Inchiquin, long loyal to the directives of the London
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Parliament as they were fed through Dublin, defeated the Catholic army of the Lord Taafe at Knockanoss in Munster. The 1648 uprisings in England, and the shift in allegiance of part of the Scottish leadership, led to changes in Ireland too. Inchiquin went over to the royalists, Ormond returned in September to lead a royalist army, and the stiff hand of Rinuccini was removed from O'Neill when the Italian left Ireland in February 1649. Six months later, Cromwell landed and entered Dublin.
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