Confederates, and this infighting hampered their preparations to resist a Parliamentarian invasion. In August 1649, a large English Parliamentarian army, led by Oliver Cromwell, invaded Ireland. It besieged and captured many towns from the Confederate–Royalist alliance. Cromwell's army massacred many soldiers and civilians after storming the towns of Drogheda and Wexford. The Confederate capital Kilkenny was captured in March 1650, and the Confederate–Royalist alliance was eventually defeated with the capture of Galway in May 1652. Confederates continued a guerrilla campaign until April 1653. This saw widespread killing of civilians and destruction of foodstuffs by the English army, who also brought an outbreak of bubonic plague. After the war, Ireland was occupied and annexed by the English Commonwealth, a republic which lasted until 1660. Catholicism was repressed, most Catholic-owned land was confiscated, and tens of thousands of Irish rebels were sent to the Caribbean or Virginia as indentured servants or joined Catholic armies in Europe. Overview The war in Ireland began with the Rebellion of 1641 in Ulster in October, during which many Scots and English Protestant settlers were killed. The rebellion spread throughout the country and at Kilkenny in 1642 the Association of The Confederate Catholics of Ireland was formed to organise the Catholic war effort. The Confederation was essentially an independent state and was a coalition of all shades of Irish Catholic society, both Gaelic and Old English. The Irish Confederates professed to side with the English Cavaliers during the ensuing civil wars, but mostly fought their own war in defence of the Catholic landed class's interests. The Confederates ruled much of Ireland as a de facto sovereign state until 1649, and proclaimed their loyalty to Charles I. From 1642 to 1649, the Confederates fought against Scottish Covenanter and English Parliamentarian armies in Ireland. The Confederates, in the context of the English Civil War, were loosely allied with the English Royalists, but were divided over whether to send military help to them in the war there. Ultimately, they never sent troops to England, but did send an expedition to help the Scottish Royalists, sparking the Scottish Civil War. The wars produced an extremely fractured array of forces in Ireland. The Protestant forces were split into three main factions (English Royalist, English Parliamentarian and Scottish Covenanter) as a result of the civil wars in England and Scotland. The Catholic Confederates themselves split on more than one occasion over the issue