[5] However, the outbreak of the First English Civil War in August 1642 meant Ormonde could no longer receive reinforcements or money from England, and by mid-1643, the Catholic Confederacy held most of Ireland, with the exception of Ulster, Dublin and Cork City.

Protestants saw this as a threat, while many Confederates felt they were on the verge of victory and gained nothing from the truce, particularly since any concessions Charles made to Catholics in Ireland undermined his position in England and Scotland.

Ormonde transferred 6,000 troops from Ireland to the Royalist army in England, including Jones; on discovering this, he withdrew from the Commission and joined Parliamentarian forces under Sir William Brereton in Cheshire.

In Ulster, there was a three sided war between Ormondist Royalists, Gaelic Catholics under Eoghan Ó Néill, and Presbyterian militia, known as the Laggan Army, supported by Scots Covenanters led by Robert Munro.

[9] This made loyalties extremely complex, as demonstrated by Michael's brother Theophilus, commander of a Royalist garrison at Lisburn; although hostile to the Confederacy, in May 1644 he refused entry to Munro, his nominal ally, and later disregarded orders from Parliament.

The nature of this warfare is demonstrated by a raiding party he led through Herefordshire in April 1645, which stole 6,000 sheep, 500 cows and killed 21 people, most of whom died in defence of their property.

[12] He also prevented relief forces reaching the city at Denbigh Green in November, and was appointed Governor when Chester finally surrendered on 6 February 1646.

Named Governor of Dublin, Jones landed on 6 June 1647 with 2,000 troops and quickly enforced a series of measures, including the expulsion of Catholics and arrest of Protestant Royalists; in late July, Ormonde himself was exiled.

On 8 August, Jones won a crushing victory at the Battle of Dungans Hill; more than half of Preston's army of 8,000 was killed or captured, along with their artillery and baggage, and the Confederates lost control of Leinster.

On 22 July, he arrived outside the town with 11,000 men; four days later Jones received reinforcements from Chester under Robert Venables, increasing his strength to 4,000 infantry, and 1,200 cavalry.

'[18] One of the Royalist officers captured at Rathmines was Richard Elliott, son of Michael's sister Mary; Jones demonstrated the bitterness engendered by over eight years of war by executing his nephew.

[21] He also displayed typical energy in immediately seeking to take advantage of this success by marching on Drogheda, but the town refused to surrender and he had insufficient troops to storm it.