1641, he joined the Royal Army raised to suppress it, and fought under the Earl of Ormonde, who was loyal to Charles I. He took part in a number of outpost skirmishes around Lismore, County Waterford, quickly becoming known as an energetic and capable leader of cavalry. 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. Charles was anxious to use his Irish troops to help him win the war in England, and in September 1643, Ormonde agreed a truce or "Cessation" with the Confederacy. Factions on both sides objected to the terms, which included limited freedom of worship for Catholics and constitutional reforms. 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 Kingdom of Scotland|Scotland]]. Nevertheless, in early 1644 the Confederacy sent a delegation to the Royalist war-time capital in Oxford to begin talks. Now a Major in the Earl of Kildare's regiment, Jones was selected by his Protestant colleagues as part of an informal Commission to represent their views. 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. While his reasons are disputed, the consensus is he believed only a Parliamentarian victory could secure the Church of Ireland, and opposed negotiations with the Confederation. Despite his own dislike of the truce, his brother Henry remained loyal to Ormonde and was rewarded by being appointed Bishop of Clogher in 1645. The war in Ireland cut across religious and political lines, with both Ormonde and the Confederacy claiming to be loyal to Charles. 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. 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