Irish Confederate Wars; 1641 to 1653

Almost nothing is known of Jones' career prior to the outbreak of the Irish Rebellion in October 1641; like his brothers Michael and Oliver, he joined the Royal Army raised to suppress it, commanded by the Earl of Ormond. His brother Henry was taken prisoner at the family home in Ballinagh; released in December, he prepared a report of alleged Catholic atrocities, titled "A remonstrance of divers remarkable passages concerning the church and kingdom of Ireland". Later published by the Parliament of England, it played a key role in shaping English and Protestant views of the rebellion.^[4]

In December 1641, Theophilus was appointed captain in Lord Edward Conway's regiment, an infantry unit raised in Ulster.^[5] Ormond's forces in the north were supported by Scots Covenanters under Alexander Leslie, who captured Dungannon in September 1642; Jones was appointed garrison commander before the Catholic Confederacy took it back in spring 1643.^[2] The outbreak of the First English Civil War in August 1642 meant the Irish Army could no longer receive reinforcements or money from England; by mid-1643, the Confederacy held most of Ireland, apart from Ulster, Dublin and Cork City.^[6]

Charles I wanted to use troops from Ireland to defeat his Parliamentarian opponents in England, and in September 1643, Ormond agreed a truce or "Cessation" with the Confederacy.^[7] Factions on both sides objected to the terms, which included negotiations on freedom of worship for Catholics and constitutional reforms. In Ulster, it created a three-way contest between Ormond's Royalists, Confederate troops under Gaelic Catholic leader Eoghan Ó Néill, and Presbyterian militia, known as the Laggan Army, supported by Covenanters under Robert Munro, who were allies of Parliament.^[8]

Michael Jones was among the Irish troops sent to England and defected to Parliament; although they shared his opposition to the truce, Henry and Theophilus remained loyal to Ormond. In return, Theophilus was knighted in early 1644, while Henry was appointed Bishop of Clogher in 1645.^[2] Promoted to Lieutenant-Colonel, Jones was made governor of Lisburn in early 1644. In May, he refused entry to troops led by Munro, appointed Parliamentarian commander in Ulster, but despite refusing to acknowledge orders issued by Parliament the two sides generally co-operated. Jones' regiment was present when Munro was defeated at Benburb in June 1646, although it is not clear whether he was.^[5]

Scarrifholis

Dublin

Lisburn

Ballinagh

Dungannon

Kells

Dundalk

Cloughoughter

Benburb

Theophilus Jones; 1641–1653 campaigns in the North

The First English Civil War ended a few days later when Charles surrendered, and with his approval Ormond signed an alliance with the Confederation to restore him to the throne. However, non-negotiables for Charles, Ormond and Irish Royalists like Theophilus and his brothers was the supremacy of the Protestant Church of Ireland, and acceptance of land settlements made prior to 1641. As a result, the terms were rejected by Ó Néill, whose estates in Ulster had been confiscated in 1610, and a rebel faction who insisted on Catholicism as the national religion.^[9]

Placed in command of Kells, County Antrim, Jones was taken prisoner when it was captured by Ó Néill in December 1646. In June 1647, his brother Michael was appointed Parliamentarian Governor of Dublin in place of Ormond, and the revitalised Protestant army won decisive victories at Dungans Hill and Knocknanauss in August and September 1647. The Confederation now re-opened talks with Ormond, once again opposed by Ó Néill, who agreed a separate truce in August 1648 with Michael Jones; negotiated by Henry Jones, its terms included the release of Theophilus.^[10]

Now firmly on the side of Parliament, Theophilus was sent to London in October to raise fresh troops and money and was present at the Execution of Charles I on 30 January. This action led to an alliance between Ormond, the Confederation, the Laggan Army and Munro's Covenanters, with the objective of restoring his son Charles II.^[11] In early summer, Theophilus returned to Dublin and took part in the Battle of Rathmines, a decisive victory won by his brother Michael over the Ormond-Confederate alliance. After Oliver Cromwell landed with the main expeditionary force in August, Theophilus was left in Dublin; Michael accompanied Cromwell on his autumn campaign and died of disease in December.^[12]

For the next three years, Jones served with Robert Venables in the campaign to subdue Leinster and Ulster, including the battles of Scarrifholis and Lisnagarvey. In April 1653, the last of the rebel leaders in Ulster surrendered to him at Cloughoughter Castle.^[13]

Post 1653

With hostilities at an end, Jones and his brothers remained active in politics, although both Henry and Ambrose refused to accept the removal of bishops from the Church of Ireland. Scotland and Ireland were made part of the Commonwealth of England, with one unified Parliament and in 1656 he was elected to the Second Protectorate Parliament, representing a combined seat for Westmeath, Longford, and King's counties. He also sat in the short-lived Third Protectorate Parliament in 1659, before falling from favour and joining with Henry, Charles Coote and others in overthrowing the Commonwealth government in Ireland.^[2]

Following the Restoration of Charles II in 1660, Jones was appointed to the new Privy Council of Ireland and made Clerk of the Pells in the Exchequer of Ireland. He succeeded his brother Henry as Scoutmaster-General of Ireland in 1661 and represented County Meath in the restored Parliament of Ireland from 1661 to 1666; his brother Oliver was MP for Knocktopher. The diarist Samuel Pepys records having dinner with him in London in September 1661, along with Sir George Ayscue and Sir William Penn, senior officers in the Royal Navy who served in Ireland with Cromwell.^[14]

He helped suppress a Presbyterian-backed plot to seize Dublin Castle in 1662, and effectively retired from public life in 1664; thereafter, much of his time was spent on legal battles over Lucan Manor, an estate awarded to him in 1654. This had been confiscated from Patrick Sarsfield, a senior commander in the Confederacy, whose eldest son Wllliam married Mary Croft, sister of Duke of Monmouth, an illegitimate son of Charles II. William used this connection to have the family lands returned in 1674 and Jones was compensated with lands elsewhere.^[2]

He died in Osbertstown, County Kildare on 2 January 1685, leaving his property to his son Arthur.^[15]