[3] 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".

[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.

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.

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.

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.

[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.

[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.