Jones, Sir Theophilus (d. 1685), scoutmaster-general of the army in Ireland, was youngest of the five sons of Lewis Jones (qv) (c.1560–1646), bishop of Killaloe, and Mabel Ussher, daughter of Arland Ussher and his wife Margaret Stanihurst. He was in England in the service of the earl of Leicester, the recently appointed lord lieutenant of Ireland, when rebellion broke out in October 1641, and was appointed captain in Lord Conway's (qv) ‘British regiment’, which was established for service in Ulster by the English parliament in December 1641. He campaigned mainly in north-east and mid Ulster, rose to effective command as lieutenant-colonel, and was knighted by Ormond (qv) early in 1644.
When Robert Monro (qv) received a parliamentary commission to command all the Ulster forces, Jones refused to admit him to Lisnegarvey in May 1644. He subsequently coordinated his efforts with those of Monro, but he continued to uphold Ormond's authority in Ulster, refused to subscribe to the covenant, defied the authority of the parliamentary commissioners who arrived in the province in October 1645, and resisted the parliamentary appointment of Lord Blaney as colonel of the regiment. After the first Ormond peace in July 1646 he moved to Leinster, where he was surprised at Kells by Henry Roe O'Neill early in 1647. He remained a prisoner till August 1648, when he was released under the terms of a cessation between Owen Roe O'Neill (qv) and the parliamentary commander, his brother Michael (qv), negotiated by his brother Henry (qv), bishop of Clogher. Some months later, he went to England to recruit soldiers on Michael's behalf.
In the early summer of 1649 he was sent to Ireland with provisions and money in advance of Cromwell's expeditionary force. He served briefly as governor of Dublin before returning to the north, where he contributed to the defeat of George Monro (qv) and the royalists near Lisnegarvey (November 1649). After Michael's death (December 1649) Theophilus took command of his regiment and served till the end of the war, when he forced the surrender of the last garrison to fall, Cloughoughter in Co. Cavan, on 27 April 1653. Later in that year Jones was appointed major of the regiment of Lieut.-gen. Ludlow (qv) and he subsequently commanded the lifeguard of Henry Cromwell (qv).
He was a member of all three protectorate parliaments and voted for the kingship petition in 1657. In the summer of 1659, when the ‘Rump’ of the Long Parliament regained power, Jones was cashiered. He was one of the leaders of the coup d'état in Dublin in December 1659 and played an influential part in the meeting of the council of officers that called for the readmission of the excluded members of the Long Parliament on 16 February 1660. In the general convention of Ireland he represented Co. Dublin, where he had received a grant of the forfeited Sarsfield estate in 1654. With Col. Arthur Hill (qv), Theophilus and his brother Henry were reported to the king as being in control of the army, and both signed an invitation to him to come to Ireland. Theophilus was one of the commissioners sent by the convention to negotiate with Charles II in May 1660.
He was appointed clerk of the pells (July), a privy councillor (December), scoutmaster-general (February 1661), and a member of the commission for executing the king's declaration for settling Irish lands (April). In the restoration parliament, he proposed the contentious private bill to raise £30,000 for the use of the duke of Ormond on his appointment to the lord lieutenancy in 1662. In the following year, he disclosed an attempt on the part of discontented former army officers to secure his support for a plot to seize Dublin castle and kidnap Ormond.
Thereafter, though he retained his military duties, Jones chiefly attended to his private affairs. In January 1661, with others who had distinguished themselves in the king's interest, Jones had been confirmed in all the lands ‘settled or intended to have been settled’ on him ‘by any gift, grant or order of any power or usurped power’ (CSPI, 1660–62, 189). In the event, the interests of the Sarsfield claimant to the Dublin estate were favourably ruled on by the court of claims and protected in the act of explanation in 1665, leaving Jones with only a life interest. In 1674, after the reversionary heir married the duke of Monmouth's sister, the crown bought Jones's interest and granted him £800 a year in concealed land to be discovered elsewhere. He appears to have devoted much of his energy to finding suitable land, and had succeeded in completing the transaction before his death. The interests that he had acquired in Co. Sligo were confirmed to him in February 1670.
Jones died in Osbertstown, Co. Kildare, on 2 January 1685 and was buried at Naas. He was survived by his wife, Alice, daughter of Arthur Ussher and Judith, daughter of Sir Robert Newcomen, and by their son Arthur and daughters Judith and Mabella.