Jones, Henry (1605–82), churchman, was eldest of five sons of Lewis Jones (qv), bishop of Killaloe, and Mabel Ussher, daughter of Arland Ussher and his wife Margaret Stanihurst of Dublin. Henry entered TCD in 1616, commenced BA in 1621, and proceeded to MA in 1624, when he was elected to fellowship. He resigned in the following year when his father presented him to the deanery of Ardagh in Cavan. He exchanged this office for the deanery of Kilmore in 1637 (after the combined dioceses of Ardagh and Kilmore were separated in 1633), apparently because he wished to resume his association with its innovative bishop, William Bedell (qv), whose controversial determination to evangelise the Irish in their own language deeply influenced him. In 1638 he was appointed archdeacon in his father’s diocese of Killaloe. Jones was taken prisoner when rebellion broke out in October 1641 and sent to Dublin early in November to deliver a remonstrance to the government, leaving his family as surety. Within weeks of his return he escaped and made his way back to Dublin, where he argued the need to create an official record of losses resulting from the rebellion, to serve as a basis for future restitution or compensation.
On 23 December eight clergy were commissioned to register the claims of the dispossessed and to certify their losses, under Jones's direction. From information about the background to the rebellion contained in depositions collected from refugees, the commissioners concluded that the rebellion was part of an international conspiracy directed by Rome and aimed at the extirpation of both protestants and protestantism. On 19 March 1642 Jones presented a report of the commission's preliminary findings to the English commons, characterising the rebellion as the work of Antichrist and asserting that a massacre of the protestant settlers had been intended. His address was published by order of the house, with an appendix of depositions, and contributed powerfully to the popular perception of the rebellion.
Jones's commission continued to collect depositions until 1647, and Jones deployed the information they contained again when a cessation was concluded with the rebels in September 1643. In an attempt to influence attitudes towards the impending negotiations he presented the Irish council with a lengthy disquisition in which he reviewed the deposition evidence and developed the twin themes of irredeemable Irish barbarism and universal catholic guilt against God. Although the English parliament canvassed his support, Jones remained loyal to the king. He was consecrated bishop of Clogher on 9 November 1645 and appointed vice-chancellor of Dublin University in succession to his uncle, Archbishop James Ussher (qv), in 1646.
The parliamentary commander who replaced Ormond (qv) in June 1647 was Jones's brother Michael (qv). Jones worked closely with him for the next two years, performing confidential secretarial and other tasks, including the negotiation of the release from captivity of their brother Theophilus (qv) as part of a cessation agreement with Owen Roe O'Neill (qv) in August 1648. In 1649 he was appointed scoutmaster-general by Oliver Cromwell (qv) and regularly attended meetings of the army council thereafter. His collection of depositions proved doubly useful. It provided the bulk of the evidence available to the high courts of justice constituted in 1652, at Jones's prompting, to try those responsible for atrocities, and it provided much of the information needed to assess the degrees of guilt and entitlements of the catholic proprietors who were transplanted to Connacht. Jones was officially engaged as a commissioner in both activities from 1652. In 1653 he assisted in the attempt to impose the oath of engagement on Scots presbyterian ministers in Ulster and served on a commission which prepared a plan to move the Scots out of Ulster to a more remote part of Ireland. Inside Trinity, he promoted the revival of arrangements, introduced by William Bedell as provost, to equip students of the ministry with a knowledge of the vernacular.
Late in 1655 he fell out of favour, apparently because he was using his position as scoutmaster to keep watch on baptists as well as on catholics and royalists: in October he was removed from his post and appointed official historian at a reduced salary. In March 1657, on the direct orders of Oliver Cromwell, he received a grant of the tithes of nine abbeys and rectories. Despite his extensive collaboration, Jones's commitment to the regime was strictly secular. While welcoming its anti-catholicism, he was not willing to accept its version of protestantism or its tolerance of radical dissent. He defiantly used his episcopal title until he was ordered to stop doing so in September 1651 and he did not minister in the new state church.
When Richard Cromwell was overthrown in May 1659, Jones was one of three agents sent to London to represent the interests of protestants in Ireland, and in December, with his brother Theophilus, he was among the leaders of the coup d'état which took control of the government and army, and acted as secretary to the council of officers. In the general convention of Ireland he represented Co. Meath, where he had acquired property at Summerhill. In April 1660 he was one of the eight signatories of an invitation to the king to come to Ireland and in the same month Jeremy Taylor (qv) reported that the Jones brothers and Col. Arthur Hill (qv) were in effective control of the army. On 24 May, Henry conducted the thanksgiving service for Charles's restoration in Christ Church. For some time thereafter, his position was uncertain. Through the influence of Sir Charles Coote (qv) he was confirmed in his property acquisitions in November 1660, but he was removed from the vice-chancellorship of the university and allowed to play only a minor part in the concelebrated consecration of two archbishops and ten bishops in January 1661, which marked the reconstitution of the Irish hierarchy.
On 9 April, however, on the recommendation of Archbishop Bramhall (qv) of Armagh, Charles rewarded him for his contribution to the restoration by ordering his translation to the bishopric of Meath, which carried with it a seat on the Irish council. Jones conducted himself circumspectly. Presiding at the installation of his brother Ambrose as bishop of Kildare in June 1667, he took the opportunity to display his own orthodoxy by refuting the scriptural and historical arguments for presbyterianism and affirming his belief in the apostolic nature of episcopacy. It seems to have been at this time that he presented the illuminated manuscript books of Kells and Durrow to Trinity College.
He devoted an increasing amount of his attention to promoting the preparation for publication of the Gaelic translation of the Old Testament that William Bedell had presided over, the manuscript of which he himself had saved. In 1676 he delivered and published A sermon of Antichrist in which he avowed his unaltered conviction that the Antichrist was at work in Rome and insisted that the way to defeat him was to make the word of God available to catholics in their own language. Two years later, preaching at the funeral of the archbishop of Dublin, he briskly dispatched the deceased and presented William Bedell, who had had the will to convert the Irish and the wisdom to do so in Irish, as a model of apostolic episcopacy. The ‘Popish plot’ energised Jones. A London edition of Antichrist was published in 1678, his assistance was courted by Shaftesbury, and he became involved in the proceedings against Archbishop Oliver Plunkett (qv), who was accused of complicity in a plot to bring a French invasion force to Ireland. He befriended the accusers, arranged for witnesses and information to be sent to the opposition in England, and helped to have the trial removed to London, where Plunkett was convicted and executed in 1681.
Jones died on 5 January 1682 and was buried in St Andrew's church in Dublin. He was married twice: first, to Jane, daughter of Sir Hugh Culme of Cloughoughter, Co. Cavan, with whom he had two sons and a daughter, and who was alive in 1641; secondly (1646) to Mary, daughter of Sir William Piers of Westmeath and Martha Ware, with whom he had two sons and five daughters.