The process by which the TCD collection was assembled and organized has yet to be fully reconstructed. When the ‘Athlone commissioners’ were appointed on 28 December 1654 to adjudicate the cases of proprietors who claimed to qualify for transplantation to estates in Connacht under the terms of the Act for Settling Ireland (12 August 1652), the information provided to them included the original Dublin and Munster depositions, together with various indexes and abstracts of their contents. Since these aids included an index to the examinations taken by the high courts of justice (MS 841), it is reasonable to infer that the examinations themselves were also made available. When the commissioners completed their task in September 1656 the ‘books’ of evidence were returned to Dublin where in due course they were lodged in an office of ‘discriminations’, in the care of seven sub-commissioners for discriminations appointed to execute the King’s declaration of 30 November 1660. Extensive use of the material was made by the Court of Claims, which was appointed to administer the Act of Settlement (27 September 1662), and its records show that the miscellaneous examinations taken by government officers in the 1640s were then included in the books.

John Temple, The Irish rebellion: or, an history of the beginnings and first progress of the general rebellion raised within the kingdom of Ireland … in the year 1641 (London, 1646), produced by the courtesy of the Board of Trinity College, Dublin.

Henry Jones, A remonstrance of divers remarkable passages concerning the church and kingdom of Ireland (London, 1642), produced by the courtesy of the Board of Trinity College, Dublin.

In 1670 the books were delivered into the custody of the clerk of the council, Matthew Barry. Eight years before, on 19 December 1662, Henry Jones and Henry Brereton had presented Barry, on behalf of the council, with the county sets of Waring copies. At an unknown date, Barry, who continued as clerk until he was replaced by James II (27 August 1689) and who died in 1696, sold the parts of the archive that now comprise the ‘1641 depositions’ to the collector John Madden. The remainder, which included invaluable captured records of the Confederate Catholics and the records of the “Athlone Commission’ itself, was not included in the transaction. Madden died in 1702 and his widow sold his manuscript collection, sometime before 1708, to John Stearne, later bishop of Dromore and Clogher (1713-17, 1717-45), who presented them to Trinity College Dublin in 1741 in commemoration of the centenary of the rebellion. They were at once bound in volumes according to the county to which each document referred. Whether this indiscriminate shuffling together of the distinct sets of records took place at the time when the original archive was divided for the sale to Madden, at the time of binding, or sometime in between is as yet unknown.