Lee, Thomas (c.1550–1601), army captain and author, was second son of Benedict Lee of Oxfordshire, England, and cousin of the influential Elizabethan courtier Sir Henry Lee; his mother was Margaret, daughter of Robert Packington of Worcestershire. He first came to Ireland in 1573 with his kinsman, the 1st earl of Essex (qv), serving as a captain of horse and provost-marshal in the ‘enterprise of Ulster’ and as warder of Carrickfergus (May 1574–October 1575).
He was arraigned for highway robbery in Oxfordshire in May 1580 and reappeared in Ireland in 1581 as a captain of horse in the forces that put down the Baltinglass rebellion. He was credited with the capture of Thomas Eustace, brother of Viscount Baltinglass (qv). An incursion into the Tipperary territory of Thomas Butler (qv), earl of Ormond, where his company ran amok, earned him the earl's enduring hostility. Lee's company was cashiered as soon as peace was restored, but he was modestly rewarded in 1583 with a custodiam of confiscated Baltinglass land on the southern border of the Pale. He exchanged this a year later for a lease on assorted monastic property, acquired an estate at Castlemartin, Co. Kildare, through his marriage to Elizabeth Peppard, and secured a lease on enfeoffed lands at Castle Rebane in the same county. These acquisitions were accompanied by continuous quarrels with other interested parties, in the course of which he repudiated his wife in 1587 and spent some time in Dublin castle in the same year.
His relations with the Dublin administration were equally fraught. Late in 1583, against its wishes, he received a commission to defend the borders of Kildare with a force of fifty foot and twenty-five horse. His actions in this role were subject to repeated criticism and interference, chiefly prompted by Sir Nicholas White (qv), Ormond's client on the Irish council. Lee responded with repeated complaints, and in 1590 brought charges against White to the privy council in London.
In the autumn of 1593 Lee fought alongside Hugh O'Neill (qv) in the forces sent to suppress the revolt of Hugh Maguire (qv) in Ulster, and was extravagantly praised by him for his valour in the battle of the Erne ford. A friendship developed between the two, and in the following March, when a government commission entered into negotiations with O'Neill in a bid to prevent conflict in the north, Lee acted as intermediary. O'Neill submitted a list of grievances protesting against the corruption and arbitrary manner of the administration of the lord deputy, Sir William Fitzwilliam (qv). Lee was sympathetic to this view of Fitzwilliam and shortly afterwards developed the theme in a lengthy attack on Fitzwilliam's government in which he enumerated acts of misgovernment, criticised the conduct of the war against Maguire, and recommended that an independent commission should inquire into the lord deputy's record. In May 1594 he declared his intention of attending the royal court, but Fitzwilliam took steps to prevent him from being received by the queen.
Lee's riposte was to prepare a diffuse treatise on the government of Ireland in which he elaborated his original thesis, attributed the present crisis to a well founded breakdown of trust, and proposed to resolve it by mediating between the queen and O'Neill. At the same time, he advertised his suitability for this task by commissioning from Marcus Gheeraets an allegorical portrait which evoked Livy's passage on Caius Mucius Scaevola, who was captured by the rebel Etruscans and succeeded in concluding a peace treaty with them, for which he was rewarded with a grant of land. Lee seems to have presented his treatise to Elizabeth late in 1594; but the secretary of state, Lord Burghley, was anxious to protect Fitzwilliam, and this ingenious job application, of which the pictorial element now hangs in the Tate Gallery, London, was unsuccessful.
Lee resumed his position as captain of horse in Ireland, where Fitzwilliam's successor, Sir William Russell (qv), appointed him general of the kerne in February 1596. With the queen's approval he held a brief, exploratory meeting with O'Neill in August 1596, but it yielded nothing. He scored a notable success in May 1597 when his company hunted down and killed the Wicklow rebel chief Fiach MacHugh O'Byrne (qv). Lee received the queen's commendation and a custodiam of a large part of O'Byrne's land, but the departure of Russell left him exposed. Through Ormond's influence the custodiam was quickly revoked and Lee was removed from his command, accused of treason, and (February 1598) committed to Dublin castle. The charges, which referred to both his conduct in Wicklow and his familiarity with O'Neill, were numerous but unsustainable and he was released on bail in July 1598. He retired to Castle Rebane and became involved in a conspiracy against Ormond, which he disclosed to Bishop Neylan of Kildare, who informed the Irish council. After a hearing at Dublin castle at which he denounced Ormond as the instigator of the rebellion, Lee was again committed to prison, in November 1598. His release was ordered by his cousin, the new lord lieutenant, the earl of Essex (qv), in April 1599, on condition of a public apology to Ormond and he was restored to his command.
He played an active but subordinate part in the subsequent campaign, and had an opportunity to put his influence with O'Neill to the test when the two men met secretly in early August, with the knowledge of the marshal of the army, Sir Christopher Blount (d. 1601). At the meeting, arranged at O'Neill's request, Lee encountered a transformed O'Neill. No longer concerned to make use of Lee's influence at Elizabeth's court, O'Neill was arrogant, boastful, and uninterested in compromise or negotiation: the object of the meeting was to use Lee as a means of conveying the strength of his confidence to the government. Although Lee never admitted that he had been duped into becoming an apologist for O'Neill, his third and last treatise leaves little doubt of his disillusionment.
‘The discovery and recovery of Ireland with the author's apology’ was written under house arrest after Lee had accompanied Essex on his unauthorised return to England in September 1599. The ‘discovery’ section repeated his previous analysis of the causes of the war, with the addition of accusations against secret traitors, the majority of whom were Anglo-Irish gentry and great lords, and the chief of whom was an unnamed figure clearly identifiable as the earl of Ormond. In the ‘recovery’ section he abandoned his earlier preoccupation with outlining the conditions under which the Irish might be conciliated, and set out a detailed strategy for the reconquest of the country, claiming for himself the initial task, the assertion of control over Leinster, for which his local knowledge qualified him. The ‘apology’ was a prolix defence of his record. Neither the treatise nor the mediation of Sir Henry Lee succeeded in rehabilitating Lee in the queen's favour. He was not a party to Essex's attempted coup d'état on 8 February 1601, but four days later he canvassed support for a plan to seize the queen and force her to release Essex. He was arrested the same day and executed for treason at Tyburn on February 14.
Lee was married twice, first to Elizabeth Eustace (antea Peppard), and secondly to Kinborough Valentine, both of whom were catholics; he had at least two children, a son and a daughter.