Captain Thomas Lee died 1601

Thomas Lee, an English Protestant who was a half-first cousin to Sir Henry Lee, Quarendon, Buckinghamshire, came to Ireland as an undertaker in 1574, and was given land.
His lineage is as follows: Sir Robert Lee who died 1539, married firstly, a Miss Cope, and there were two sons, Anthony, who married a Miss Wyatt, and died in 1549, having had Sir Henry Lee, born 1588 died 1611, and Robert's other son was Francis Jesse(?).
Sir Robert secondly married in 1531, Lettice Poniston, who died 1557, and there were three children, Benedict, Elizabeth, and Margaret. Benedict, who married Margaret Pakington, had William, who married Judith Wirley; and Thomas.
By the terms of his grant Thomas Lee gave an 'undertaking' to maintain his principal dwelling on his estate, to use English language and dress, to keep in his employ or as a tenant no Irishman able to bear arms who was born outside the county, and not to part with any of his lands without the consent of the Lord Deputy. Any female of his family who married an Irishman should forfeit her inheritance or dowry.
He married Elizabeth Eustace, wealthy widow of John Eustace, whose maiden name had been Peppard, who was described as a 'mere Irish' (ie native: from merus, which is Latin; pure, unmixed; but, contrarily, her maiden name and married name were Anglo-Norman), and who acted as his translator. They had two children, Henry who died in 1657, and Margaret, who married a Charles Manners.
He and Elizabeth separated in 1587, when, while translating for him, she discovered and revealed his plot to capture Walter Reagh Fitzgerald by deception, but they were reconciled some time later.
When Elizabeth died, he married, secondly, Kinborowghe Valentine.
He was employed by the Crown to protect the borders of the Pale against raids by the Irish, and he campaigned against the O'Moores and O'Tooles, as Captain-General of the Kern (foot-soldiers). He owned a substantial estate in Kildare, and bought or built a castle at Castlereban, on the river Barrow, north of Athy, on a site obtained from Sir Walter Fitzgerald, otherwise known as Sir Walter de St Michael.
He was active in the campaign in which Sir Henry Bagenal and Hugh O'Neill were slightly injured while suppressing the revolt of Hugh Maguire in a rout at Beleek on 10th October 1593, and he was on friendly terms with them, to the extent that he allowed both to claim credit for his own efforts.
In 1594, he wrote a tract entitled A Brief Declaration of the Government of Ireland, in which he described the hanging of Hugh Gaveloc O'Neill by the Earl of Tyrone, to clear the way for his own leadership of the O'Neill;
'And where the earl's adversaries have, in times past, incensed your majesty against him, for hanging and cutting off one Hugh Gaveloc, a notable traitor, and son to Shane O'Neale, informing your majesty the said Hugh was your majesty's subject; it shall be well proved that he [Gaveloc], was ever a traitor against your majesty, a daily practiser with foreigners [as the Scots and others], for the disturbances of that kingdom, and one who sought, by all means, to overthrow the earl who, by martial law, which he then had, did cut him off for his offences. For the doing whereof he did incur your highness's displeasure; and the said martial law, which kept the whole country in awe, was taken from him; the want whereof has made his country people grow insolent against him, and careless of observing any humanity or duty; which hath bred the outrages now in practice, so that in my poor opinion, it were requisite the same authority were restored unto him.'
Lee accompanied Sir William Russell into Wicklow to hunt for Fiach McHugh O'Byrne early in 1597. Relatives of the outlaw had given away his hiding place, and on 8 May, when O'Byrne was attempting to escape from Russell's column, he ran into Lee. O'Byrne was captured and killed by Lee's men when he hid in a cave.
Lee had the outlaw's head preserved in salt and sent to the Queen, to claim his reward, signing his letter 'your bog Irishman'. The impropriety of dealing directly with Elizabeth in this manner became a cause for anger when the court officials needed to defend themselves against criticism for the embarrassing loss of the outlaw's head, which had been found in a tree in someone's garden, in Enfield Chase.
Lee became more disenchanted with the English court, his sympathies began to change towards the Irish, and he 'went native', wearing the garb of a Gaelic chieftain, and becoming involved in skirmishes with various landowners and sheriffs.
His friendship with O'Neill and Bagenal became a problem after they became enemies.
Hugh O'Neill had eloped with Henry Bagenal's sister Mabel, and then married her under circumstances of dubious legality, as he had at least one other wife. By the time Bagenal and O'Neill met at the Yellow Ford in August 1598, the cause of Ireland may have been intertwined with an in-law squabble, as O'Neill's womanising had by now driven Mabel to run away. She was to return to live with him again for a time before her early death.
Bagenal's forces were already close to defeat when he was shot in the face and killed, after he lifted the visor of his helmet to have a look around.
Also killed was a Thomas Leigh, (or Lee in some versions), who was one of the captains of an advance party with Bagenal's army. The advance force was wiped out.
[Thomas Leigh had two brothers, Urian Leigh, and Ed. Leigh. Sir Urian Leigh is mentioned by a traveller in Ireland, William Brereton, who arrived in Carrickfergus in 1635, and while suffering from constant diarrhoea, was advised by Leigh to burn sage wood on hot coals in a container, which he should then place under himself while on the toilet. Brereton concluded that drinking whiskey was more efficacious.]
After the defeat, Thomas Lee's friendship with O'Neill came under suspicion, and he was jailed in Dublin castle for a few months, suspected of aiding the Irish with information.
On 12 February 1601 Lee was arrested in England, having gone there in support of Robert Deveraux, second Earl of Essex, returning from a disastrous and expensive campaign in Ireland. Essex was in disgrace for having made peace with O'Neill, when he had been expected to defeat him. Essex had attempted to foment a rebellion against Elizabeth.
Lee was apprehended while secretly watching the Queen in her chamber (according to one version, in Notes and Queries, 1943, he waited under her bed), as part of his plot to hold her to ransom his friends the Earls of Essex and Southampton, who were both under suspicion of conspiracy against the Queen. He was tried the day following his arrest, was found guilty, and was hanged drawn and quartered the next morning at Tyburn, at the site of Marble Arch, in London.
Essex, being of noble birth, was spared the hanging, and was beheaded for treason.
In the Genealogical Office, in Dublin, there are manuscript letters regarding Lee's views on the problems of Ireland. There are also records of letters from his cousin, Sir Richard Lee, supported by Richard's brother, Sir Harry Lee, to Elizabeth I, asking her not to confiscate the property in county Kildare, because of the suffering which would be caused to Lee's son.
Other subsequent letters applying for a grant of the land, indicate that it was indeed confiscated, as part of the punishment for treason.
Thomas Lee's portrait, painted in 1594 by Marcus Gheevaerts, showing him in an exaggerated pose and the attire of a Gaelic chieftain, is in the Tate gallery, London. The same artist was commissioned by Sir Henry Lee to paint Queen Elizabeth at Ditchley, suggesting a close connection between the two men.

Portrait of Captain Thomas Lee  1594
Oil on canvas
support: 2305 x 1508 mm
Purchased with assistance from the Friends of the Tate Gallery, the National Art Collections Fund and the Pilgrim Trust 1980

Thomas was related to Sir Henry Lee, Elizabeth I's Champion and creator of imagery for her annual Accession Day celebrations. Henry may have helped devise the complex symbolism of this portrait. Thomas served in the English colonial forces in
Ireland . His bare legs are a fantasy evocation both of the dress of an Irish soldier, and that of a Roman hero.
Thomas was suspected of treachery to
Elizabeth and visited London in 1594 partly to refute this. The Latin inscription in the tree refers to the Roman Mucius Scaevola, who stayed true to Rome even when among its enemies. Lee implies that he too is faithful.  (From the display caption February 2004)

In simple terms, Thomas Lee was a manifestation of the problem of an ambassador who comes under the sway of those he should wield influence over; but he also lived at the point of contact between the forces for old and new; the old being the policy of the Crown of persuading the Irish to adopt English ways, and the new being the Crown's growing impatience with the old Gaelic system, and a people increasingly depicted by contemporary English writers as immoral, warlike, and beyond civilising, an attitude which would lead to the disaster at Kinsale, and the Flight of the Earls.
Descendants may not have wished to be known as the children of a traitor, so finding records of them may be difficult. His children would have been contemporaneous with the Leighes given land in Tyrone in 1609.
In some texts, he is titled Sir Thomas Lee, but this is probably in error; there was a Baronet of that name and title who died in 1691, who had been an MP for Aylesbury, and later, Bucks, in England.
He was known to O'Neill and others as Tom, and in many cases, his surname is spelt Lea.
He was a kinsman to Sir Ralph Lane.