Thomas Morgan of Llantarnam (or Bassaleg, a branch of the Morgan of Tredegar) (1546–1606), of the Welsh Morgan of Monmouthshire, was a confidant and spy for Mary, Queen of Scots, and was involved in the Babington plot to kill Queen Elizabeth I of England. In his youth, Thomas, a staunch Catholic, worked as Secretary of the Archbishop of York until 1568, and then for Lord Shrewsbury who had Mary under his care at this time. Morgan's Catholic leanings soon brought him into the confidence of the Scottish queen and Mary enlisted Morgan as her secretary and go-between for the period extending between 1569 -1572 which coincinded with a series of important conspiracies against Elizabeth. Morgan was imprisoned for 3 years in the Tower of London before exiling himself to France.
In 1584 Morgan was dispatched to Paris with letters from Mary to her supporters at the French court. He met up with Dr. William Parry and the pair hatched a plan to kill the queen. Parry was arrested in England and charged with High Treason but he pleaded that he was a secret agent trying to discover the Catholic's treasons. One of the charges brought against Mary in 1586 involved her involvement with Morgan, charge no. 8 read 'Her Servant Morgan practising with Parry for the killing of her Majesty and the favouring and maintaining of him, since the said Queen did know that he was the principal persuader of Parry to attempt that most wicked act'. Morgan strenuously denied his involvement in his secret letters to Mary who chose to believe him. Thomas Morgan had a secret correspondence with Mary who was imprisoned in England, and was plotting the assassination of Queen Elizabeth. In 1584 he may have been involved in the production of Leicester's Commonwealth, a scurrilous tract attacking Robert Dudley, 1st Earl of Leicester, Elizabeth's powerful favourite. The book was widely circulated in England. It contained a detailed argument that Mary should succeed Elizabeth to the throne. Francis Walsingham, the chief of Elizabeth's intelligence service, believed him to be the author.
Morgan and Charles Paget recruited Anthony Babington, a young English nobleman ready to give his life for Mary, to murder Queen Elizabeth I in the famous Babington plot. Lewes Lewkenor described Morgan as 'a man not inferior to any of them all in drifts of policy'.