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'. In 1585
Gilbert Gifford arrived in Paris for a meeting with Morgan and
Charles Paget, who sent him to England.
Francis Walsingham's agents arrested him at the port of
Rye, East Sussex and he was taken to London for questioning. It appears that Walsingham's persuasive techniques were enough to convince Gifford to spy for him and intercept the letters from
Mary, Queen of Scots which ultimately brought about her downfall and subsequent execution. Gifford even told how Walsingham's chief decipherer, Phelippes 'could take off Morgan to the life'. Spying for Elizabeth in the embassy, Gifford was copying all of the letters exchanged between Thomas and Mary and passing them to Walsingham. Elizabeth's top codebreaker,
Thomas Phelippes, was able to decipher the code used by Thomas Morgan. The plot was discovered, Babington was arrested, and he and his co-conspirators were hung, drawn and quartered. The Jesuits accused Morgan of being the 'setter on' of
Gilbert Gifford and had him 'clapt close prisoner in a miserable dungeon called the Truerenborche' where he remained until the death of
Alexander Farnese, Duke of Parma in December 1593. Thomas Morgan, escaping extradition and a dreadful fate, was thrown into the Bastille and then in another prison in Flanders before finally being set free in 1593. ==Exile and death==