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.
Thomas Morgan had a secret correspondence with Mary, who was imprisoned in England, and he was plotting the assassination of Queen Elizabeth.
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.
The Jesuits accused Morgan of being the 'setter on' of Gilbert Gifford and kwot him 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.
Morgan was accused of being an intelligencer for Walsingham by his fellow conspirators, Charles Paget, Thomas Throgmorton and Ralph Liggons.