He was not there long. Even though England was totally safe for him, and he had already been preferred by a king who admired him, and had married an English girl, complaining that he was not accepted by the Protestants and could not find advancement because of them he set sail for Rome with his wife. Pope Paul V immediately drew what may have been the correct conclusion and threw him into prison as a spy. However, the good pope changed his mind shortly, perhaps still hoping to reconvert the son of Mary, Queen of Scots, and decided accept the matter graciously, placing Thomas in Italy. He used his influence with Cosimo II de' Medici, Grand Duke of Tuscany, to get Thomas appointed to the professorship of the "Pandects" at Pisa. The Grand Duke commissioned him also to write a definitive work on the Etruscans.