Thomas Smith was a supporter of Elizabeth I. He plotted to remove Mary I from power in 1554. He was also one of Evelyn Smythe's distant ancestors.
Shortly after the the Sixth Doctor's arrival, it was revealed that Thomas was secretly married to Lady Sarah Whiteside, one of Queen Mary's ladies-in-waiting, who was pregnant with his child. Although the Queen disapproved of this, the Doctor changed her mind. Thomas discovered his child would be named John Smith, one of the Doctor's aliases. His son later became a prominent member of Queen Elizabeth's court. (BFA: The Marian Conspiracy)