Thomas Smith was a supporter of Elizabeth I and plotted to remove Mary I from power. He was also one of Evelyn Smythe's ancestors.
When the Doctor arrived, it was revealed that Thomas was secretly married to Sarah Whiteside and she was pregnate with his child. Althought the Queen dissaproved of this, The Doctor managed to change her mind and Thomas discovered his child would be named John Smith. the alias of the Doctor. (BFA: The Marian Conspiracy)