You went with major to kill Owen but after. Thomas would later be brought back as a super human being by Owen Routh as part of a secret project with Hans. This project began in the early 1990's, and it involved the use of DNA from Pacari and Hally Salako, resulting in the latter's death. This Thomas would then be stored in the container in Shed 17. After being freed from his container, Thomas proceeded to heal Major Hartley's wound and resurrect Toby, Gordon, Percy, Henry, Keith, and everyone at the Sodorland Border that was affected by the plague

Thomas just stands there being idolised like a guard by the humans Not saying anything