Dr. Thomas Wayne is the posthumous overarching antagonist in Batman: The Telltale Series. A billionaire and doctor based in Gotham, he was the father of Bruce Wayne. When Thomas and his wife, Martha, were murdered by Joe Chill, they inspired Bruce to pursue a life of crime fighting. During the events of the series, it was revealed that Thomas had ties to crime lord Carmine Falcone and corrupt mayor Hamilton Hill.
Thomas Wayne was a prominent doctor in Gotham, and, to the public, a humanitarian. However, in reality, he was an associate of the Falcone Crime Syndicate and was partners with both its leader Carmine Falcone and Mayor Hamilton Hill. While Carmine acted as a fall guy and collected profits for the others, Hamilton controlled City Hall and its politics, and Thomas laundered the money and legalized many of the operations. The group also used hitmen that worked for Falcone, such as Joe Chill to take care of competition, including Theodore Cobblepot, who ran against Hill as Mayor. He would also make deals with arms dealer, Rumi Mori, which the latter owed various favors for him. While Martha was aware of his double life, Thomas kept the information away from Bruce.
The group also collected large amounts of psychogenic chemicals and modified them to induce violence in whoever was infected with them.
During his time working with Falcone and Hill, Thomas used Arkham Asylum, Gotham's local mental hospital, convicted people, and took control of their land and money to make himself and his partners even richer. To make sure that their "insanity" looked plausible, he injected them with the chemicals they collected to make them act violently. Among one of his many victims was Esther Cobblepot. Shortly afterwards, the trio built the Wayne Enterprises tower on Esther's property. Thomas also ordered the assassination of the Arkham family when they objected to his use of the Asylum.
Eventually, Martha found out about Thomas' use of Arkham and objected to it. She threatened to reveal his crimes to the public if he didn't stop and close all ties with Falcone and Hill. Thomas would have agreed, but word of that got to Hill. As Thomas, Martha, and Bruce returned from an annual showing of "The Mark of Zorro", at the Monarch Theatre, Chill, who had been hired by Hill to assassinate them, ambushed the Waynes in an alleyway.
As Thomas begged for his life and tried to protect his family from Chill, whom he incorrectly believed was sent by Falcone, he was shot twice in the torso. After he stated that it was nothing personal, Chill shot Thomas again, that time straight through his left eye, and killed him. Chill then murdered Martha, and took her pearls that she wore to make it look like a mugging gone wrong, but was forced to flee before he could kill Bruce.
Following their deaths, Thomas and Martha were looked upon by Gotham as martyrs and many of Gotham's elite became inseparable to make sure that none of them suffered a similar fate. That also forced Falcone to begin to use his own resources to manage his empire. Their deaths also inspired Bruce to become the vigilante Batman, who hoped to clean up Gotham in their name.
However, the public's unknowing of Thomas' dealings lead to the Arkham's daughter, Victoria, to become the terrorist, Lady Arkham, and form the Children of Arkham, a group that she commanded. On the twentieth anniversary of Thomas and Martha's deaths, the Children of Arkham leaked information about Thomas' dealings with Falcone by leaking an account that was managed by him and the crime lord was leaked to the press, possibly through Hill (whom they blackmailed) or a member of the group. With that, the Wayne family's legacy was tarnished and Bruce was forced to suffer from those consequences, but took the responsibilities that were directed at him. After the Children of Arkham's defeat, Bruce's public image would recover, but Thomas and his reputation were ruined beyond repair.
Initially, Thomas Wayne was seen by many as a wise, respectable, and caring man and father who devoted many of his resources of Wayne Enterprises to make the lives of Gotham's citizens better.
Sadly, that all changed when Thomas' criminal connections to Hill and Falcone were discovered. Throughout the series, Thomas was revealed to have committed various atrocities, including drugging Esther Cobblepot, committing people to Arkham Asylum in order to steal their lands and wealth, and had the Arkhams assassinated when they opposed his amoral actions. As described by Falcone, Thomas was "more ruthless than any of them" when people got on his bad side. Also, as described by Alfred Pennyworth, Thomas had a strong desire for control, regardless of the consequences, indicating he entered crime to gain as much power as possible.
Despite his ruthlessness and cruelty, Thomas was not without a heart, genuinely cared about Martha and Bruce, and often gave him anything that he wanted. That was shown when Bruce recalled seeing the film 'The Mark of Zorro' countless times at the Monarch Theater, where Alfred revealed that Thomas and Martha had arranged the screenings themselves. He was willing to protect his family if necessary, even attempting to save the two from being murdered, showing that deep down, for all his cruelty, Thomas was not completely ruthless.
- Thomas can be considered the main antagonist of the game, as Lady Arkham's motives for her actions directly involved retribution for his crimes.
- In The Long Halloween, it was shown in a flashback that Thomas had saved Falcone's life when the crime lord was in critical condition. However, there were no indications that Thomas was involved in criminal activities.