Thomas Wayne was a prominent doctor in Gotham, and, to the public, a humanitarian. However, in reality, he was a member 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. While Martha was aware of his double life, Thomas kept the information away from Bruce.
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. To make sure that their "insanity" looked plausible, he injected them with a special substance that made them act violently. Many of his victims included Esther Cobblepot. Thomas also ordered the assassination of the Arkhams when they objected to his use of the Asylum.
Eventually, Martha found out about Thomas' use of Arkham and objected to that. She threatened to reveal that to the public if he didn't stop and to 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 believed that he 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, Vicki Vale, 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.
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 then any of them" when people got on his bad side.
Despite his ruthlessness and cruelty, Thomas genuinely cared about Martha and Bruce, and often gave him anything that they wanted. That was shown when Bruce recalled seeing the film 'The Mark of Zorro' countless times at the Monarch Theatre, where Alfred Pennyworth revealed that Thomas and Martha had arranged the screenings themselves.