Dr. Thomas Wayne was one of the most respected patrons in all of Gotham City. He inherited his family's ancestral home Wayne Manor and took charge of the family business Wayne Enterprises. A skilled surgeon and philanthropist, Thomas Wayne also established the charitable Wayne Foundation. He was the husband of socialite Martha Wayne and the father of Bruce Wayne, the future Batman.

Some thirty odd years ago, Thomas and Martha were traveling across the Midwest when they witnessed a glowing light falling from the sky into a nearby field. Thomas went to inspect the item and discovered a strange alien crystal. Upon physical contact with the artifact, his consciousness was transported through space and time to the planet Krypton. There, his astral self met Kryptonian scientist Jor-El. Jor-El explained to Thomas that the item he discovered was a Kryptonian probe, one of dozens that he had sent out throughout various yellow-sun star systems. He told Thomas of the pending destruction of Krypton and that he was searching for a suitable world in which to send his infant son Kal-El. Jor-El instantly developed a fondness and respect for Thomas Wayne and because of him determined that Earth was the perfect world to send his son. He then sent Wayne's subconscious mind back into his body on Earth. 

Only a few months later, Thomas and his wife Martha gave birth to their only son, Bruce. Thomas never forgot his astral experience on Krypton and began writing a journal of his experiences. Still in possession of the Kryptonian probe, he reverse-engineered the technology and was able to use some of it to save Wayne Enterprises from bankruptcy. Nobody ever knew about the alien heritage from which the thriving company prospered from. Thomas was careful that his journal would never fall into the wrong hands, so he hid it in a secret grotto in the caverns beneath Wayne Manor. He always intended to give the journal to his son so that he might learn the truth about the family's legacy.

Thomas Wayne was the father of Bruce Wayne and husband of Martha Kane. After his son Bruce was murdered by a robber, whom Thomas severely beat, the grief caused Thomas to become Batman but more brutal and using guns. Martha couldn't handle the trauma and she went insane, becoming the Joker. However when the Everything Universe event collided, Bruce Wayne alive and was also the Batman. Colliding from the flashpoint paradox to the Everything Universe.