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I'm not the hero of this story. I'm a man who's been corrupted by his own unbearable pain. I'm a man who has too much blood on his hands to be called good. I'm a man who had nothing to live for--until the day I met The Flash.
~ Thomas Wayne
Thomas Wayne in the Flashpoint timeline is an alternate incarnation of the Batman. He is a more older version of himself who has become very bitter, argumentative and lonely. He also owns a chain of hotels and Wayne Casino.
Rather than Thomas and Martha Wayne being gunned down by Joe Chill, it was Bruce that died in crime alley that fateful night, leaving Thomas Wayne alive and broken. Following the tragic event, Thomas Wayne took on the Batman mantle himself, seeking for vengeance. Unlike his son, however, Thomas has no sense of mercy and remorse for criminals, and has no qualms about killing them.
Running a casino as a way to track various criminals as well as commanding the GCPD, Thomas operates out of a small Bat-Cave under his old mansion, delivering bloody vigilante justice when night falls. Most villains have likely perished under his rule, but still, The Joker still remains, this time being the mentally-shattered version of his former wife. On his way to rescue her hostages, Havery Dent's twin children, he kills a henchwoman by dropping her off a skyscraper.
With the help from Jim Gordon and Selina Kyle/Orcale, Thomas discovers that they are being held in his old mansion. Gordon rushes in alone, but he is tricked into shooting one of the children dead before dying by The Joker's hands. Rushing onto the scene, Wayne confronts his wife, who tells him about the canon timeline. Thomas trying to stop her insane mayhem, Martha asks her about his son's fate, and after telling her his identity as Batman, she runs aware in sadness only to trip and fall into a fissure to her demise.
When The Flash awakens and discovers Batman's existence, The Flash tries to find him for help. Once he discovers his true identity, the two, along with Cyborg and Element Woman, and Thomas go to the house of Shazam's children, thinking that their power could help Barry with his memory issues. Discovering the war between Wonder Woman and Aquaman, Barry asks Thomas to help him in the fight, which he agrees on after The Flash pointing out that's what Bruce would do. However, the battle failed miserably, as Wonder Woman killed Billy Batson and the Enchantress kills most of the resistance and wounds Thomas. Despite being injured, he manages to stop Professor Zoom by shooting his in the back of his head. Before dying due to Aquaman's nuke, he gives The Flash a letter for Bruce, asking him to fix the timeline.
Despite The Flash's success in fixing the timestream, the Flashpoint timeline continued to exist, held in place by a mysterious force. The Flash returns to this timeline along with Thomas' son Bruce Wayne while investigating the existence of a button found embedded within the walls of the Batcave. Thomas immediately attacks them upon their arrival as he thought them to be a trick. But Flash convinces him that they traveled to his world using the Cosmic Treadmill and need his help to repair it. After fixing the Treadmill, the Flashpoint timeline suddenly begins to vanish around them. Bruce is held back by The Flash as he begs his father to come with them to their world. However Thomas refuses and instead tells Bruce to give up the Batman mantle so he can pursue a happier life. The timeline then seemingly disappears completely along with Thomas Wayne.
Although he was supposed to be erased by Dr. Manhattan, Thomas Wayne was saved by the Reverse Flash as punishment for his previous death during the events of Flashpoint. Reverse Flash knew it would torment Thomas to see his son grow up and become Batman, so the villain stranded him in the mainstream timeline to witness just that instead of the fate he chose. Thomas continued to watch Bruce from the shadows out of concerned for his well being, and soon deduced that his son was the target of a big conspiracy. He later approached the Joker, who had been critically wounded at a church, and told him he would save his life if the madman revealed who he was working for.
Thomas discovered Bane was behind the conspiracy against his son. But instead of stopping him, Thomas decided to join him in his plans to psychologically and emotionally break Batman, so that Bruce would give up his crusade.
Powers and Abilities
Thomas in the Flashpoint timeline, demonstrates peak athletic strength and combat skills. He can effortlessly lift a grown man above his head, which is demonstrated in the confrontation with Barry. Also in that scene, it is shown that Thomas is able to throw Barry with a single arm, with enough force to shatter a wooden table to pieces. Later in the Flashpoint story, Thomas is shown of being very combat proficient by fighting and defeating well armed and elite soldiers trained to fight superhumans such as Superman. He is shown to have the strength to kick down a wooden door, shattering it into pieces and breaking the door frame and closely surrounding walls, all with a single kick. It is also implied in the final battle that he is capable enough to fight against Amazon warriors as well as Atlantian soldiers, though no such scenes are actually shown.