- 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.
- -- Batman (Thomas Wayne) src
This section of the history takes place during Flashpoint, a massive crossover event set in an alternate timeline to the mainstream DCU. History was completely changed when Professor Zoom finally found a way to erase his nemesis the Flash without harming his own legacy.
In the alternate timeline of Flashpoint Paradox, robber Joe Chill kills the young Bruce Wayne rather than his parents. As a result, Thomas Wayne wishes revenge so takes up to mantle of Batman, but unlike his son he is far more ruthless in his actions as he is happy to kill any criminal that gets in his way. Thomas tracked down Chill and was going to poison him but decided to beat him to death with his bare hands. His wife Martha Wayne is so traumatized by the event she cut her face into a garish grin and soon enough, descends into insanity and becomes the altered timeline's Joker.  On her crime-spree, she kidnaps the twin children of Judge Dent. When he tracks down one of her partners in crime Yo-Yo, he interrogates her to find his wife's location, but she refuses to cooperate he throws her off the building. However at that moment Cyborg arrives to catch her and Batman jokes "she slipped". Cyborg asks Thomas to join him in stopping the war between the Amazons and the Atlanteans that has devastated Europe, but he refuses.
Later that night the powerless Barry Allen is looking for Batman, and enters the Batcave, but Thomas attacks the intruder. He is taken back when Barry kept calling him Bruce and says he knows he is Batman. Thomas is shocked but wished to learn more about his son and his life in the alternate time line. Barry convinces Thomas to help to re-write the timeline and the first step was getting Barry's powers back. Thomas creates a device that will recreate the accident that created the Flash, the first attempt was a failure leaving Barry badly burnt, but after one more attempt, it the procedure proves a success and Barry becomes The Flash once again.
Thomas Wayne Wayne secretly funds his war on crime through his Wayne Casinos. He works closely with Chief Jim Gordon, the head of Gotham Security, as a few years ago the police force was privatized. He works closely with Oswald Cobblepot the head of security for all his casinos.
Batman is called by Chief Gordon, who tries to convince him that he does not have to fight villains by himself, however Batman refused. Later, Batman is shocked that the Joker had footage of his friend James Gordon being killed. She tricks Chief Gordon into shooting Dent's daughter by taping her mouth shut and disguising her as the Joker. Before Batman confronts her, she slashes Gordon's throat. After Gordon's murder Batman turns-up to face his ex-wife.  Batman tells her he has discovered a way rewrite history so Bruce was never killed. He told her about Barry Allen and how he helped him restore his powers. Martha with this knowledge is shocked to learn the hardships her son will go through, she runs to her death off a cliff near Wayne Manor. 
Thomas works with the Barry to recruit a team to alter the Reverse-Flash changes to the timeline. Batman contacts Cyborg and attempt to find Project Superman the government branch responsible for raising an alien Kal-El who is supposedly the most powerful being on the planet. When they find him all they see is a pale skinny man but when he is exposed to sunlight his powers activate and he flies away.
The group of heroes escape the facility with the help of Element Woman, but Barry's memories begin to change and Thomas is forced to inject him with a drug which slows down his brain processes.The heroes head to Fawcett City to find the team known as S.H.A.Z.A.M. a group of Teenagers who can combine their powers to become Captain Thunder.
Using the powers of Billy Batson they are able to slow down the effects of the combination of the Speed Force and the altered timeline itself on Barry's brain. The team decide to stop the war between Wonder Woman and Aquaman, because there is no guarantee that they would win against Professor Zoom. Thomas reluctantly agrees and the heroes head for New Themyscira in the Batplane, they also recruit Enchantress for the mission. Wonder Woman and Emperor Aquaman are locked in battle when the team arrive.
Batman stabs Professor Zoom in the back with a sword and while Professor Zoom gloats that Barry had created the timeline not Zoom. The Flash did this when he attempted to go back in time save his mother, but Batman is fatally wounded by the Enchantress, who was truly an Amazonian spy. Before the Flash can run to the past in an attempt to stop his younger self from altering the timeline, Thomas, realizing what Flash was planning to do after despite learning his inadvertent role, thanks him for all he has done and gives the Barry a letter addressed to his son, and accepts his fate.
After Barry apparently restores the timeline to an approximation of its prior self, he visits Bruce Wayne and gives him a letter from his father, and told him he could not of done it without his help. Bruce is deeply touched that his father has sacrificed his existence itself for him.
- 23 Appearances of Thomas Wayne (Flashpoint Timeline)
- 12 Images featuring Thomas Wayne (Flashpoint Timeline)
- 8 Quotations by or about Thomas Wayne (Flashpoint Timeline)
- Character Gallery: Thomas Wayne (Flashpoint Timeline)
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