Barry enters the Batcave, expecting to find Bruce but is immediately attacked by this far more violent Caped Crusader, against whom he's no match without his speedster abilities.

[2] Allen reveals to Batman that the timeline he's living in is an altered version of his own, with significant changes resulting in a much darker and more violent world.

This story is set after the first, failed attempt to restore Barry's powers and fills out the backstory of how different this version of Gotham is and how Thomas operates as Batman.

Local judge Harvey Dent is distressed when his twin children are kidnapped by the Joker, so he calls in Thomas and James Gordon, the Chief of Gotham's privatised police force, owned and funded by Wayne.

Dent blames Wayne for the kidnapping as it was he who convinced him that privatising the police force was a good idea, and threatens to take both it and his casinos away if his children aren't found.

He consults with Selina Kyle, a paraplegic in this world and fulfills the role of Oracle, and follows a clue to track down where the Joker is holding the children: the long abandoned Wayne Manor.

During their fight, Batman explains to the Joker that he has the chance to re-write history, to save their son but at the cost of both their lives which is why he feels obligated to ask if he should go through with it.

[7] After a second attempt successfully restores Barry's powers, Batman works with the Flash to rally a team to oppose Eobard Thawne's changes to history.

[9] Batman stabs Professor Zoom in the back using an Amazonian sword and learns that altered timeline was actually created by the Flash as part of an attempt to save Nora Allen.

[11] In the Convergence crossover, when the alternate Brainiac miniaturized the reality of the Flashpoint universe, Thomas Wayne had returned alongside Captain Thunder, Kal-El, Abin Sur and Cyborg.

[13] Following the conclusion of the Convergence, all parallel universes and alternate timelines are restored and composed as the new multiverse, including the Flashpoint reality and thus Thomas remains existing as the result.

Left to ponder in the Batcave, Thomas waited for the joint Atlantean and Amazonian hit squad to arrive so he may sacrifice himself and them with explosives, until he encounters the Flash and Batman.

Thomas teams up with his son to hold off the Atlantean-Amazonian hit squad to give the Flash time to fix the Cosmic Treadmill.

As the Flash and Batman disappear, Thomas is satisfied upon seeing his son alive and accepts his fate; he hopes that Bruce would move on from the past.

Once he judged Bruce to be suitably psychologically broken, he broke into the Batcave, knocked out Alfred, and trapped his son in a nightmarish sequence in Arkham Asylum.

Holding the gun to Bruce, Thomas tries to convince his son to give up being a vigilante and live a long and happy life with Selina.

Returning from Earth-23, Thomas and Calvin find Machinehead rebuilding the crashed ship as it is suspected that Lex Luthor had help from someone in another part of the Multiverse.

[25] When Bruce Wayne enlisted Mime and Marionette to steal the snowglobe containing the Flashpoint reality from Rip Hunter sometime after Thomas had faded, the Flashpoint was restarted where the Atlantean and Amazon war was made worse, Super-Man was released from his capsule earlier by Batman, and there are claims of threats from space coming to Earth.

With the Time Sphere, Martha plans to make it so that Bruce survives and she and Thomas didn't after learning about the other timeline from a displaced Psycho-Pirate who she killed.

After the Time Sphere exploded and Gilda was killed, Batman's gamble with Rip Hunter came out positive as both Thomas and Martha accepted that the world would be better without Bruce enabling the Flashpoint reality to be stabilized.

After Bruce sacrifices himself to save Earth 2 from an Apokoliptan invasion, Thomas takes up the "mantle of the Bat" to fight crime and uses Hourman's Miraclo pill to enhance his strength and agility.

[28] Amidst "Convergence", Earth 2 is destroyed, though Thomas joins Dick Grayson and a group of survivors in traveling to Telos's world,[29] where the former finds a pre-Flashpoint Gotham City and has a conversation with its version of Bruce before sacrificing himself to defeat the Club of Villains.