Flashpoint details an altered DC Universe in which only Barry Allen seems to be aware of significant differences between the regular timeline and the altered one, including Cyborg's place as the world's quintessential hero much like how Superman is in the main timeline, with Superman himself being held captive as a lab-rat by the United States government within an underground facility in Metropolis. In addition, a Thomas Wayne version of Batman, whose son Bruce Wayne is dead instead of him and his wife Martha (who becomes The Joker), spends his days "running Wayne Casinos" in order to help fund his vigilante activity.
Consisting of a 61 issue run, the series crossed over with Booster Gold, sixteen separate three-issue miniseries, and a number of one-shots beginning in June 2011. DC announced that Flash #12 would be the last in the series; a thirteenth issue had been announced for sale on May 25, 2011, but was withdrawn.
Barry Allen wakes up to discover everything and everyone around him has changed. He is not Flash nor does he have powers, his mother Nora (deceased in his own timeline) is alive; his father, Henry, died of a heart attack three years ago (instead of in prison). Captain Cold is Central City's greatest hero, the Justice League is never established, and even Superman is seemingly nonexistent.
In Gotham City, Batman throws a criminal off a building. Cyborg and Batman have a conference with a group of superheroes to discuss how Wonder Woman's Amazons have conquered the British Isles, while Aquaman's Atlanteans have sunk the rest of Western Europe, and the battle between the two has caused massive death and destruction. America is similarly endangered. The heroes cannot cooperate to find a solution, and the meeting is ended.
Barry Allen drives to the Batcave, where Batman attacks him. Batman is revealed to be Thomas Wayne—in this timeline his son, Bruce, has died instead of his wife and him.
In the flooded remains of Paris, Deathstroke captains a pirate ship in search of his daughter. Emperor Aquaman appears and stabs Deathstroke in the chest and attacks Deathstroke's crew (Sonar, Icicle, and Clayface). Sonar is able to remove a piece of the trident from Deathstroke's chest and heal him.
At Wayne Manor, Barry tries to explain to Thomas about his secret identity as the Flash and his relationship to Bruce Wayne. Barry's memory begins to spontaneously realign itself to the altered timeline and Barry realizes that the world of Flashpoint is not a parallel dimension, but an alternate reality. Barry's ring ejects Eobard Thawne's Reverse-Flash costume and causes Barry to believe that his enemy is responsible for changing history. Barry decides to recreate the accident that gave him his powers in a bid to undo the damage caused by Thawne, but his initial attempt fails and leaves him badly burned.
In London, Steve Trevor is waiting at a rendezvous for Lois Lane but is attacked by Wonder Woman and the Amazons. Wonder Woman catches him by the neck with her Lasso of Truth and begins interrogating him. He explains that he was hired to extract Lane from New Themyscira because she was sent to gather information on the Amazons for Cyborg. The U.S. president informs Cyborg that Steve Trevor sent a signal to the Resistance but was intercepted because of a traitor among the heroes that Cyborg tried to recruit. Cyborg is relieved of duty as Element Woman sneaks into the headquarters. Meanwhile, in New Themyscira, Lane encounters the Resistance.
A second attempt at recreating Allen's accident restores his powers and health. He concludes that the Reverse-Flash changed history to prevent the formation of the Justice League. He also learns that Kal-El was taken by Project: Superman. Flash, Batman and Cyborg join the cause to stop Wonder Woman and Aquaman. The three find a pale, weakened Superman at the Project and realize that he may well have been in a containment cell since he was a child—possibly never even seeing a human being before. After being rescued, Superman flies off in seeming fright in the midst of a battle with the guards, leaving the three in the sewers to be rescued by Element Woman. Flash's memories continue to change.
The president announces Cyborg's failure to unite the world's superheroes and the U.S. enters into the Atlantean-Amazon war. Flash, Batman, Cyborg and Element Woman break down the door in need of the Marvel Family's help and Batman asks Billy to use his lightning to prevent Flash's memories from changing even further. The group hears of the failed air assault on England due to the Amazons' Invisible Plane air force. Hal Jordan is the first casualty, and a giant Atlantean-generated tidal wave threatens the rest of New Themyscira. Flash tells Batman that if he fails to stop Thawne, the world will destroy itself. Despite reservations, Batman joins Flash as the group heads off to New Themyscira. Enchantress joins them en route. Wonder Woman and Aquaman are fighting one-on-one until Flash and his team arrive.
The Marvel Family transform into Captain Thunder, also transforming Tawky Tawny. Captain Thunder attacks Wonder Woman and appears to be winning until Enchantress reveals herself as the Amazon spy in the Resistance and uses her magic to restore the Marvel Family to their mortal forms. Penthesilea (who was secretly one of the conspirators of the Atlanteans-Amazons war, along with Orm) kills Billy Batson, causing a massive explosion that cripples the opposing forces.
In the wake of the devastation, Thawne appears in front of Flash. The Reverse-Flash reveals that Flash himself created the Flashpoint timeline by traveling back in time to stop him from killing Barry's mother. Barry pulled the entire Speed Force into himself to stop Thawne, transforming the timeline by shattering the history of his allies. Thawne resets Barry's internal vibrations, enabling him to remember this. According to Thawne, these actions transformed him into a living paradox, no longer requiring Barry to exist and allowing him to kill the Flash without erasing his own existence. Thawne continues to taunt Barry with this knowledge until Batman kills him with an Amazonian sword.
As the fight continues, Superman arrives and begins to aid the heroes, first by landing hard enough to crush the Enchantress under his feet. Thomas insists that Barry puts history back to normal to undo the millions of deaths. Meanwhile, Cyborg detects seismic activity which he claims could destroy the world. Waves start to approach. Now knowing the point of divergence, the Flash restores the timeline. As he enters the timestream, a dying Thomas thanks him for giving his son a second chance and gives Barry a letter addressed to Bruce. Barry then meets with his mother and bids a tearful farewell to her.
Traveling back in time, Barry merges with his earlier self during the attempt to stop Thawne. While traveling through time, Barry realizes he can see three different timelines — DC (New Earth), Vertigo (Earth-13), and WildStorm (Earth-50). A mysterious hooded figure (later revealed to be a cursed immortal Pandora) tells him that the world was split into three to weaken them for an impending threat, and must now be reunited to combat it. The DC, Vertigo, and Wildstorm universes are then merged, creating a brand new DC Universe. Barry then wakes up in a similar manner to the beginning of Flashpoint, also retaining all his memories from the alternate timeline. Believing that everything is over, Barry remembers Thomas' letter and gives it to Bruce, who is still the Batman in this timeline. Bruce, deeply touched by his father's sacrifice to ensure his son's life, cries and expresses his gratitude to Barry for informing him of the events that transpired before the timeline was reset.
Flashpoint: The World of Flashpoint Featuring The Flash (collects Grodd of War #1, Kid Flash Lost #1-3, Legion of Doom #1-3, Reverse Flash #1 And Citizen Cold #1-3, 256 pages, paperback, March 2012, ISBN 1-4012-3408-9)
Flashpoint: The World of Flashpoint Featuring Wonder Woman (collects Emperor Aquaman #1-3, Outsider #1-3, Lois Lane and the Resistance #1-3 And Wonder Woman and the Furies #1-3, 272 pages, paperback, March 2012, ISBN 1-4012-3410-0)
Flashpoint: The World of Flashpoint Featuring Superman (collects World of Flashpoint #1-3, Booster Gold #44-47, The Canterbury Cricket #1 And Project Superman #1-3, 256 pages, paperback, March 2012, ISBN 1-4012-3434-8)
Flashpoint: The World of Flashpoint Featuring Batman (collects Batman: Knight of Vengeance #1-3, Deadman and the Flying Graysons #1-3, Deathstroke and the Curse of the Ravager #1-3 And Secret Seven #1-3, 272 pages, paperback, March 2012, ISBN 1-4012-3405-4)
Flashpoint: The World of Flashpoint Featuring Green Lantern (collects Hal Jordan #1-3, Abin Sur - The Green Lantern #1-3, Frankenstein and the Creatures of the Unknown #1-3, and Green Arrow Industries #1, 224 pages, paperback, March 2012, ISBN 1-4012-3406-2)
Several allusions to Flashpoint are made during the first two seasons of The Flash television series. The character Farooq/Blackout appears in the season one episode "Power Outage". In "Rogue Time", the Flash is warned that going back in time to save his mother's life would have a terrible ripple effect on the timeline, and in the season finale, "Fast Enough", Flash is told not to do so by his own future self, and shares a conversation with his dying mother that is similar to the one in the comic. In the season two episode "Welcome to Earth-2", it is revealed via a new report that on Earth-2, Oliver Queen died on the Queen's Gambit instead of his father Robert, leading Robert to become the vigilante the Arrow, mirroring Thomas Wayne becoming Batman instead of Bruce in the comic. In "Rupture", a de-powered Barry attempts to recreate the accident that gave him his powers using a method similar to the one featured in Flashpoint. The season two season finale, "The Race of His Life", begins a loose adaptation of Flashpoint when Barry, grief stricken after Zoom kills his father Henry, travels back to 2000 and stops Eobard Thawne/Reverse-Flash from killing Nora, thus radically altering the timeline. In the season three premiere, "Flashpoint", Barry has been living in the new timeline (dubbed 'Flashpoint' by Eobard, who is kept imprisoned in a carbine cell by Barry) for three months with both his parents alive and begins dating Iris, while Wally West protects the city as the Flash. However, Barry discovers that Joe is a reclusive alcoholic frequently missing shifts at work, Cisco Ramon is a self-centered billionaire tech genius with no interest in helping Barry, and Caitlin Snow is not a biologist but a pediatric ophthalmologist. As in the comic book story, Barry begins losing his memories as the Flashpoint timeline starts to overwrite the timeline he's familiar with. Eobard tries to convince Barry to release him so they can fix what he did, but Barry refuses to listen and tries to make things better by helping Wally stop his archenemy, Edward Clariss/The Rival. Barry succeeds in stopping Edward, who is killed by Joe, but not before Wally is critically wounded. Realizing the effects of Flashpoint are only going to get worse, Barry releases Eobard, who kills Nora in 2000 and returns Barry to the corrected 2016. Before leaving, however, Eobard leaves a taunting hint that things aren't exactly the same (as evidenced by Eobard being alive in 2016 whereas he was erased from existence in 2015 when Eddie killed himself). In the following episode, "Paradox", several differences from the original timeline are revealed. Cisco is angry with Barry after his brother died in a car accident and Barry refused to go back in time to save him. Iris and Joe West have a strained relationship after Iris discovered that Joe concealed from her that her mother was still alive. John Diggle has a son, John Jr., rather than a daughter, Sara. Barry has a colleague in the forensics department named Julian Albert who he's been apparently working with for a year. Caitlin has metahuman ice powers that she has been concealing from the rest of the team. Barry attempts to go back and reset the timeline again, but is pulled out the time stream by Jay Garrick. Acting as a stern mentor to Barry, Jay explains the consequences of time travel by comparing the timeline to a broken coffee cup - even after it has been repaired, it will never be completely the same. Jay advises Barry that he must live with the mistakes he made when he created "Flashpoint" and move forward with his life. When he reveals what he did to the timeline to the others. Cisco and the others forgive him and help battle enemies from Flashpoint. Barry is currently unaware that Thawne continues to trouble the Legends of Tomorrow, working with Damien Darhk and Malcolm Merlyn to change their histories.