While visiting his mother's grave, lamenting his inability to save her when she was killed in a home invasion when he was a child, Barry Allenthe super-speed superhero known as the Flashis alerted to a break-in at the Flash Museum by Captain Cold, Captain Boomerang, Heat Wave, Mirror Master, and The Top. Defeating the Rogues, he discovers that they have been hired by his arch-enemy, the time-traveling Professor Zoom, to lure him in as part of a plan to destroy Central City. With the help of his allies in the Justice League of America, Barry foils Zoom's plot.
The next day, Barry awakens to discover that the world has radically changed around him: his powers have disappeared, his mother is alive, and the Justice League does not exist. In this new timeline, Aquaman and his Atlantean forces have sunk most of Western Europe, while Wonder Woman has led the Amazons in conquering Great Britain, and both armies are at war with one another after a failed attempt at peace resulted in Wonder Woman murdering Aquaman's wife Mera. Government agent Cyborg has put together a team to end the war by taking out the two leaders, and approaches Batman to join them, but he refuses, causing the President to abandon the plan. Instead, pilot Hal Jordan is assigned to fly an alien spacecraft in a bombing run on the Atlanteans.
Barry visits Wayne Manor, but is attacked by Batman, who he realizes is not Bruce Wayne (who died in this reality) but his father Thomas Wayne. Attempting to explain things to an incredulous Thomas, Barry retrieves his Flash costume from the ring in which it is kept, but Professor Zoom's costumes appears in its place, causing Barry to believe Zoom is responsible for changing history. Convinced to help Barry by the knowledge that Bruce lived in the original timeline, Batman helps him recreate the accident that gave him his Flash powers, only for Barry to wind up being severely burned.
In London, Steve Trevor attempts to exfiltrate undercover reporter Lois Lane, but is discovered by the Amazons and killed. With Trevor's information, the Amazons hunt Lane down, but she is rescued by the local resistance, and falls in with them. Meanwhile, amongst the remains of Paris, Deathstroke and Lex Luthor are attacked and killed by Aquaman's forces while tracking the energy trail of their new superweapon: a captured and weaponized Captain Atom.
Realizing that his memories of the original timeline are fading, the injured Barry insists Batman recreate the accident again, this time resulting in the successful restoration of his powers. Discovering that he is unable to travel through time himself, Flash seeks to recruit more allies, beginning with Superman, who in this world is a prisoner of the government after his ship crashed into Metropolis, rather than Smallville. With the aid of Batman and Cyborg, they break into the bunker in which the withered Superman is held and liberate him. Empowered by the sun, Superman holds off the government agents who confront the group, but then flies off in fear and confusion. Flash collapses as his memories continues to alter, and is taken to the home of Billy Batson and his foster siblings to recover. Learning of Jordan's failed attack and the beginning of the final battle between the Atlanteans and the Amazons, Flash convinces Batman to join them in an attempt to stop the war.
Onboard Batman's jet en route to Britain, Batman shows Flash a message intercepted from Lois Lane of a super-speedster she captured an image of, who Flash identifies as Zoom. As they wonder why Zoom would let Lois live if he saw her, the jet is show down by the Atlantean fleet, and the battle begins. Batson and his siblings combine into Captin Thunder to fight Wonder Woman, while Flash and Batman occupy Aquaman, only for Batman to be gravely wounded. At this point, Zoom reveals himself to Barry, and explains it was not he, but Barry himself who was responsible for changing the timeline, when he went back in time to save his mother, and caused the fabric of reality to fracture. The battle continues around themwith Wonder Woman killing Captain Thunder, and Superman arriving too late to save Cyborg from Aquamanculminating in a wounded Aquaman giving the order to trigger the Captain Atom bomb. As the explosion tears across the landscape, Zoom mocks the Flash, when he is suddenly shot through the head and killed by the injured Batman. Batman urges Barry to fix everything, giving him a letter addressed to Bruce. Barry races back in time, and stops his earlier self from preventing his mother's death.
Barry reawakens at his desk, and finds that everything is back to normal. He visits Batman to tell him about everything that occurred, and gives him the letter from his father, prompting the tearful Batman to tell him: "You're one helluva messenger."
In a post-credits scene, a Boom Tube opens in space above Earth and a horde of Parademons emerges, foreshadowing Justice League: War.