While visiting his mother's grave, Barry Allen, known as the Flash, is alerted to a break-in by Captain Cold, Captain Boomerang, Heat Wave, Mirror Master, and Top at the Flash Museum. Defeating the Rogues, he discovers that they have been hired by his archenemy, Professor Eobard "Zoom" Thawne, as part of a plan to destroy Central City. With the help of the Justice League, Barry foils Thawne's plot, but Thawne's taunts over the death of his mother still haunt Barry as he departs.
The next day, Barry discovers that the world has radically changed: his powers are gone, his mother is alive, his wife Iris is married to someone else, and the Justice League does not exist. Aquaman and his Atlantean forces have sunk most of Europe, while Wonder Woman has led the Amazons in conquering Great Britain, and both forces are now at war after an attempted alliance between them resulted in Wonder Woman murdering Aquaman's wife Mera. Cyborg has assembled a team to eliminate both parties and approaches Batman to join them, but his refusal leads the government to scrap the plan, and instead recruit pilot Hal Jordan to fly an alien spacecraft to bomb the Atlanteans.
Barry visits Wayne Manor, but is attacked by Batman—who he realizes is not Bruce Wayne but his father Thomas; in this alternate reality, Bruce was killed by Joe Chill, and Martha Wayne became the Joker. Attempting to explain things to the elder Wayne, Barry retrieves his costume from his ring, but Professor Zoom's costume appears, causing Barry to believe Thawne is responsible for the timeline alteration. Barry convinces Batman to help, and Batman helps him recreate the accident that gave him his powers, but the attempt fails and Barry is severely burned.
In London, Steve Trevor attempts to extricate reporter Lois Lane, but is discovered by the Amazons and killed. The Amazons hunt down Lane, but she is rescued by the local resistance. Meanwhile, in the remains of Paris, Deathstroke and Lex Luthor are attacked and killed by Aquaman's forces while tracking the energy trail of Aquaman's new weapon, which is powered by the captive Captain Atom.
At the Batcave, after realizing that his memories are changing, Barry asks Batman to recreate the accident again. The second attempt results in success and Barry's powers are restored, but he discovers he cannot travel through time because Thawne is also using the Speed Force. Barry recruits more allies, beginning with Superman, who is a prisoner of the U.S. Government after his ship crashed into Metropolis. With the aid of Batman and Cyborg, they liberate Superman, who is empowered by Earth's yellow sun for the first time and fends off the facility's security then flies off in fear and confusion. Barry collapses as his memories continue to change.
Barry is taken to Billy Batson's home to recuperate, and learns that Jordan's attack has failed and that the final battle between the Amazons and Atlanteans has begun. Barry convinces the superheroes to help stop the war and they depart for Britain aboard Batman's jet, only to be shot down upon arrival. Batson and his siblings combine into Captain Thunder to fight Wonder Woman, while Barry, Cyborg and Batman occupy Aquaman. After killing Black Manta alongside Grifter, Batman is wounded by Ocean Master. Thawne reveals himself and after fighting and brutally defeating Barry, explains that Barry himself is responsible for this alternate timeline: Barry traveled back in time to save his mother, fracturing the fabric of reality. Wonder Woman uses her lasso to force Captain Thunder back into Batson and kills him; Superman returns but cannot save Cyborg from Aquaman, who then remotely detonates his Captain Atom-powered bomb. As the explosion tears across the landscape, Thawne mocks Barry but is killed by Batman. The dying Batman urges Barry to run, giving him a letter addressed to his son. Barry races back in time and stops his earlier self but again fractures time, creating another alternate timeline.
Barry awakens at his desk and finds that reality is apparently back to normal. After spending a moment with Iris at his mother's grave, Barry visits Bruce Wayne to tell him about everything that occurred. Barry gives Bruce the letter from his father, and Wayne thanks him. Barry then runs off.
In a post-credits scene, a Boom Tube opens in space above Earth and a horde of Parademons emerges.
The soundtrack to Justice League: The Flashpoint Paradox was released on September 10, 2013. The music was composed by Frederik Wiedmann.
Justice League: The Flashpoint Paradox received very positive reviews. The review aggregator website Rotten Tomatoes reported a 100% approval rating based on 5 reviews.
Critics and audiences said that the film stays true to its source material. It is generally praised for its mature story line and the way Flash obtains justice, but criticized for its excessive violence and use of blood that exceeds the comics it is adapted from. Some questioned its PG-13 rating because of the graphic nature of Professor Zoom's death, and the gruesome deaths of other characters, including children.
IGN gave a Justice League: The Flashpoint Paradox 8.5/10, and said it has outdone its source material. It called the style "sleek and hard-hitting", praised C. Thomas Howell's voice acting which it said brought "unnerving dread", and stated that it is the "most hardcore DC animated movie to date", although it also warns against the level of violence and said the numerous cameos "detract from the main story".