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The movie begins in an alternate universe where Lex Luthor and a heroic analogue to The Joker named The Jester are stealing a device from the Crime Syndicate headquarters. After securing the "Quantum Trigger," Luthor and The Jester attempt to escape. The Jester sacrifices himself to allow Luthor a chance to get away, killing J'edd J'arkus (the Martian Manhunter's opposite) and Angelique (Hawkgirl's counterpart) in the process. Lex Luthor is confronted by the remaining Syndicate members, only to activate his dimensional travel device and escape to the Earth of the heroic Justice League.
Once there, he turns himself over to the police, who he knows will think he's the evil Luthor and thereby summon the Justice League. Superman's x-ray vision confirms Lex Luthor's reversed organs mean that he's from a parallel Earth, and that Lex Luthor is still in the Stryker's Island prison, so the League agrees to hear Lex out. Lex tells his story and asks the League for help: his Earth is being extorted by the Syndicate, who have taken control of all crime on Earth and systematically eliminated Luthor's League members. The only thing holding them in check is the threat of a nuclear response. While waiting outside the League's meeting room, he hides the Quantum Trigger. All members of the League agree, except for Batman, who argues that the League is spread too thin for the problems of their own world, let alone Luthor's. Luthor transports the remaining members of the League to his universe, while Batman stays behind to finish building the Watchtower.
Arriving at Justice League headquarters on Lex's parallel Earth, they find the Syndicate and must soon retreat. Regrouping at Jester's base, they make plans to attack Syndicate targets, and they even capture Ultraman. However, United States President Slade Wilson orders his release, to the outrage of Lex and the Justice League. Wilson explains that he didn't "roll over" for the Syndicate, and that acceding to the Syndicate's demands saves millions of lives. His daughter, Rose, regards him as a coward. J'onn J'onzz inadvertently reads her mind and explains that Wilson isn't, that as a military man he actually holds life more dear than others. J'ohn Jones later saves Rose's life during an assassination attempt, and they start to fall in love.
Owlman (Batman's counterpart) is building a weapon, the Quantum Eigenstate Device or QED, which the Syndicate intends to use as the equalizer to the nuclear threat. When pressed by Superwoman (Wonder Woman's counterpart), Owlman admits the weapon can destroy entire worlds. Operating under the theory that there are many parallel Earths, and that each one develops from the choices that every single person makes, he begins seeking Earth-Prime, the first Earth. Owlman, a nihilist, believes that destroying all of the Earths is the only action that would have any purpose, as it is the only action that would not result in another alternate universe where a different choice was made. Owlman plans to use his weapon to destroy Earth-Prime, causing a chain reaction that would erase the entire multiverse. Superwoman notes that even as a "murdering psychopath," she thinks Owlman is much crazier than she is. When the League eventually arrives at the moon base of the Crime Syndicate, it becomes a free-for-all fight as everyone is matched up against their alternates and, in some cases, have to help each other gain the upper hand. Eager to put his plan into action, Owlman initiates the QED and takes it to Earth-Prime. Batman deduces which universe holds Earth Prime, but without a way to get there, it appears that everyone is doomed. A plan is hatched in which Johnny Quick (Flash's counterpart) uses his speed to eventually match the temporal vibration, opening another portal to Earth-Prime so that Batman can engage Owlman.
Owlman and Batman are mental equals, but Owlman has clear advantages: his powered exoskeletal suit, and Batman's injuries from fighting Superwoman. However, Batman outwits Owlman at the last moment, sending him and the QED to an uninhabited world just before the bomb detonates. Owlman has the opportunity to disarm it in the last seconds, but in the end does nothing, saying, "It doesn't matter."
Back on the Crime Syndicate's world, Johnny Quick dies after the vibrating caused him to age rapidly. Batman had anticipated that, which is the real motive behind claiming Flash was too slow. The remaining members of the Syndicate (Ultraman, Superwoman, and Power Ring) are arrested by the U.S. Marines, led personally by President Wilson after J'ohn.
Wilson thanks the Justice League for giving them back their world and they are sent back to their own dimension. When they return, Wonder Woman keeps the still-cloaked plane that she stole from Owlman. Because of the League's forces being spread too thin, Batman thinks about a membership drive and opens the door to the heroes (Aquaman, Red Tornado, Black Lightning, Firestorm, and Black Canary) that he had summoned for help earlier and keeps them around to start expanding the League.