Crime is on the run as the newly formed Justice League keeps Metropolis safe and this makes evil genius Lex Luthor very unhappy. Together with Black Manta, Sinestro and a gang of ruthless recruits, Lex builds his own league and declares them the Legion of Doom.
In an alternate universe where evil usually triumphs over good and where the roles of the heroes and villains are reversed from their counterparts in the mainstream DC Universe, heroic analogues of Lex Luthor and the Joker (called the Jester) are attempting to steal a device, the "Quantum Trigger", from the headquarters of the Crime Syndicate. The pair trip an alarm but manage to secure the device. The Jester sacrifices himself to allow Luthor to escape and kills J'edd J'arkus and Angelique (alternate versions of Martian Manhunter and Hawkgirl respectively) with a radioactive bomb. Luthor is confronted by the remaining Syndicate members (Ultraman, Superwoman, Power Ring, Johnny Quick and Owlman) but escapes to the Earth of the heroic Justice League by activating a dimensional travel device.
In an alternate universe, the Justice League is a brutal force that maintains order on Earth. This universe has its own versions of Superman, Batman, and Wonder Woman:
The Justice League, with assistance from Cyborg, stop the Royal Flush Gang as they attempt to rob a diamond vault using complex technology that allows them to pass through solid objects. Wonder Woman uses her lasso of truth on the leader to find out who gave them the technology. The leader, despite being under the influence of the lasso, says that he doesn't know who gave them the technology. Martian Manhunter uses his mental powers to scan the minds of each member of the gang, none of them know the origin of the device. Meanwhile, Vandal Savage plots to exterminate the greater part of the human population and start a new civilization, having discreetly given the technology to the Gang in order to test it. To ensure that the Justice League is unable to stop him, Savage hires Mirror Master, who hacks into the Batcomputer and steals contingency plans devised by Batman to incapacitate his League teammates should they ever go rogue. When Mirror Master asks if he wants him to find Batman's true identity, Savage declines stating that he already knows the true identity of Batman. Savage assembles Mirror Master and a group of other supervillains (consisting of Bane, Cheetah, Ma'alefa'ak, Star Sapphire, and Metallo) with personal vendettas against the heroes and pays them to simultaneously attack the members of the League using the stolen plans, albeit altered to be lethal. When the supervillains agree with Savage's plan, he welcomes them to the Legion of Doom.
A series of strange abductions have occurred in Gotham City, Central City, Coast City and Metropolis among others. Video footage suggests that Batman, a wanted, costumed vigilante, is behind the incidents. When a mysterious, burly, cloaked kidnapper abducts a woman, Green Lantern (Hal Jordan) arrives to confront the kidnapper and saves the woman when she is dropped from above. Green Lantern then attacks the kidnapper, revealing it to be a monstrous Parademon. The creature defeats Green Lantern soundly, and as he is about to be killed, Batman appears and attacks the Parademon, trying to interrogate it. The Parademon then attacks both heroes. They escape from the city's police and chase the creature into the sewers, where it charges a Mother Box and explodes. Batman and Green Lantern examine the box, deduce that it is of extraterrestrial origin, and decide to ask Superman for an answer. Another Mother Box, supplied by The Flash (Barry Allen) is being studied at S.T.A.R. Labs. Doctor Silas Stone, father of Vic Stone, deliberately misses his son's football game so he can study the box. Arriving in Metropolis, Batman and Green Lantern fight Superman—who has fought a Parademon previously and believes the heroes are working with it. The battle spreads over a portion of the city; it finally stops when Batman calls Superman "Clark". Superman uses his x-ray vision and recognizes Batman as billionaire Bruce Wayne. The three heroes then begin to collaborate. On planet Apokolips, Darkseid orders Desaad to begin an invasion of Earth in response to the superheroes' discovery of his plans.
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 the Top at the Flash Museum. Defeating the Rogues, he discovers that they have been hired by his archenemy Professor Eobard "Zoom" Thawne, the Reverse-Flash as part of a plan to destroy Central City. With the help of the Justice League, Barry foils Zoom's plot, but Zoom's taunts over the death of his mother still haunt Barry as he departs.
In the Atlantic Ocean, the USS California submarine picks up incoming human-like threats approaching the sub by sonar. The sub is attacked, leaving the entire crew dead by the invading hostiles. At S.T.A.R. Labs' Justice League headquarters, Cyborg is given news by Colonel Steve Trevor over the sunken sub. Cyborg decides to check it himself, deciding against Trevor's idea of calling the other superheroes, as he puts it "there is no Justice League".
The film, set between 1953 and 1960, opens with an unknown entity (Keith David) narrating that it has witnessed the evolution of life on Earth and has decided to eradicate mankind because of its capacity of violence and destruction. At the end of the Korean War, United States Air Force pilot Hal Jordan (David Boreanaz) and his wingman, Kyle "Ace" Morgan (John Heard), are attacked by enemy pilots. Hal is shot down, ejects to safety and is forced to kill a North Korean soldier, causing him to be hospitalized for mental trauma. At Gotham Observatory, scientist Dr. Saul Erdel inadvertently teleports J'onn J'onzz (Miguel Ferrer)—the last survivor of the Green Martian race—to Earth. The shock of J'onn's sudden appearance causes Erdel a heart attack. Unable to return to Mars, J'onn disguises himself as Erdel and takes his wallet and identification.
Doomsday, monstre provenant de l'espace, atterrit sur Terre à bord d'une météorite. Écrasant la totalité de la Ligue des Justiciers avec une déconcertante facilité, Superman se voit devenir le seul être capable de venir à bout de la créature. Seul son courage et sa détermination viendront à bout de la créature extraterrestre, y compris le sacrifice si cela s'avère être la seule solution possible.
Six mois après la mort de Superman après avoir vaincu Doomsday, quatre nouvelles versions du héros apparaissent: Superboy, Steel, Cyborg, Superman et Eradicator. Chacun d'entre eux est différent dans sa personnalité et son style de combat du crime par rapport à Superman, laissant le monde entier se demander lequel est le vrai Superman. Lois Lane, encore sous le choc de la mort de Clark, décide de mener une enquête. Lex Luthor tient une conférence de presse présentant Superboy comme le véritable Superman, sponsorisé et financé par LexCorp. Lois assiste à la conférence avec Steel et se faufile dans l'un des laboratoires de LexCorp. Là, Lois apprend du scientifique Dabney Donovan que Superboy est un clone de Superman. Soudainement, la conférence est attaquée par l'éradicateur, qui cherche à "éradiquer" Luthor. Superboy et plus tard Steel tentent de l'arrêter, mais sont vaincus jusqu'à l'arrivée à temps de Cyborg Superman, qui se bat et chasse Eradicator. Beaucoup le voient comme le vrai Superman, provoquant la colère de Luthor. Lois écrit un exposé révélant que Superboy est un clone et demande si tous les Supermen sont des faux. Cela conduit à une rencontre entre elle et Cyborg Superman, lui disant qu'elle sait qu'il n'est pas le Superman qu'elle a connu et aimé.
Bruce Wayne and Lex Luthor are both nominated for the Man of the Year award, and Wayne wins. As he is making his speech, the Joker breaks in with the Riddler, Harley Quinn, the Penguin, Two-Face, Poison Ivy, Bane, Catwoman, and steals the award, as well as money and gems. Batman arrives and stops everyone except the Joker, who escapes on his boat, but Robin's helicopter picks up Batman. When the rope holding Batman is broken, he calls in the Batwing and defeats the Joker. Meanwhile, Luthor is running for president, but his poll figures are terrible. He learns that the Joker knows how to produce more Kryptonite, and can make a gas that makes people love him, which will help Luthor win the election and defeat Superman. He breaks the Joker out of Arkham Asylum and promises him the use of Luthor's De-Constructor weapon to defeat Batman by dismantling all his gadgets and vehicles.
Batman doit faire face au plus grand défi de sa vie : les vacances ! Le chevalier noir accepte à contre-coeur de laisser Batgirl et Nightwing l'emmener pour un repos longtemps repoussé loin de la lutte contre le crime, laissant Gotham City sous la protection de Superman et de la Ligue des Justiciers. Rien ne se déroule comme prévu lorsque les vacances de Batman sont écourtées par des dangers provenant de son passé et des envahisseurs du centre de la Terre. Superman et les autres membres de la Ligue des Justiciers réalisent très vite la quantité de travail qu'a Batman dans sa lutte quotidienne contre le crime à Gotham.
Superman’s clone Bizarro has become an embarrassing problem. Chaos and destruction follow Bizarro everywhere as he always hears the opposite of what is said, says the opposite of what he means and does the opposite of what is right. And when the citizens of Metropolis keep confusing Bizarro with Superman, the Man of Steel decides it’s time to find a new home for him....on another planet! It’s up to the Justice League to come to terms with their backward counterparts and team up with them to stop Darkseid and save the galaxy!
In the present day, Lex Luthor and his Legion of Doom try to use cryogenic rays from orbital satellites to expand the Earth's polar ice caps in the Arctic Ocean, causing a massive drop in sea levels and creating new islands they intend to rule. Superman and the Justice League confront the Legion, dividing their forces to fight the Legion and destroy the satellites. In the ensuing space battle, Robin purposely crashes his spacecraft into the satellite array. Refusing to accept defeat, Captain Cold overloads the remaining satellite, which falls back to Earth and entombs Luthor in an ice sheet shortly before the satellite explodes. The League is triumphant and believes Luthor to be dead.
The Tiny Toon Adventures characters leave for their summer vacations after their term at Acme Looniversity ends. Babs and Buster Bunny have a water pistol fight, which eventually escalates into their flooding Acme Acres. The bunnies, along with Byron Basset, float from flooded Acme Acres down to the southern United States, where they continuously avoid getting eaten by the river's residents.