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.
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.
La Ligue de justice d'Amérique est contrainte de faire appel aux services spécifiques de John Constantine et de ses camarades spécialistes de l'occultisme pour contrer une importante menace d'invasion.
Alimenté par sa foi restaurée en l’humanité et inspiré par le sacrifice de Superman, Batman constate l'arrivée d'éclaireurs extraterrestres — appelés "Paradémons" et attirés par la peur de leurs victimes — et comprend que l'attaque majeure prophétisée par Lex Luthor (dans le film Batman v Superman : L'Aube de la justice) est imminente, or Superman est mort et ne peut plus protéger l'humanité. Conscient de ses propres limites, il contacte Diana Prince/Wonder Woman et tente de former avec elle une ligue de super-héros. Il part retrouver Arthur Curry, dit Aquaman, qui habite à Atlantis, tandis que Diana va approcher Victor Stone, footballeur devenu à moitié machine après un accident et capable d'influer sur les technologies, mais les deux hommes refusent de les aider. Barry Allen, jeune homme doté de super-vitesse, accepte avec enthousiasme l'offre de Bruce Wayne.
Gotham City-based vigilante Batman travels to Metropolis to preemptively combat Superman, fearing what would happen if the latter is kept unchecked, while another threat endangers humankind.
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.
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.
The documentary looks at the story behind Superman Lives, a film that was cancelled only three weeks before filming was set to begin. In the film Schnepp interviews several people involved with the development of the project and shows artwork and designs that would have been featured in Superman Lives if it had been made. Though the Run time is 104 minutes, there is an extended version of the film.
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".
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:
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!
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.
In the Lego universe, the wizard Vitruvius attempts to protect a superweapon called the "Kragle" from the evil Lord Business. He fails to do so, but prophesies that a person called "the Special" will find the Piece of Resistance capable of stopping the Kragle.
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 planet Krypton faces imminent destruction due to its unstable core; the result of depleting Krypton's natural resources. The ruling council is deposed by the planet's military commander, General Zod, and his followers during a coup d'état. Knowing that artificial population control and isolationism have ruined their civilization, scientist Jor-El and his wife Lara launch their newborn son, Kal-El, the first naturally born Kryptonian child in centuries, on a spacecraft to Earth after infusing his cells with a genetic codex of the entire Kryptonian race. After Zod kills Jor-El, he and his followers are captured and exiled to the Phantom Zone. However, they are indirectly freed after Krypton explodes, rendering the Kryptonian race extinct apart from Zod and his forces.