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.
Barbara Gordon traque les criminels de Gotham City dans le costume de Batgirl. Une nuit, elle tente d'arrêter des braqueurs seule mais échoue ; Batman intervient et capture l'un des voleurs en fuite. Les deux justiciers identifient l'organisateur : Paris Franz, neveu du parrain du crime Lord Francesco, qu'il souhaite évincer pour prendre sa place, et qui commence à être obsédée par Batgirl. Batman demande à sa protégée de le laisser faire mais elle refuse. Quand Franz piège Batgirl en la menant vers le cadavre de Francesco, Batman lui interdit de s'impliquer dans l'affaire. Furieuse, Batgirl commence à frapper Batman et le plaque au sol avant de l'embrasser, puis ils couchent ensemble. La nuit sème la confusion dans la relation entre Batman et Batgirl. Franz se manifeste à nouveau, piégeant Batman, et Batgirl intervient mais manque de le tuer. Barbara se rend compte que Batman avait raison et abandonne son costume.
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.
When Gotham is plagued by crime committed by an animal-themed villain squad composed of The Penguin, Silverback, Cheetah, Killer Croc and Man-Bat, Batman and other heroes band together to stop them.
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 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".
During an investigation of missing children, Damian Wayne, still fighting crime as Robin, has taken the Batmobile out to an abandoned toy factory without Batman's consent, where he finds Anton Schott, who is responsible for the children's disappearance and has also transformed some of them into grotesque, mutilated "Dolls". Damian's father, Bruce, arrives as Batman to aid Damian in the resulting battle, with Damian chasing after the Schott while Batman knocks out the Dolls with gas and frees the remaining children. Damian chooses to spare Schott, only for an owl-masked assassin to kill him, telling Damian to never doubt his instincts. The assassin leaves Damian and the Schott's body behind, leading Batman to accuse Damian of murdering him when he arrives. Damian insists he spared Schott out of respect for Batman, and after inspecting the body further, Batman discovers an owl feather.
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!
It’s Halloween night in Gotham City and Scarecrow, Clayface, Silver Banshee and Solomon Grundy have hit the streets to stir up trouble! Batman is on the trail of the city’s spookiest villains while, further complicating matters, the clown prince of crime himself, The Joker, is ruling over this mysterious crew of misfit criminals. It’s up to the Dark Knight to stop this gruesome gang before they unleash “digital laughter,” a computer virus that’s part of a diabolical plan to jeopardize all of Gotham City’s vital technology. Batman, Green Arrow, Cyborg, Nightwing and Red Robin must combine forces to battle these baddies and save the city.
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.
At the headquarters of the League of Assassins, Ra's al Ghul grooms Damian Wayne (son of his daughter, Talia, and Batman) to succeed him as head of the league. The league is attacked by a group of assassins led by Slade Wilson, Ra's al Ghul's initial choice for successor before Ra's met Batman. Feeling betrayed, Slade decided to seize power. During the battle, Ra's is fatally burned in a missile strike explosion, dying inches away from reaching the Lazarus Pit. Although Damian stabs Slade in the eye, Slade escapes, vowing vengeance. Talia takes Damian to Gotham City to protect him with his father's help.
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.
Batman rescues Riddler from a black ops assassination ordered by Amanda Waller, returning him to Arkham Asylum. Invoking Priority Ultraviolet, Waller captures criminals Black Spider, Captain Boomerang, Deadshot, Harley Quinn, KGBeast, Killer Frost and King Shark forming the Suicide Squad. Their mission is to break into Arkham Asylum and recover a thumbdrive in the Riddler's cane. While in Waller's employ, Riddler copied information on the squad, and is planning to make it public. She forces them to comply by threatening to detonate nano-bombs implanted in their necks. KGBeast, who believes the bombs are a bluff, walks out on Waller and is killed as an example to the others.