À Gotham City, les quatre plus grands criminels (le Joker, le Pingouin, le Sphinx et Catwoman) font peser une terrible menace. Les super-héros Batman et Robin vont faire face à ces méchants et devront même aller dans l’espace pour contrecarrer le plan diabolique de leurs ennemis.
Bruce Wayne returns home to Gotham City after 12 years abroad, and Lieutenant James Gordon moves to Gotham with his pregnant wife, Barbara, after a transfer from Chicago. Both are swiftly acquainted with the corruption and violence of Gotham City, with Gordon witnessing his partner Detective Arnold Flass assaulting a teen for fun.
Alors que Bruce Wayne et Selina Kyle (et leurs alter égo, Batman et Catwoman) entament une relation amoureuse, un nouvel ennemi apparait; un ennemi qui a manipulé des criminels aussi puissants que Bane, Poison Ivy, L'Épouvantail, Gueule d'argile, Harley Quinn ou encore le Joker; un ennemi qui a découvert la véritable identité de Batman et tous ses secrets; un ennemi qui a un plan pour détruire le justicier, ses proches et ses alliés définitivement: Silence...
After the death of his protégé Jason Todd, billionaire industrialist Bruce Wayne was forced to retire from his Batman persona. Ten years later, Gotham City is overrun with crime and terrorized by a gang known as the Mutants. The 55-year-old Wayne maintains a friendship with 70-year-old retiring Police Commissioner James Gordon, while the Joker (Batman's archenemy) has been catatonic in Arkham Asylum since Wayne's retirement. Arkham inmate and former district attorney Harvey Dent undergoes plastic surgery to repair his disfigured face. Although he is declared sane, he quickly goes into hiding following his release. Dent's disappearance, news stories of the crime epidemic throughout the city and the memory of his parents' deaths drive Wayne to become Batman once more. He combats serious crimes, rescuing 13-year-old Carrie Kelley, but now struggles with the physical limitations of age.
Batman and Robin struggle against Dr. Daka, a Japanese scientist and agent of Hirohito who has invented a device that turns people into pseudo-zombies and has a base in a funhouse of horrors in a Japanese area of the city. Daka makes several attempts to defeat the Dynamic Duo before finally falling to his death when Robin hits the wrong switch, opening a trapdoor to a pit of crocodiles.
Since his last encounter against Batman, Mr. Freeze has found a home in the Arctic and started a family (of sorts) with the still cryogenically-encased Nora, an Inuit boy named Kunac, and two pet polar bears, Hotchka and Shaka. Nora's condition begins to rapidly deteriorate due to a submarine accidentally emerging from underwater directly underneath them, shattering her containment vessel. Freeze returns to Gotham City with his companions. He enlists the help of Dr. Gregory Belson to find a cure. Belson determines that Nora needs an organ transplant, but due to her rare blood type there are no suitable donors available.
As a child, Bruce Wayne falls down a dry well, where he is attacked by a swarm of bats; he subsequently develops chiroptophobia. While watching an opera with his parents, Bruce is frightened by performers masquerading as bats, and asks to leave. Outside, the family is targeted by a mugger, Joe Chill, who murders Bruce's parents, leaving him to be raised by the family butler, Alfred Pennyworth.
Batman et Robin sont invités à une démonstration très secrète animée par le professeur Hugo Strange et son assistant, le Dr Harleen Quinzel, qui pourrait éventuellement changer à jamais le futur de Gotham. En cours de route, Batman s'arrête au pénitencier d'État de Gotham pour rendre visite à Catwoman (dont la tentative de suicide du premier film a échoué) pour lui remettre un livre de poésie d'Elizabeth Barrett Browning. C'est quelque chose qui la tiendra occupée pendant les 36 prochains mois de sa vie jusqu'à ce qu'elle soit définitivement libérée de prison. Au laboratoire, ils rencontrent le procureur et allié de Bruce Wayne dans la guerre contre le crime Harvey Dent, célèbre pour avoir arrêté un gang de contrefacteurs de pièces tout en conservant un quartier à deux faces en souvenir de l'affaire.
The Joker and the Penguin break out of Arkham Asylum and race each other to find a stash of stolen money hidden within a crypt in Gotham Cemetery after an inmate, who had hidden it, told them about it. The Joker is quickly intercepted by the Batman and is electrocuted when he falls into a river by his super-charged joy buzzers while the Penguin takes the opportunity to enter the cemetery himself. While searching through a crypt, the Penguin accidentally cuts his hand while using his umbrella-sword to open a coffin he hopes contains the money, finding a body instead. Blood from his hand drips on the corpse's heart, which brings it to life; it is none other than the vampire lord Count Dracula, his body having been moved from Transylvania to Gotham City after his "death." After attacking and turning a watchman at the cemetery into a vampire, Dracula hypnotizes the Penguin into becoming his non-vampiric servant so that he may lead him through Gotham to feed and guard his coffin during the day while he regains his strength.
During a conference of crime bosses held in a Gotham City skyscraper, gangster Chuckie Sol is killed by a mysterious cloaked figure, shortly after Batman bursts in on the meeting. Due to the killer's resemblance to Batman, the Dark Knight is blamed for Sol's death. Councilman Arthur Reeves tells the media that Batman is a public menace (despite Commissioner Gordon's protests), then later attends a party at the mansion of billionaire Bruce Wayne, Batman's secret identity. Reeves teases Bruce about his bad luck with women and for having allowed an old girlfriend, Andrea Beaumont, to get away.
Batman, Batgirl et Robin forment une alliance avec les Tortues Ninja pour affronter Shredder qui s'est apparemment joint à Ra's al Ghul et sa Ligue des Assassins, afin de pouvoir prendre le contrôle de la ville.
At a manor in Sarajevo, Ra's al Ghul ruefully realizes his mistake in allying himself with the Joker, while his assistant informs him that the Joker has captured Jason Todd, the second Robin. In a warehouse, the Joker brutally beats Jason with a crowbar while Batman races there. Joker then leaves the warehouse and traps a half-dead Jason inside. Although Jason attempts to escape, a planted explosive destroys the building before Batman can rescue him.
Batman and Robin fail to stop Mr. Freeze from stealing a cache of diamonds. They learn that Freeze was once a scientist named Victor Fries, who became dependent on a diamond-powered subzero suit following an accident in a cryogenics lab while working to save his wife, Nora, from a terminal illness called MacGregor's Syndrome.
The Dynamic Duo face off against the Wizard, a hooded villain with an electrical device which controls cars and a desire to set challenges for the Dynamic Duo, whose identity remains a mystery throughout until the end.