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.
Adam West and Burt Ward go in search of the Batmobile after it is stolen, and along the way find themselves forced to consult their memories to decipher clues left by the criminals, evidently people they had known from filming the Batman television series. Memories include affairs, one of which led to Burt being chased by a knife-bearing lover, medicine Burt was forced to take so his genitals would not be so visible in his tights, and Adam meeting the actress who played Batgirl (Yvonne Craig) and accidentally placing a hand on her breast during filming. As it turns out, the villains who stole the Batmobile were the actors who once played the Riddler (Frank Gorshin) and Catwoman (Julie Newmar).
The Joker escapes from Arkham Asylum, causing a nurse to be taken to intensive care after spraying some of his lethal gas in her face. Upon arriving in Gotham City, he kidnaps Councilman Johnson and his son shortly after brutally murdering the Councilman's wife. Determined not to let his archenemy murder anyone else, Batman hunts him through the city. After Councilman Johnson is found dead while his son remains in The Joker's captivity, Batman questions whether his crusade against evil does more bad than good. Batman tracks The Joker to a carnival, where he thwarts the villain's plot of bombing a ferris wheel. He then races to the location of The Joker and the councilman's son, but when the young boy kills The Joker with his own gun, Batman debates if his greatest nemesis' death is a step toward Gotham's peace, or rather a sign that things are getting worse.
Batman, Robin and Nightwing investigate a string of incidents where a mysterious assailant has been taking down numerous crime organizations all over Gotham City. In their findings, they discover that while the thugs were taken down and no cash was stolen in the crime scenes, The Riddler and The Scarecrow have been lethally drugged with a botanical neurotoxin found only in the Far East. Moreover, blood splatters in the crime scenes indicate that the assailant was reckless, not caring about sustaining gunshot wounds during the fights while drugging the villains. Batman concludes that the assailant is Batgirl, who is being manipulated by Poison Ivy; the gunshot wounds she sustained were her failed attempts at breaking the spell. Batman and Robin confront Poison Ivy, who attempts to kill Batman with a lethal dose of the neurotoxin. An injured Batgirl, however, briefly breaks Poison Ivy's spell on her to block the shot as the villainess makes her escape and Nightwing rushes to the scene with the antidote.
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.
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.
Mister Freeze et Le Pingouin sont de retour à Gotham City. Après avoir réfrigéré la ville, le scientifique transforme Bane et Killer Croc en monstres géants dévastant tout sur leur passage. Afin de les combattre, Bruce Wayne élabore un robot géant de Batman et le combat commence. Dans sa quête pour ramener la paix, le super héros sera suivi dans son affrontement par Robin, Green Arrow, Nightwing et Flash.
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.
Alors qu'il combat Gorilla Grodd, Batman est pris dans sa machine temporelle et est envoyé au Japon féodal. Il y est chassé par des samouraïs au service du Joker. En s'échappant, il rencontre Catwoman, elle aussi prise dans le temps depuis deux ans, qui lui apprend que les criminels de Gotham sont tous là et sont devenus des Seigneurs féodaux après avoir abusé le daimyō. Batman et Catwoman doivent donc intervenir pour empêcher les vilains de ré-écrire l'histoire.
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.
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...
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".