While touring Powers Industrial,
Barbara Gordon witnesses a power generator being stolen by the
Foot Clan and also spots four creatures during the robbery that she refers to as
metahumans. She reports this back to Batman, who decides that if the culprits want high tech, he will set a trap with it. The Foot Clan then attacks
Wayne Enterprises to steal an experimental
cloud seeder machine, but are ambushed by
Batman, who fends off the Foot and their leader,
Shredder. Meanwhile, it is revealed that the four metahumans Batgirl sighted are actually the
Teenage Mutant Ninja Turtles, currently tracking Shredder's actions to Gotham City, having learned he has allied with an unknown party. After defending Wayne Enterprises from the
Penguin, the Turtles encounter and fight Batman, as each side believes the other is the enemy. Batman is able to overpower the Turtles, who then retreat.
Donatello researches Batman and his sighted locations, and uses this information to figure out the location of the
Batcave. After a brief scuffle with
Robin, Batman and Batgirl arrive, and the Turtles introduce themselves and explain their reason for coming to Gotham. The two groups agree to work together against their common enemies, and Robin reveals that Shredder and the Foot Clan are working with
Ra's al Ghul and the
League of Assassins. Shredder and Ra's meet and strike a bargain: Ra's will give Shredder access to the Lazarus Pit to become immortal, in exchange for Shredder building a machine that will spray the Techno Cosmic Research Institute (TCRI) mutagen over Gotham, transforming the citizens into monstrous mutants that will destroy the city. With Shredder's failure to steal the cloud seeder, Ra's hires the Penguin to intercept it, while he and Shredder go to
Arkham Asylum and release the
Joker. The two trade Joker a vial of the TCRI mutagen for the Joker Venom formula, which combined with the mutagen will drive the mutated insane, and Joker uses the mutagen on Arkham's inmates. The Bat-Family and the Turtles are alerted about an alarm at Arkham by
Commissioner Gordon and investigate. After fighting their way through various mutated members of
Batman's rogues gallery, they confront
Harley Quinn and Joker, mutated into a
spotted hyena and a
king cobra. Joker injects Batman with a mixture of Joker venom and mutagen, transforming him into a mutant
vampire bat who attacks the others in a frenzy, throwing Two-Face out a window. The heroes are able to inject Batman with an anti-mutagen and restore him, and subdue Harley and Joker. Batgirl learns about the cloud seeder's theft by Penguin, and they realize the incident at Arkham was a distraction. Aware that Shredder and Ra's will be using Joker venom, they deduce they will be at
Ace Chemicals to create it. At Ace Chemicals, the Bat-family and the Turtles fight through the Foot Clan and the League of Assassins with the
Batmobile and the Turtle Van. While Batman fights Shredder and
Leonardo engages Ra's, Donatello and
Michelangelo sabotage the cloud seeder as it launches. Leonardo subdues Ra's, and Batman is able to defeat Shredder with a distraction from
Raphael. The cloud seeder crashes into the facility and explodes, knocking Shredder into a vat of Joker venom and destroying Ace Chemicals. At the Batcave, the Turtles prepare to return to New York until Batman reveals a surprise pizza party to celebrate their victory. In a
post-credits scene, Shredder emerges from the rubble of Ace Chemicals, now possessing a Joker-like appearance and laughing maniacally. ==Voice cast==