In Gotham City, a series of tech company robberies put Batman on high alert, leading him to believe that a new threat has invaded his city. Meanwhile, the Teenage Mutant Ninja Turtles—Leonardo, Raphael, Donatello, and Michelangelo— arrive in Gotham, pursuing their enemy Shredder, who has joined forces with the infamous Ra's al Ghul and The League of Assassins. As Batman encounters the Turtles, they clash due to a misunderstanding of each other's intentions. During this initial conflict, Batman proves to be a formidable opponent to the Turtles, who are caught off guard by his expertise and gadgets.

The Turtles' search for Shredder leads them to infiltrate Arkham Asylum, where more pieces of a sinister plan come to light. The unusual activity in Arkham draws Batman's attention, and he begins to piece together Shredder's alliance with Ra's al Ghul. Batman's straight-laced sense of justice contrasts with the Turtles' more easygoing and unconventional approach to heroism. Despite their differences, the Dark Knight and the heroes in a half-shell find themselves needing to put aside their misunderstandings. They must work together if they intend to stop Shredder and Ra's al Ghul's destructive plot unfolding within the shadows of Gotham.