The film begins with a young Bruce Wayne falling into a well on the Wayne estate. His father rappels down to get him after the young boy has been frightened by bats. Flash forward 14 years we see that Bruce is in prison in Bhutan for theft; he was stealing Wayne Enterprises goods. He meets Ducard, who bids him to come find him and train with him in The League of Shadows. Bruce gets out of prison and ascends the highest mountain to find The League waiting for him.
He trains with them and must pass a final test which he is under the influence of the hallucinogen from the rare blue flower that grows on the face of the mountain. He passes the test but learns that Ducard wants him to lead a group from The League into Gotham City in order to destroy it so that it can be rebuilt from the ashes. Bruce then fights all of the trainees and kills who he thinks is Ra's Al Ghul when the training temple is destroyed. Ducard who is knocked out cold is saved by Bruce.
Wayne returns to Gotham City in order to fight the crime and reclaim the city for good. He enlists the help of Lucius Fox, Wayne Enterprises archivist who was also a good friend of Bruce's Dad. In order to maintain a facade Bruce pretends to be a playboy in public so no one will believe that he is the Batman at night. Eventually Ra's Al Ghul comes to Gotham and Bruce learns that Ducard is Al Ghul and was misdirecting him the entire time he trained him.
The League of Shadows seeks to contaminate Gotham's water supply with the help of Dr. Jonathan Crane, aka Scarecrow, who is head of Arkham Asylum. Crane uses the hallucinogen from the blue flower in order to manipulate the minds of his patients, and The League is using it to contaminate Gotham's water. Batman enlists the help of Detective Jim Gordon, the one trustworthy cop in the Gotham Police Department, in order to help him stop the crime and eventually to stop The League from destroying the city. Batman is able to stop the attack and defeat Ra's Al Ghul. He even gives away his identity to Rachel, his longtime best friend and the woman he loves. But she cannot be with him knowing that he is Batman.
The end of the film shows Gordon using the Bat-Signal to call for Batman who arrives on the roof of the building of the Police Department. Gordon tells the Batman that there is a new criminal in town who leaves a calling card: a joker from a deck of cards. Batman says he will look into it and disappears into the night.
