When playing with Rachel, eight-year-old Bruce Wayne develops a fear of bats after falling into a well where he is attacked by swarms of bats. Having left the opera early, both Wayne's parents are shot dead after being mugged. The murderer is arrested, but Wayne still blame himself for the accident because it's him who urged his parents to leave.
Back from college, Wayne is furious to hear that Chill(the murderer who killed his parents) is about to be paroled after he testifies against mob boss Felcone. Carrying a gun, he is waiting outside the court, intending to kill Chill. But while he is hesitating, Chill is shot by a female assassin who is apparently sent by Felcone. After scolded by Felcone for being innocence of the desperate lives, Wayne resolves to travel the world to experience poverty and crime; he is apprehended by Chinese police and put in jail until approached by Ducard, who frees him and invites him to join his group: the League of Shadows. In the temple where the group assemble, Wayne meets the leader of the group, Ra's al Ghul, and he is trained to conquer his fear by Ducard. After refusing to execute a farmer, Wayne sets the temple on fire and engages in a fight with Ra's. A beam falls down crushing Ra's to death; Wayne saves his unconscious mentor and jumps out the temple before it explodes.
Returning to Gotham, Wayne prepares to fight the corrupt city. With the help of Alfred(his butler) and Fox(former board member of his father's company), he designs a black suit with bat as a symbol and other paraphernalia; Batman was born. Felcone and his henchmen are uploading drugs at a dock when Batman interferes. Felcone is tied to a searchlight forming a bat symbol in the sky.
Rachel confronts Dr. Crane, who is a psychopharmacologist at Arkham Asylum and a partner of Felcone, about Felcone's convenient mental breakdown after his arrest. Crane reveals that he has invented a type of fear-inducing drugs which can cause hallucinations upon inhaling, and they are putting it into Gotham's water supply to purge the city. Rachel is drugged. Batman then comes to the rescue, bring her back to his manor driving his Batmobile, just in time to inoculate her.
At Wayne's birthday party, Ducard shows up revealing himself as the real Ra's al Ghul. Wayne delivers a insulting speech to the guests and disperses them before Ducard sets his manor on fire. Alfred saves an unconscious Wayne and they narrowly escape the explosion.
Meanwhile, at the Narrow section of Gotham, Ducard and his followers are installing a microwave emitter which will vaporize Gotham's water, eventually resulting in releasing the fear-inducing drug into the air. All prisoners at Arkham Asylum are set free by Ducard's men, including Dr. Crane, who proceeds to chase Rachel, but she manages to stave him of with a razer. With the water vaporized, the drug is releasing into the air, all the people are infected except for Ducard, the ninjas, sergeant Gordon and Rachel. Batman arrives, and after rescuing Rachel from a group of infected people, he intimates to her his identity then takes off with Rachel shouting his name.
Ducard carries the microwave emitter on a monotrain, heading to the center of the city, vaporizing water all the way. Batman enlists Sergeant Gordon's help to devastate the base of the monorail in order to prevent him from approaching the water main. Driving the Batmobile, Gordon suscessfully destroys it. On board the train, Batman picks up a fight with Ducard. After defeating him, Batman jumps out of train, leaving Ducard crash with it.
Back at the ruins of his manor, Wayne decides to rebuild it. Rachel comes over and they kiss each other. But she then makes it clear that she can't accept his dual identity. Gordon using the searchlight to form a bat symbol to pay homage to Batman, and though the drug is under control, the city is suffering from the aftermath, as half of the prisoners of the Arkham Asylum are at large; especially a psycho who left a joker at the crime scene, and Batman agrees to take care of it. Leaving a cliffhanger for the sequel.