Bruce Wayne returns home to Gotham City after 12 years abroad, mostly people don’t know he was training really hard to fight his war on crime and Lieutenant James Gordon moves to Gotham with his pregnant wife, Barbara, after a transfer from Chicago. Both are swiftly acquainted with the corruption and violence of Gotham City, with Gordon witnessing his partner Detective Arnold Flass assaulting a teen for fun.
Bruce goes in disguise on a surveillance mission in the seedy East End, where teenage prostitute Holly Robinson propositions him. He is drawn into a brawl with her pimp and several prostitutes, including domina.trix Selina Kyle. One of the two reporting police officers shoot him and take him in their squad car, but a dazed and bleeding Wayne maneuvers his handcuffed hands in front of himself, and demands the police get out. The cops try to subdue him, but the ensuing struggle causes the police car to careen out of control, and flips. Wayne flees, but not before dragging the police to a safe distance. He reaches Wayne Manor, barely alive, and sits before his father’s bust, requesting guidance in his war on crime. A bat crashes through a window and settles on the bust, giving him inspiration.
Gordon works to rid corruption from the force, but on orders from Commissioner Gillian Loeb, several masked officers attack him, including Flass, who threatens Gordon’s pregnant wife. Gordon tracks Flass down, beats him up, and leaves him naked and handcuffed in the snow.
As Gordon becomes a minor celebrity for his bravery on the job, Batman strikes for the first time, attacking a group of thieves and gaining experience. Batman soon works up the ladder, even attacking Flass while he was accepting a bribe. He gains a reputation of being a supernatural being and inhuman, due to his use of speed and darkness to conceal himself. Two months after Batman arrived, the crime and corruption has declined. After Batman interrupts a dinner party attended by many of Gotham’s corrupt politicians and crime bosses, including Carmine “The Roman” Falcone to threaten their criminal organization, Loeb orders Gordon to bring him in by any means necessary.
As Gordon tries in vain to catch him, Batman attacks Falcone, stripping him naked and tying him up in his bed after dumping his car in the river. Assistant district attorney Harvey Dent becomes Batman’s first ally and he conceals this from Gordon.
Detective Sarah Essen suggests Wayne as a Batman suspect and she and Gordon witness Batman save an old woman from a runaway truck. Essen holds Batman at gunpoint, but Batman disarms her and flees to an abandoned building. Loeb fraudulently orders a bomb dropped on it, forcing Batman into the fortified basement. A SWAT team is sent in, led by trigger-happy Lieutenant Branden, whom Batman attempts to trap in the basement. Branden manages to climb out of the trap through a collapsed chimney, and joins in the gun battle. Enraged as the team’s careless gunfire injures several people outside, Batman beats the team into submission, but is wounded during the fighting. Using a signal device to attract the bats of his cave to distract the police and conceal himself, Batman escapes amid the chaos. Selina Kyle, after witnessing him in action, dons a costume of her own to begin the life as Catwoman.
Gordon has a brief affair with Essen, while Batman intimidates a drug dealer for information. The dealer goes to Gordon to testify against Flass, who is brought up on charges. Loeb blackmails Gordon with proof of his affair against pressing charges. After taking Barbara with him to investigate Wayne’s connection to Batman Gordon confesses the affair to her. Bruce avoids Gordons suspicions by appearing with a woman over and heavily drinking, though he is actually faking all of it.
Batman sneaks into Falcone’s manor and overhears a plan against Gordon but is interrupted when Catwoman, hoping to build a reputation after her robberies were pinned on Batman, attacks Falcone and his bodyguards, aided by Batman. Identifying Falcone’s plan as the morning comes, the un-costumed Bruce leaves to help Gordon.
Gordon tries to rebuild his relationship with his family after Essen leaves Gotham. While leaving home, Gordon spots a motorcyclist enter his garage. Suspicious, Gordon enters to see Johnny Vitti (Falcone’s nephew) and his thugs holding his family hostage. Gordon realizes if he lets them go, they will most likely kill his wife and son. Therefore, Gordon shoots the thugs and chases Vitti, who has fled with the baby. Bruce Wayne, on a motorcycle, also rushes to chase Vitti. Gordon blows out Vitti’s car tire on a bridge and the two fight, with Gordon losing his glasses, before Vitti and James Gordon Jr. fall over the side. Bruce leaps over the railing and saves the baby. Gordon realizes that he is standing before an unmasked Batman, but says that he is “practically blind without [his] glasses,” and lets Bruce go.
Gordon and his wife start attending marriage counseling. Loeb is forced into early retirement and that means he is arrested and on trial and so is Falcone who is the hospital and will be head to prison pretty soon when he heals, while Flass makes a deal with prosecutors to testify against him. Gordon, meanwhile, is promoted to Captain. When a criminal who “calls himself the Joker” threatens to poison the city’s reservoir, Gordon summons Batman with the Bat-Signal and waits on a rooftop for the Dark Knight to arrive.