Bruce Wayne is the eight-year-old son of Dr. Thomas Wayne, who is running for Mayor of Gotham City, and Martha Arkham-Wayne. After receiving death threats, Thomas calls his friend, Alfred Pennyworth, to become the head of security at Wayne Manor. Thomas and Alfred fought together in the battlefield, where Alfred saved Thomas' life, and, in gratitude, Thomas created a prosthetic leg to replace the one that Alfred lost in an explosion. Alfred learns that Thomas, Martha and Bruce go to the movies every Wednesday and tries to convince Thomas not to go, because it would make him an easy target. Thomas, however, does not want to disappoint Bruce, and leaves.
During the movie, the movie theater runs out of power, and Thomas decides to return home, fearing Alfred might be right. However, Bruce demands to watch the movie immediately, and rushes out of theater, bumping into a criminal on the way out. The criminal recognizes him as "the Wayne kid" and takes his hostage, demanding that the Waynes give him their money. When he attempts to remove Martha's pearl necklace, Thomas tries to intervene and the criminal shoots them both in front of Bruce.
Later on, at Wayne Manor, Alfred learns that Thomas and Martha named him Bruce's legal guardian in case something happened to them, and that Bruce will be put into foster care if Alfred refuses to accept this role. To honor his best friend, Alfred agrees to become Bruce's guardian and presents himself to Bruce as his butler.
A teenage Bruce befriends his classmate, Jessica Dent, and develops a rivalry with her twin brother, Harvey Dent. He also learns about Arkham Manor, where Martha lived as a child. Martha's mother suffered a mental breakdown when Martha was twelve, murdered her husband with a sledgehammer and committed suicide by jumping off the balcony. Because of this, Arkham Manor, which was built like a maze, is believed to be cursed, causing all members of the Arkham bloodline to become insane. One night, Bruce decides to enter his parents' mausoleum and is attacked by hundreds of bats, an experience that frightens him. After seeing a statue of a Japanese samurai wearing a bat-like mask after the bat attack, Bruce is struck with inspiration.
Shortly afterwards, Bruce convinces Alfred to train him in various forms of hand-to-hand combat and acrobatics, and Bruce finds the death threats his father received. Bruce also self-teaches himself in the field of investigation. Bruce believes that Mayor Oswald Cobblepot had his parents assassinated. Years later, Bruce's investigation leads him to Jacob Weaver, a police detective who was the first to the crime scene at the Waynes' murder and left the police to work at the Mayor's office three weeks later. Bruce also finds a picture of Weaver using a golden lighter that Bruce had given to Thomas for Christmas.
Bruce dons a bat-themed costume (inspired by his experience at the mausoleum) to disguise himself and to frighten his parents' alleged killers. He attacks Weaver, but the grapple gun he develop malfunctions, and Weaver escapes. Bruce then seeks Lucius Fox, a twenty-two year-old intern at Wayne Medical, who agrees to repairs his equipment in exchange of funding for a project to develop artificial limbs for amputated people, which Fox wants to use to give a new arm to his five year-old niece.
Meanwhile, Detective James Gordon of the Gotham City Police Department is investigating a string of disappearances in which the victims are teenage girls between thirteen and fifteen. The case is shortly put on hold so Gordon can meet his new partner, Harvey Bullock, an LAPD detective and star of a recently cancelled reality show called "Hollywood Detectives", who has come to Gotham to solve the Waynes' murder in order to relive his fading career, much to Gordon's dismay. One day, Bullock spots a local drug dealer called Axe beating one of his clients and attempts to arrest him, but is stopped by Gordon, who apologizes to Axe. Axe tells Gordon he will take Gordon's payment because of that, and Bullock is disappointed to learn Gordon is corrupt.
Gordon and Bullock are called to provide security detail to a beneficent party organized by Mayor Cobblepot. Bruce attends to the party to find Weaver, who goes to the roof to smoke. Bruce changes into his costume and confronts Weaver, but is attacked by Cobblepot's bodyguards and escapes, wounded, after a fight with Gordon, Bullock and other police officers. In the aftermath, Bruce's alter ego is named "Batman" by the press and becomes a public sensation.
Cobblepot, infuriated by Batman's actions, tell his men to have "Birthday Boy" take care of Weaver. Birthday Boy is a serial killer, responsible for the kidnappings Gordon had been investigating. He abducts his victims and takes them to a "playroom" in the abandoned Arkham Manor, where he gives them a birthday cake. After urging them to "make a wish", Birthday Boy disembowels them with a butcher's knife.
Birthday Boy murders Weaver and Batman's investigation leads him to Arkham Manor. Meanwhile, Bullock uses Gordon's name to take the files about the Waynes' case from the GCPD cold case archive. Cobblepot's informants at the police station inform him of this, and Cobblepot has Axe kidnaps Gordon's seventeen year-old daughter, Barbara, and take her to Birthday Boy. Gordon learns that Bullock is responsible for this, and reveals that he also tried to solve the Wayne murders, but Cobblepot forced him to abandon the investigating by arranging Gordon's wife's death in a fixed car crash. Gordon confirms he has been overlooking Axe's crimes to protect Barbara, and an apologetic Bullock helps Gordon find Axe. They beat Axe and force him to reveal Barbara's location.
At Arkham Manor, Birthday Boy prepares to kill Barbara, but she fights back and manages to stab him with a piece of wood. Meanwhile, Batman and Gordon join forces to cross the maze and find the Playroom. Batman attacks Birthday Boy while Gordon rescues Barbara. However, Bullock gets lost and runs into Batman and Birthday Boy fighting across the building. Bullock ends up in the attic, where he finds the decaying mutilated corpses of Birthday Boy's previous victims: The daughters of all of Cobblepot's enemies, including police officers who tried to investigate his criminal activities. Batman overpowers Birthday Boy, who is arrested by Gordon and Bullock.
Batman then goes to Cobblepot's office and confronts him. Cobblepot stabs Batman with a blade concealed in his umbrella and unmasks him. Cobblepot then reveals that he intended to have Weaver murder the Waynes that night (Weaver cut the power of the movie theater), but they were accidentally killed by a mugger. Cobblepot then prepares to kill Bruce when Alfred appears and shoots Cobblepot, causing him to fall off a window to his death.
Gordon and Bullock expose Birthday Boy's connection with Cobblepot, and Birthday Boy is transferred to the Crane Institute for the Criminally Insane, runs by Dr. Jonathan Crane. The Birthday Boy’s identity is revealed Ray Salinger, an escapee from Crane's hospital who is obsessed with teenage girls who resemble his first victim, a fifteen year-old debutante Amanda Grant. Gordon arrests Axe, having decided he has had enough of allowing corruption rampant throughout the city, while Barbara idolizes Batman, begins studying martial arts and criminology, and sketching potential "Batgirl" costumes. Bullock, on the other hand, has traumatized by what he saw at the attic and becomes a suicidal alcoholic. Fox, after seeing Batman uses the grapple he repaired for Bruce on the news, deduces that the young billionaire is the vigilante and begins building a bat-themed arsenal for him, hoping to become a part of the action. Because of Batman's actions leading to the corrupted mayor's downfall, Gotham's residents believe that their city now has a defender, inspires hope to the decent but also brings fear towards the guilty.
Jessica replaces Cobblepot as the Mayor, while Harvey continues his activities as District Attorney. Bruce though disappointed of the truth behinds the circumstance of his parents' death, despite initially had not intend to be a vigilante crusader, but after seeing the differences he made as Batman, and with Alfred's help, Bruce decides that he will become the hero the city believes him to be.
After more of Batman's exploits made headlines throughout the news, he attracts the attention of a mysterious man that becomes obsessed with discovering the hero's secret identity, which he deems "the ultimate riddle".
- Bruce Wayne/Batman (Flashback and Main Story)
- Jacob Weaver (First Appearance)
- Alfred Pennyworth (Flashback and Main Story)
- Stanley (In Flashback Only)
- Thomas Wayne (In Flashback Only)
- Martha Arkham-Wayne (In Flashback Only)
- Joe Chill (In Flashback Only)
- James Gordon
- Barbara Gordon
- Harvey Bullock
- Gillian B. Loeb
- Jessica Dent (Flashback and Main Story)
- Harvey Dent (Flashback and Main Story)
- Lucius Fox
- Axe (First Appearance)
- Oswald Cobblepot/The Penguin (Dies in this issue)
- Amy (First Appearance)
- Ray Salinger/The Birthday Boy (First Appearance)
- The Riddler