At a museum displaying the treasures of magic, the curtains come alive and capture the guards. The villainous Abra Kadabra arrives to steal the exhibit, but Batman attacks him… with an assistant, Zatanna. Abra Kadabra tosses a mystical blast her way and Batman gets her out of the way. He then turns the audience into puppets, turns them against the heroes, and gags Zatanna. Batman is quickly overwhelmed and dropped into a water trap, but he frees himself and knocks away Abra Kadabra's wand. Zatanna snaps it and then traps the villainous sorcerer in her top hat.Years ago, the Waynes emerge from a movie theater and young Bruce Wayne asks if he can be Zorro. As he runs ahead, an armed figure emerges from the shadow and demands Martha's necklace. He shoots first Thomas when he tries to intervene, and then Martha. Later, Bruce swears vengeance as the Waynes' family retainer, Alfred, looks on. Bruce perfects his mind and body and finally takes on the guise of Batman.
Two omnipotent figures, the Phantom Stranger and the Spectre, watch from limbo. The Spectre insists that there must be vengeance to stop evil. The Phantom Stranger insists that Batman cannot turn to vengeance, but the Spectre warns that they are there to watch a critical moment in Batman's life. The Spectre offers a wager: if Batman kills the man who killed his parents, he gains the Caped Crusader as an agent of divine retribution. If the Phantom Stranger wins, Batman is free to go his own way and continue on his path to protectng those who cannot protect themselves, always fighting for justice.
A priest comes to see a dying criminal, Moxon, in the prison hospital. He asks if Moxon has anything to confess, and the criminal boasts of how he ran Gotham's rackets for 40 years. Finally he confesses that he hired a hitman to kill Thomas Wayne. However, the killer killed Martha as well when he wasn't supposed to. The priest demands the killer's name and Moxon wonders why he's so interested. Moxon agrees to talk and can only whisper the word "Chill" before dying. The priest goes outside… and removes his clothing to reveal Batman beneath.At a criminal bar, Gotham's underworld gather to honor Moxon, but Batman arrives and breaks up the wake. He captures one of them and demands to know who killed the Waynes. More criminals attack and Batman easily disposes of them, He starts to lose control and a voice in his head suggests that he restrain himself. Batman releases the crook and the Phantom Stranger appears. The Stranger warns that Batman is losing control and offers him knowledge of his parents. He gestures and they find themselves over 30 years in the past at a charity costume ball. The Waynes enter, in costume, and the Stranger explains that Batman can't alter the past. Batman remembers the bat costume that his father wore, and that he took as inspiration. Thomas and Martha introduce themselves and Batman embraces his unwitting mother. Moxon and his thugs break in to steal the donations and Batman and Thomas attack them. A man who Batman who realizes is his parents' killer grabs Martha and holds her hostage, and Moxon goes for the money. Working together, Batman and Thomas bring down a giant bat exhibit but the killer flees. When Batman chases after the killer, he finds himself in a black void. The Spectre appears and asks what Batman will do once he finds the killer. Batman admits he doesn't know, and wonders why the Spectre won't reveal the killer's identity. The Spectre gestures and Batman finds himself in Blackgate Penitentiary. The killer, Joe Chill, comes to visit and Batman realizes Chill is the killer. He watches as Moxon threatens Chill unless he evens the score. Moxon casually agrees, telling him to make it look like an accident. Batman wonders where justice is, and demands the Spectre take him to the Batcave. They appear and Batman tracks down Chill. The Spectre asks what he'll do, and Batman says that it will end before dawn. Batman tracks down Chill, who now sells weapons to super-criminals. At a warehouse, Chill offers a sonic disruptor to a horde of villains. They refuse to bid and Chill uses it to demolish an armored car. The villains begin bidding but are interrupted when Batman drops in a gas grenade. The villains attack but Batman easily subdues them, using the smoke as cover. Chill tries to flee but Batman easily corners and disarms him. The Caped Crusader accuses him of the Waynes' murder to Chills shock, Chill asks him how he could know about something that happened years ago. Batman tells him he knows because he was there, because he is the son of the man Chill murdered, He knows because he is Bruce Wayne, and tells the dumbstruck man that Chill is the reason he grew up to become the Batman.
A horrified Chill tries to fight back but Batman beats him down. The Phantom Stranger and the Spectre appear and urge Batman on to serve justice and vengeance, respectively. The Spectre notes that if Chill lives, he will reveal Batman's secret identity. Batman considers… and then releases Chill.Chill runs inside and begs the villains for help. He explains that he killed a man and because of what he did that mans son grew up to be Batman. The criminals point out that Chill is the reason for their arch-nemesis. They attack him, but Batman arrives and the villains attack. Batman takes them down but the Joker grabs the sonic disruptor. In the struggle, the beam goes wild, bringing down the building. Everyone escapes except for Chill, who is crushed beneath the rubble. Batman goes to his side, and the dying Chill admits that Batman got him after all.
In Limbo, the Phantom Stranger notes that karma delivered the final blow to Joe Chill. He comments that it's ironic that Chill was caught in the collapse, and the Spectre merely smiles and claims ignorance.
Batman returns his father's costume to a display case in the Batcave, and announces that his parents' murder has been solved.