The episode begins with the murder of Thomas Wayne and his wife Martha, while their young son Bruce looks on in horror. That night, Bruce tearfully swears to avenge his parents' death by battling crime. As he grows up, he studies criminology and martial arts, eventually becoming Batman. In the present day, The Spectre and The Phantom Stranger debate what Batman will do once he confronts his parents' murderer, which he will do on this night. They eventually wager on it: if Batman upholds justice, he is free to live his life the way he always has. On the other hand, Spectre wages that if Batman gives in to vengeance, he himself will become like Spectre.
That evening, Batman (disguised as a priest) tries to learn from Lew Moxon, a dying gangster who ordered the hit on the Waynes, the name of the killer. Moxon manages to say "some guy named... chill" before dying. Batman then heads to a bar to interrogate other criminals for further information, but they claim to know nothing. After Batman threatens to kill a man he is interrogating, the Phantom Stranger restrains him, taking him back to a charity costume party that his parents attended, revealing the reason for Batman's costume as being based on young Bruce's subconscious memory of his father's "Bat-man" costume. For a joyful moment, Batman is reunited with his parents. The gala is interrupted by thugs led by Moxon who show up to rob the party. Batman and Thomas fight together against the gang, managing to capture Moxon. One of the other thugs, who Batman recognizes as the killer, holds Martha hostage only to be rescued by Batman and Thomas. Batman races after the escaping thug, only for the Spectre to appear before him. He asks what Batman will do once he identifies his parents' killer. Batman has no easy answer. Spectre then shows Batman a meeting between Moxon and the other man at Blackgate Penitentiary. The man, who Moxon calls "Chill", offers to kill Thomas Wayne for Moxon in retaliation for his interference. Moxon casually agrees. Batman realizes that the dying Moxon had identified the killer to him - "Chill", and vows that "This ends tonight".
Returned by Spectre to the Batcave, Batman uncovers that Joe Chill now sells exotic weapons to supervillains. Batman interrupts that night's sale, fighting off the assembled villains while focusing on his true target: Chill. Batman corners Chill in an office, disarming him and revealing that he is the son of Thomas Wayne. Bruce now has Chill at his mercy, and the Phantom Stranger and Spectre each appear to persuade him, respectively, to uphold justice or exact vengeance. Ultimately, Bruce spares Chill's life. Panicked, Joe Chill begs to the villains for protection against Batman, revealing that he is indirectly responsible for the hero's existence. However, before Chill can reveal Batman's true identity, the villains turn on him in a blind rage, resulting in a brawl that accidentally sets off the sonic laser Chill was trying to sell them earlier. The weapon's beam sends the ceiling crashing down on Chill, killing him. The Stranger says that Batman made the proper choice and that fate ultimately overtook Chill. He then mentions how convenient it was that Chill just happened to be under the collapsing ceiling at just the right moment. The Spectre only smiles and says "I wouldn't know anything about that".
The episode ends with Bruce enshrining his father's bat costume within the Batcave and declaring "Case... closed."
The episode features a number of guest appearances. Kevin Conroy, Mark Hamill and Richard Moll all appear from Batman: The Animated Series as The Phantom Stranger, The Spectre and Lew Moxon, and Adam West and Julie Newmar appear as Thomas and Martha Wayne.
- Actually Pretty Funny: The Joker openly laughs at how Joe Chill inadvertently created Batman.
- Adaptational Badass: In the past, Thomas could hold his own against some thugs. It was just that Chill took him by surprise.
- Ambiguous Situation: It's unknown if the Spectre killed Joe Chill or it's merely an accident.
- Asshole Victim: Joe Chill is a horrible person, being a hitman and currently selling weapons to murderous supervillains, and seeming to view his murder of the Waynes as just another job. The Spectre tries to coax Batman into killing him for this very reason, and when Batman refuses it's implied the Spectre may have finished Chill himself. It's hard to argue Chill didn't deserve it.
- Bittersweet Ending: With his parent's killer finally paying for it, Bruce hangs up his father's party costume in a display case and solemnly says, "Case closed."
- Bear Hug: In both a sweet and heartbreaking moment, Batman hugs Martha.
- But for Me, It Was Tuesday: Downplayed. When Batman furiously confronts Joe Chill over the murder of his parents, Chill does remember killing the Waynes, but states, "That was a lifetime ago!" He also simply calls them 'a guy I killed on a job.'
- Continuity Snarl: The episode "Invasion of the Secret Santas!" revealed that Bruce's parents were killed after seeing a Swashbuckler movie, not The Mask of Zorro.
- Darker and Edgier: The darkest episode of the entire series. This "love letter to Silver Age comics" is noted for being the first time in an animated series that Batman confronts Joe Chill.
- Did Not Think This Through: Joe Chill tells the villains he created Batman. He didn't realize it until it was too late that they might be more interested in taking revenge on him than helping him. It's only Batman's intervention that saves him.
- Dramatic Unmask: Batman does this to himself when explaining to Chill why he's after him. It is the first time Bruce's adult face has ever been shown on the series.
- Even Evil Has Standards: Lew Moxon while he felt justified taking out a hit on Thomas Wayne he did genuinely feel bad that Martha was also gunned down, leaving their son Bruce without a Mother.
- Good Angel, Bad Angel: Both Phantom Stranger and Spectre acts as this to guide Batman to either becoming a hero of Justice or an agent of Vengeance.
- Harmful to Minors: As in other versions, Bruce sees his parents gunned down.
- He Who Fights Monsters: Batman is slowly becoming this which worsens when Phantom Stranger and Spectre brought up his parents' murder.
- Heroic Vow: "I swear by the spirits of my parents to avenge their deaths by spending the rest of my life warring on all criminals."
- Internal Reveal: Bruce reveals his identity to the man who murdered his parents.Batman: I am the son of the man you murdered. I am Bruce Wayne!
- Little "No": Joe Chill's reaction to the Internal Reveal.
- Karmic Death: Joe Chill is killed when the ceiling collapse on him as he tries to escape triggered by the very weapon he was trying to sell. Justified, as it's implied the Spectre may have arranged for Chill to get what he deserved.
- Mythology Gag: The flashback at the beginning is reminiscent of Detective Comics #33.
- No-Holds-Barred Beatdown: Batman delivers one to Joe Chill.
- Oh, Crap!: Joe Chill reacts in horror that Batman is Bruce Wayne.
- Save the Villain: Batman interrupts the villains' attempt to kill Joe Chill.
- That Man Is Dead: Batman maybe gone but Bruce Wayne will live.
- Thou Shalt Not Kill: The wager between the Phantom Stranger and the Spectre hinges on whether or not Batman will uphold his number one rule.Phantom Stranger: He is beaten. Let your devotion to justice temper your rage.
Spectre: He took your parents. Ruined your life. Fulfill your destiny. Become what you have trained to be: an agent of vengeance. He knows who you are. If this man lives, Batman dies.
Batman: Batman may die, but Bruce Wayne? [drops Chill] Never.
- Villainous Breakdown: After Joe Chill basically confessed that he created Batman, the super villains are none too happy and viciously attacked him.