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Jean-Paul Valley sees visions of his dead father, who had programmed him at birth to be a deadly weapon. These visions tell Jean-Paul to avenge his father's death, while at the same time trying to stop a gunrunning organization that used to be run by Carlton LeHah, who had killed his father. He eventually comes to believe that Selkirk, a Gotham mobster who has taken over the remnants of Lehah's organization, is a puppet for LeHah, running things behind the scenes.
Returning to Gotham, Bruce meets Robin. He is impressed enough with Jean-Paul to let him remain as Batman but when Robin tells him of Abattoir's death, Bruce sneaks into the Batcave and demands that Jean-Paul step down. Jean-Paul refuses and threatens to kill Bruce if he ever returns. In response, Bruce asks the deadly assassin Lady Shiva to retrain him. Since Bruce had once been the only person capable of surviving a fight with her, he figures that nobody could better prepare him to fight Jean-Paul. Shiva pits Bruce against several expert martial artists after killing their master in what would become Bruce's disguise, the Mask of Tengu (a bat spirit).
Shiva's caveat is that these attacks will continue indefinitely until Bruce Wayne breaks his solemn vow to never take a life. Finally, in the midst of another attack, Bruce uses the deadly Leopard Blow Shiva had taught him, leaving his would-be assailant dead and Shiva finally declaring him worthy of fighting her (at some point in the future). Without Bruce noticing, Robin and Nightwing had tailed him and saw the whole thing. As Shiva departed and Wayne was left to hear Nightwing chastise him over how everything Batman had ever taught was a lie, the man struck by the Leopard Blow came back around, as Bruce had merely struck him hard enough that Shiva would believe for the time being that Wayne had killed the man. Bruce had figured out that Shiva put a radio transmitter in his mask, and decided that he was back to peak physical condition and thus did not need any more from Shiva.
Bruce returns to the Batcave and dons the original Batman costume. Along with Robin and Nightwing, he tracks Valley down to Selkirk's penthouse, as the other heroes had been watching Jean-Paul for a while and knew he sought his father's killer. Coincidentally, Catwoman is chasing the same man because he owns a neural enabler that might allow a paraplegic to walk again. Selkirk already wants to kill Jean-Paul for destroying a valuable weapons cache in Gotham Harbor.
When they eventually all meet, mass fighting and gunfire ensue. The battle ends in the mobster's helicopter as Jean-Paul's grapnel gun locks one of the rotors and Catwoman knocks away a gun intended to kill Bruce and Jean-Paul. Selkirk's helicopter crashes into the Gotham Narrows Bridge; coupled with fuel from the chopper mixing with Jean-Paul's flame-thrower, Jean-Paul falls into the Gotham River. Bruce and Catwoman save Selkirk and his aides just before the helicopter explodes from the leaking gasoline. When Bruce tries to find Jean-Paul using the Batmobile, it explodes. Having realized that Jean-Paul would have booby-trapped the car, Bruce escapes just in time. After the explosion, Nightwing fears Bruce dead and takes his vengeance out on Jean-Paul on a party boat. The police arrive in time to prevent Nightwing's murder, but Jean-Paul escapes. However, to his shock, Jean-Paul finds Bruce waiting at Wayne Manor.
The final battle of the "Knightfall" saga takes place in the caverns surrounding the Batcave between Jean-Paul and Bruce Wayne: rather than beating Jean-Paul at hand-to-hand combat, Bruce escapes into a passage too narrow for Jean-Paul to go through in his armor, forcing him to remove most of it. Bruce then opens a hatch to the outside, which covered the very hole he fell into as a child, allowing sunlight to stab at the night lenses in Jean-Paul's helmet. After being momentarily blinded, Jean-Paul sees Bruce staring down at him in the original Batman costume and concedes defeat, saying "You are Batman... and I am nothing." Bruce comforts Jean-Paul, who leaves Gotham to travel the world and find his purpose as had Bruce. Bruce decides not to take Jean-Paul to the police because it was his decision to make Jean-Paul the Batman.