As new villains overrun Gotham City of the future, the aging Bruce Wayne hangs up the cape of the once invincible Batman. But when troubled teenager Terry McGinnis stumbles upon the Dark Knight's secret, a new alliance is forged. And a triumphant new Batman is born.
The Royal Flush gang, minus the reformed Ten, attempt a robbery of a Gotham city museum. Although the gang gets away with the piece, Batman stops Jack and leaves him for the police. Bruce deduces that the Royal Flush gang is working for Paxton Powers, and by listening in on Commissioner Gordon's interrogation of Jack, he and Batman also discover that there are widening rifts in the Royal Flush family. At the hideout, the King and Queen argue, with the Queen endlessly comparing King to his previous namesake, her father. Furious, the King sets another plan in motion: he kidnaps Powers and holds him for ransom, using Bruce Wayne as a go-between. Powers, reluctant to have his illegal dealings exposed, makes a deal with the gang, to eliminate Bruce, but there's more than one double-cross afoot. Angie Harmon makes her first appearance as the new voice of Commissioner Barbara Gordon.
Batman faces off against a new high-tech villain, a man in a suit that projects an impenetrable force field that repels everything Batman can throw at it. Bruce Wayne recognizes the force field as the work of Dr. Blades, a Wayne-Powers scientist who has developed what he calls iso-field generator rings, which generate an aura of energy around its wearer. While touring the Wayne-Powers lab facilities, Blades' assistant Dr. Suzuki demonstrates the rings and the aura, which are meant for use as a self-contained environment for people with immune-system deficiencies. Bruce and Terry recognize the aura immediately, and the question then becomes: who in the lab is the untouchable criminal?
Bruce Wayne is out of town, and Inque is back -- announcing her presence by disrupting the launch of a billion-dollar satellite. Newly invulnerable to water, she poses more of a threat than ever before. Terry remembers that Bruce Wayne had to save him from Inque twice before, putting both his identity and his life at risk. Wanting to prove himself, he insists on pursuing Inque himself, though he asks Max to do some detective work for him. Meanwhile, Inque's deal has gone sour, and her would-be client has weakened her with a particle destabilizer. Sick and desperate for help, she goes to the one person who she feels she can trust -- Deanna Clay, the daughter she abandoned as a child.
Shortly after Batman foils a daring, high-tech robbery of a powerful Wayne-Powers agricultural compound, Charlie "Big Time" Bigelow, one of Terry's friends from his wilder days, gets out of jail. Charlie offers Terry a chance to hook up with some contacts he made on the inside for a big job, but Terry refuses, trying to talk Charlie into staying out of trouble. Feeling guilty because Charlie went to jail and he didn't, Terry convinces Bruce Wayne to get Charlie a low-level job at Wayne-Powers. When Terry finds out that Charlie used him to get into Wayne-Powers, he confronts him, hoping to steer him straight before he has to intervene as Batman. Clancy Brown makes his first appearance as Charlie "Big Time" Bigelow.
Feeling old and tired, Bruce Wayne is reminiscing about past loves lost when Talia, daughter of R'as al Ghul, visits him in the Batcave. With her father long dead, she wishes to rekindle their romance and makes him an offer: She will give him eternal youth through use of the immortalizing Lazarus Pit, and they can spend the rest of their lives helping people through their philanthropic organizations. Worried that Bruce might give in for all the wrong reasons -- and concerned that he may lose the honor of being Batman -- Terry decides to come along to make sure everything is as it seems. When he and Bruce discover the truth behind her offer, it turns out to be more bizarre than either could have imagined.
When Batman tries to capture an eight-foot-tall gorilla that's on the loose, he's surprised at the extremely intelligent decisions it makes in order to escape. During the chase, he encounters two zoologists from Gotham State University, who say that it's their gorilla -- named Fingers -- who has escaped. Following a hunch, Batman investigates at the zoology department and discovers the scientists were using methyl glycose (the compound used for splicing) to add human DNA to Fingers for better intelligence tests. Batman must now find a giant, smart gorilla that's only getting smarter, and who has an unexplained hatred of noted conservationist James van Dyle.
Batman receives a little unexpected help in capturing Inque: Superman. Superman reunites with Bruce Wayne, and extends an offer to Terry to join the Justice League. When Batman's introduction to the League is met with hostility by the other members, Superman takes Batman aside and explains that he has reason to suspect a traitor in their midst; he asks him to keep his eyes and ears open. Terry reluctantly agrees, finding it difficult to spy on people he's idolized his whole life. When the League steps in to stop a mysterious attack on Metropolis, a missile explosion claims Warhawk's life. Batman is the only one to witness the event, which puts suspicion squarely on his shoulders.
Batman shows the League evidence of Superman's complicity in the death of Warhawk, but the idea is met with some resistance -- particularly from Barda, who flatly refuses to believe that Superman could be responsible, preferring instead to suspect Batman. Barda is convinced when Warhawk reappears, revealing that he didn't die in the explosion. Batman is only partly relieved, armed as he is with a kryptonite sample necessary to stop – and kill – Superman if he has to.
Big Time returns to Neo-Gotham, causing problems for both Batman and his alter-ego Terry McGinnis, who still feels guilty for what happened to him.
Terry is sent to Bruce's old friend Kairi Tanaka to brush up on his combat skills, and inadvertently befriends the heir-apparent to the criminal organization KOBRA.
After the leader of KOBRA kidnaps Max to be his wife, Batman is forced not only to rescue her, but to stop KOBRA's plot to revert the world back to when dinosaurs ruled it... with their gene-spliced dinosaur men as the dominant species.
Zeta returns to Neo-Gotham City to look for his creator, but falls into the clutches of Mad Stan, who turns him into a walking time-bomb. Batman and Ro must track Zeta down before time runs out.
Terry recounts to Max one of his earlier adventures as Batman, during which he revealed his face to a child and inadvertently made the boy a target of KOBRA.
