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.
When Batman intercepts a police radio call reporting that a giant is attacking an armored car, he and Bruce Wayne correctly guess that the grotesquely mutated Charlie "Big Time" Bigelow, recently escaped from prison, is responsible. What they don't know is the identity of the man he's working with. The next day, while Terry and Max are discussing Charlie's fate, Terry is jumped and kidnapped by some of Big Time's accomplices, unintentionally separating him from the knapsack with his Batman suit. Big Time takes Terry back to his hideout, again offering him a chance to work with him. When Terry instead offers Charlie a way out, he takes it -- with consequences Terry doesn't expect.
Batman has had his hands full foiling the plans of the mysterious terrorist organization Kobra. After he fails to stop some Kobra operatives from stealing a thermal bomb, Bruce Wayne recommends that he study under Kairi Tanaga, one of his old training partners, in an effort to improve his combat skills. During his training, he becomes friends with the reclusive Xander -- a skilled fighter who is shut out from the real world by his two bodyguards. One evening, Terry sneaks Xander out of the dojo to experience normal adolescent life, where, for the first time in his life, he meets someone who can beat him; Max trounces him at Sentries of the Last Cosmos. The evening is interrupted by some Jokerz, and Xander's bodyguards whisk him away as the scene unfolds. Xander never returns to the dojo, instead resuming his rightful place as the future leader of Kobra. He and his "bodyguards" have nearly completed the serum that will transform humans into reptiles, but he needs only one thing -- Max, who he wants to be his queen.
Suffering a minor concussion and four cracked ribs after trying to stop Xander from abducting Max, Terry is in no shape to go after her; but, when he and Bruce find out that Xander is Kobra's future leader, he immediately charges to the rescue. Meanwhile, Xander reveals everything to Max: his birth as a clone at the hands of Kobra, his grooming as their perfect leader, and Kobra's plan to detonate a thermal bomb that will raise the Earth's temperature. The bomb will make it too hot for humans, but Kobra's plan is to splice themselves into human/lizard hybrids to survive the holocaust -- starting with Max.
In a Zeta Project crossover, the synthoid Zeta returns to Gotham with his friend Ro. While trying to make contact with Dr. Selick, they are attacked by Agent Bennet and his federal agents. The two split up, but Bennet manages to stop Zeta by attaching a disruptor to his back. Mad Stan, fleeing a battle with Batman, saves Zeta from "feds trampling his basic human rights." After bringing him back to his hideout, Stan discovers that Zeta is a synthoid. Suspecting that he's a killer robot sent by the federal government, he sends the recovering and grateful Zeta on his way -- with a bomb planted on his back.
When Max continues to pressure Terry to reveal his identity to Dana, Terry explains that he doesn't just keep his identity secret to protect himself -- it's also for the protection of everyone else. To illustrate, he tells her about an adventure from early in his career as Batman. While foiling a Cobra bank robbery, he tried to rescue a young boy named Miguel from a burning building. However, his costume frightened the boy so much he had to take off his mask to reassure him that he wasn't a monster. Meanwhile, at Cobra's Gotham headquarters, Cobra's ringleader was using a mental imaging device to root out the operative who gave away their bank job plans. When a news report surfaced that Miguel had seen the face of Batman, the Cobra commander became very interested -- and Terry discovered the consequences of his seemingly trivial act.