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.

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.

Ian Peek is a muckraking journalist who gets footage from seemingly impossible locations, no matter how tight the security. When there's a disturbance at city hall during a secret meeting between an organized crime witness and the district attorney, Batman encounters a man who can pass through solid matter at will. In short order, he puts two and two together and realizes this new villain is Peek. Confronting Peek, however, leads to him using his power to find out Bruce and Terry's secret -- and he threatens to expose them live on the air.

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.

Terry steals the Batsuit to pursue his father's killer, a professional bodyguard named Mr. Fixx (George Takei), whose employer, Derek Powers (Sherman Howard), the current CEO of Wayne-Powers, is secretly using the company's resources to develop a biological weapon. Bruce Wayne, discovering the theft, deactivates the suit, but when seeing the now-helpless Terry being punched out reactivates it so he can continue pursuing Fixx, and in the end Wayne appears at Terry's house to hire him as a "special assistant."

Batman's already tense relationship with the law gets tenser when he accidentally messes up a major police sting operation. Fed up with Terry, who she sees as a hothead, Commissioner Gordon warns Bruce that she'll be keeping an eye on him to make sure he doesn't get into more trouble. Her worst fears are realized soon enough when she sees Batman bludgeoning Mad Stan to death with one of his own bombs. When Terry returns home, he finds the Commissioner's men looking for him, but he doesn't know why. Fleeing to Max's house, he tries to understand: how could people have witnessed him perpetrating a crime he didn't commit?

In 2019, Bruce Wayne, the original Batman, retires due to failing health when his rescue of a kidnapped woman nearly goes wrong and he must resort to almost using a gun—the ultimate sin in his eyes. Twenty years later in 2039, Terrence "Terry" McGinnis discovers Batman's identity after the aging Bruce Wayne helps him fight off a gang of Jokerz (street punks enamored by the original Clown Prince of Crime). After Terry's father is murdered, Terry seeks Bruce's help to avenge him.

Derek Powers' body is continuing to deteriorate. Desperate, he has Victor Fries (Mr. Freeze) revived, and creates a new body for him under the pretense of medical research. Finally cured, Fries is repentant, but Bruce Wayne doesn't trust him. Batman halfheartedly shadows Freeze, convinced that he has reformed. But how long can he stay reformed once he discovers that Powers is using him?

Maxine "Max" Gibson, one of Terry's classmates and a bona fide genius, has created a computer program to figure out Batman's secret identity. When Max is targeted by the Jokerz, she rewrites the code to find the Jokerzs' identities, which only puts her in more danger. Michael Rosenbaum and Jill Eikenberry make their first appearances as the voices of Carter Wilson, another one of Terry's classmates, and his mother.

While Terry is out walking Ace, Bruce Wayne's dog, Ace savagely attacks a suspicious-looking man on the street and then runs away. When Bruce traces the serial number on the man's gun, he discovers the man is none other than Ronny Boxer, a longtime purveyor of illegal sports, including dog sports. Boxer is also Ace's former owner; Bruce took him in when Boxer's dog-fighting ring was busted by the police. While Terry goes undercover to get close to Boxer, Bruce looks for Ace, all the while wondering exactly what Boxer did to Ace in the past.

When executive Robert Vance was diagnosed with a degenerative brain disorder, he arranged to have his consciousness digitized. Now, 35 years later, his grandson Bobby has awakened him before his computer is shut down. Searching for a temporary home before he can find a human host, he infects Batman's costume. Terry goes after him, hoping to answer the question -- is Batman the suit, or the man inside it?

Terry must deal with both his rejection by his girlfriend, Dana, and a group of Bruce's old enemies, the Royal Flush Gang, who pattern themselves after playing card ranks. Things look up for Terry when he meets a girl named Melanie who seems to share his problems.

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.

When all of Gotham's animals start getting agitated at the same time, Terry and Bruce Wayne figure out that sound frequencies beyond human hearing are to blame. That points to one man: Shriek. The animals prove to be the tip of the iceberg when people suddenly lose the ability to understand each other's speech. Shriek eventually turns off the interference, but makes a demand of Commissioner Gordon: the city's safety for Batman's life.

Max Shreeve, a sound engineer working for Derek Powers, develops a suit that amplifies sound waves into awesomely destructive force. Powers is uninterested in the suit until Bruce Wayne interferes with his plans for Wayne-Powers once too often. On Powers' orders, Shreeve makes an attempt on Wayne's life, taking the name Shriek. Chris Mulkey makes his first appearance as the voice of Shriek.

The Royal Flush Gang's Ten returns on a mission to rescue her family, who have been captured by the Jokerz. When Melanie approaches Terry for help, he is forced to decide whether or not to put his relationship with Dana at risk, and if Batman can really trust Ten.

Dana, who feels she has been ignored and let down by Terry once too often, begins receiving roses from a secret admirer. When she is abducted by the mystery man, a boy named Patrick Fitz who lives in the sewers because of his rat-like appearance, Batman may be the only one who can save her.

One of the hottest virtual reality arcade games is Sentries of the Last Cosmos. Max and Terry's classmate Corey Cavaleri loves the game, sometimes better than real life. When he beats the arcade's all-time record, Corey is summoned to the secluded Sentrycroft estate by the game's creator, Simon Harper. There, he and two other kids become real-life Sentries, complete with flaming swords and flying discs. After a raid on Gotham's hall of records, Harper tells the kids that Sentries of the Last Cosmos is more than a game; in a nod to The Last Starfighter, Harper -- calling himself the Wise One -- claims that the Sentries' war against the Dark Regent is real, and that the game is used to recruit trainees. Batman learns of Harper's plot to send the kids after the Dark Regent -- the equally reclusive Eldon Michaels -- and tries to stop the kids and find the connection between the two men.

An experimental military warcraft makes an emergency landing in the middle of nowhere, where it's seized by a bunch of Jokerz out initiating a new member. Batman and its designer, Dr. Price, race to stop the Jokerz before they lay waste to the city -- and before the nuclear core goes critical.

Willie Watt, a nebbishy student at Terry's high school, is pushed around by everyone -- including his construction-worker dad, who insists that he needs to toughen up. Aching for revenge against Nelson, the jock that torments him, Willie steals a remote-controlled heavy-lifting robot (or "golem"), and rampages through Gotham. Batman stops the Golem quickly, but as a result of the fight he gains the power to control the golem mentally -- much to Nelson's dismay.

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.

The Terrific Trio, a group of scientists who became superheroes after gaining powers in an experiment gone awry, make their way into Gotham and become media sensations. But Magma, Freon, and 2-D Man soon learn that the accident that gave them their powers was not really an accident. The Trio are inspired by the Fantastic Four, with 2D Man being Mr. Fantastic, Magma being a combination of the Thing and the Human Torch, and Freon can spread her molecules apart to the point where she becomes hard to see, and her ice beams can form protective shields, making her analogous to the Invisible Woman.

Terry's late nights as Batman are starting to take a toll on his personal life when he can barely stay awake during the day. When he discovers that several jocks are using "slappers" -- patches that deliver the super-steroid Venom -- he investigates, only for his mother to catch him carrying the drugs. Then he has to find a way to stop the flow of Venom into Gotham and clear his name, all while being grounded.

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.

When Dr. David Wheeler, a prominent child psychologist, opens a new ranch/group home promising to help troubled teenagers, parents jump on the bandwagon and start sending their kids away for even the most minor infractions. Max encourages Terry to investigate as Batman when their friend Chelsea is sent away for writing a letter of protest to the principal. Batman discovers that the kids are being held prisoner and brainwashed, but he is spotted and fired on. Since Batman can't get admissible evidence, he decides to get it as Terry by visiting Chelsea with a pocket recorder. When Terry is captured, he's forced to rely on a delinquent he's never gotten along with.

High school jock Nelson unwittingly smuggles a glass vial with an unknown green fluid into Gotham, which is seized at customs. In the parking lot, he's attacked by the Stalker, who demands to know the whereabouts of the vial. Batman interferes with Stalker's flight, but is in turn stopped by agent Bennet, who tells him Stalker is helping them track Falseface, an identity-switching mercenary working for Cobra, a secret organization holding Gotham hostage with a horrific chemical weapon. Despite his misgivings, Batman teams up with Stalker to find Falseface and stop Cobra's plans.

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?

Jared's stepfather, Jim "Big Jim" Tate, is a top weapons designer who likes to splurge his considerable salary on his family. When he's laid off from Wayne-Powers and hard up for work, he starts designing new weapons illegally for foreign governments. In order to steal the plans and parts he needs, he puts an array of untested weapons and his Special Forces training to use and becomes an unstoppable one-man army: Armory.

After a rare night out with his friends, Terry follows a suspicious figure out in the subway. Everyone is worried when he fails to reappear the following morning, and Bruce Wayne takes it upon himself to find him. When he asks Max about Terry's last whereabouts, she insists on coming along, despite his protests. Meanwhile, Batman wakes up in an underground tunnel under the hostile glare of a young boy, a runaway who lives in the tunnels. The boy wants Batman off of his turf as soon as possible, and tries to help him leave. It turns out that the suspicious figure is none other than Shriek's assistant, who is helping the twisted sound genius with his new plan. Shriek causes a cave-in to trap Batman and the boy, who starts to express his long-standing hostility toward Batman. As Max and Bruce work toward finding Terry, and Batman and the boy try to escape, each learns to appreciate the others' skills -- until Shriek reveals himself from the shadows.

A hooded vigilante calling himself Payback, armed with a bullwhip-like laser, has been terrorizing people under the pretext of helping the city's kids. Bruce Wayne discovers a link between two of the kids and the Gotham Youth Counseling Center. When the Center's computer proves inaccessible, Terry has to enter the Center under the guise of being dissatisfied with his treatment by Bruce. However, when his later impulsiveness as Batman gets him in hot water with Bruce, he vents at his next session at the center -- and unwittingly sets Bruce up as a target for Payback.

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.

The latest teen craze is "splicing" -- incorporating animal DNA into a human body. While some kids just get cosmetic changes like cat eyes, many opt for more major transformations. Batman investigates Dr. Cuvier, the founder of splicing, and discovers his plan to kill D.A. Young before the process can be outlawed. Cree Summer makes her first appearance as the voice of Terry's classmate Max Gibson.