| ShortSummary | - --09-14
- 1.262304E9
- A virtual-reality game designer uses three teenage fans' devotion to the game universe in order to eliminate his enemies and rivals .
- After Inque's latest employer betrays her and blasts her with an experimental weapon that causes her body to slowly dissolve, she is forced to turn to someone she has not seen in years: her daughter.
- Wayne-Powers builds a new body for Victor Fries, better known as Batman's opponent Mr. Freeze, in the hope that a similar treatment might reverse Derek Powers' transformation into Blight. Cured of his need for extreme cold, Fries tries to redeem himself, but neither the new Batman nor his former victims completely trust him, and his benefactors have plans of their own.
- Bruce Wayne's former love, Talia, returns to offer him the chance to be eternally young. However, Bruce and Terry discover a dark secret. Decades ago, after Talia sided with Bruce against her father, Ra's al Ghul was left mortally wounded beyond the Lazarus Pit's ability to heal. In order to save himself, Ra's al Ghul sacrificed his daughter by using a computer to imprint his thoughts and memories into Talia's body, erasing her consciousness and replacing it with his own. After improving the computer, Ra's al Ghul decides it is time to move into a new body: Bruce Wayne's.
- After a series of unexplainable events, all the kids in Terry's class think that the ghost of a dead student is haunting their high school. But Batman soon discovers the real cause—Willie Watt, who has developed powerful new psychic abilities.
- A new body modification trend called splicing, combining human DNA with that of animals, is taking Neo-Gotham's fashion world by storm. While the DA wishes to have it completely outlawed as it is causing a rise in aggressive behavior, Dr. Able Cuvier, the creator of the process, insists that the procedure is safe. However Batman soon discovers that Cuvier is up to no good as Cuvier is working towards attacking the DA in hopes of silencing him.
- In the future of Batman Beyond, Amanda Waller reveals to an older Terry McGinnis she created the project "Batman Beyond" to continue Bruce Wayne's work. The episode is not only the Justice League season finale, but, as a cross over, the final Batman Beyond episode as well. The episode contains many references to prior episodes of Justice League, Batman Beyond, and Batman: The Animated Series such as the death of Terry's father, Ace from the episode Wild Cards, the future Justice League, much of Terry's rogue gallery, the Gray Ghost, and Andrea Beaumont. The episode is also notable for being character driven, exploring the motivations and relationship of the two Batmen; this attribute was common in Batman: The Animated Series but rare in Justice League or Batman Beyond. The final scene in this episode bears a resemblance to the first scene in the episode On Leather Wings of Batman: The Animated Series, as the creative team thought it could possibly be the final JLU episode. Furthermore, it is notable that in the beginning of the episode Terry believed that he was a clone of Bruce Wayne but it is revealed by Amanda Waller that Bruce Wayne is Terry's biological father due to her using genetic tampering. The rift created by Terry discovering his genetic compatibility to Bruce is also healed once Terry discovers that Bruce Wayne was unknowingly his father and talks with him. The truth being revealed to Terry allows him to let go of his anger and fear. He calls his long-time girlfriend Dana in preparation to ask her to marry him, an accomplishment Bruce Wayne unfortunately never has in his own life. Terry also begins to start treating Bruce as his father.
- A deadly assassin named Curare is sent after D.A. Sam Young, husband of Commissioner Barbara Gordon. Batman's attempts to protect Young lead to conflicts with Gordon, and some surprising revelations about the past.
- 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 has mysterious visions of a young girl asking him for help. His search for her leads him into confrontation with a group of people with incredible psychic powers known as the Brain Trust.
- 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.
- 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.
- A bionics designer is forced to give a gang of street punks robotic implants after they kidnap his wife. To stop them, Batman needs a special verbal "kill-phrase" to shut down their implants, but can he convince the designer to give it to him?
- Inque is freed by a lovesick worker at the cryogenics plant where she is being held. Trapped in her mutated form, she seeks to attain the chemicals that will allow her to once again regain her human shape, and get revenge on Batman and the "mysterious old man" who aids him.
- Bruce is out of town and incommunicado when Curare returns to Neo-Gotham, hunting down the last of her former society after the failure of her last mission marked her for death. Curare's target, the last surviving member of the League of Assassins, forces Batman to protect him from Curare's wrath by planting a bomb equipped with a deadman switch somewhere in the city. Things only get more complicated as Max gets herself involved in an already volatile situation.
- A gossip reporter acquires the technology to become incorporeal and becomes the ultimate Peeping Tom. When he discovers Batman's identity, he threatens to reveal it on national television, but soon discovers the technology is having an adverse effect on his body.
- Terry is forced to take a computer-simulated "baby" with him everywhere—even as Batman—in order to make the grade in Family Studies. Meanwhile, a family of jewel thieves are plying their trade around Neo-Gotham, stealing priceless rubies.
- This episode takes place after episode 52 Countdown. The destruction caused by a fight between Zeta and Infiltration Unit 7 causes Batman to believe that Zeta is endangering his companion Ro.
- Seeking vengeance, Shriek uses his knowledge of sound to take away Neo-Gotham's ability to communicate. His price for returning things to normal? Batman's life.
- A villain known as Spellbinder uses hypnotic technology to orchestrate a string of robberies, turning his victims into his unwitting accomplices.
- A group of Jokerz steals a prototype military vehicle and goes on a rampage of destruction, while Batman and the vehicle's designer try to recover the machine before its malfunctioning reactor goes critical and turns it into a flying bomb.
- Batman reluctantly joins forces with his former enemy, Stalker, to hunt down a wily criminal named False-Face, who has stolen a dangerous virus for a criminal organization called KOBRA.
- Batman goes up against a new, seemingly invulnerable foe called Repeller, who uses technology similar to a prototype that Wayne-Powers' medical division has been developing.
- After losing his job as a weapons designer, the stepfather of one of Terry's friends turns to crime to make ends meet as a supervillain called Armory.
- The brilliant leader of a crew of Jokerz plots revenge against Max Gibson, a fellow student who outperforms him at school. Terry's efforts to help her are complicated by her efforts to find out the true identity of Batman, whom she is convinced is a student at school, and her erroneous conclusion that Terry is one of the Jokerz. This episode makes references to Batman: The Animated Series when Maxine says to Terry: "You call me Robin, and I'm out of here." to which Terry replies "No problem, Alfred."
- Batman, Wonder Woman, and Green Lantern chase Chronos to the past, where they team up with some of the greatest DC heroes of the Old West. After defeating stolen future tech in that era, they again follow Chronos to the future. Warhawk from the Batman Beyond era is revealed to be Green Lantern and Hawkgirl's son. Guest starring: Bat Lash, Jonah Hex and other DC Characters from the old west. This episode also teases with the idea of Wonder Woman and Batman having a relationship.
- Terry steals the Batsuit to pursue his father's killer, a professional bodyguard named Mister Fixx whose employer Derek Powers , 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."
- 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, Terrence "Terry" McGinnis discovers Batman's identity after the aging Bruce Wayne helps him fight off a gang of Jokerz . After Terry's father is murdered, Terry seeks Bruce's help to avenge him.
- The Royal Flush Gang return, minus Ten, in an attempt to regain their reputation. However, after they are double-crossed by Paxton Powers, both Paxton and the gang seek to increase their bank accounts through Bruce Wayne.
- Batman, Green Lantern, and Wonder Woman chase Chronos into the Neo-Gotham City of Batman Beyond, just in time to face a battle with a group of Jokerz beside that era's Justice League. The time travelers are taken to the Justice League Unlimited refuge. An older Bruce Wayne reveals the street gang they fought together was enhanced by Chronos who led them to kill the rest of the League of that era. The combined heroes defeat the retooled Jokerz, and Batman traps Chronos in a time loop, right before he started his first time travel. This episode has homages to Crisis On Infinite Earths. The only place in the JLU universe in which Hal Jordan appears as Green Lantern.
- 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.
- Howard Groote, a hopeless nerd, purchases an illegal android in the form of a beautiful girl to pose as his girlfriend. His plan soon backfires when "Cynthia", programmed to be completely devoted to Howard, becomes dangerously possessive.
- Batman reluctantly agrees to aid a genetically enhanced gorilla in finding the poacher who kidnapped his mother.
- Batman gets involved when a friend of Terry's and her adoptive father are haunted by eerie, man-shaped creatures made out of soil, and soon learns that they have a frightening connection to the girl's biological father.
- The Stalker, a cybernetically enhanced big-game hunter, comes to Neo-Gotham seeking what he believes is the only prey left on Earth worthy of his skills: Batman.
- 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 who lives in the sewers because of his rat-like appearance, Batman may be the only one who can save her.
- As Derek Powers' Blight persona slowly destroys what was left of his normal life, he turns to his son for help. Paxton Powers seems willing to help Batman bring his father in, but unfortunately, deception and greed run in the family.
- When Commissioner Barbara Gordon witnesses Batman killing an opponent in cold blood, Terry finds himself on the run from the law as he tries to discover the real culprit and prove his innocence.
- Terry, having just started to work for Bruce Wayne, faces off against Inque, a notorious mercenary who is sabotaging FoxTeca, a company formed by Lucius Fox's son.
- 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.
- When Ace goes missing, Bruce remembers the origin of Ace. Terry discovers an underground dog fighting organization.
"This episode, whilst officially part of Season Three, was released on the Season Two DVD Boxset and not on Season Three's."
- A holomorphic military android has been reported to have gone rogue, and Terry needs to find him before he kills someone. But has the android really gone rogue, or has he just gained a conscience?
This episode leads into the spin-off series The Zeta Project.
- Bruce Wayne and Terry McGinnis confront a very familiar foe.
- A new program for troubled kids is becoming a popular last resort among parents in Gotham, but "The Ranch" is not everything it seems. When Terry's friend Chelsea Cunningham gets sent to The Ranch, Terry goes to investigate, but ends up biting off more than he can chew.
- When several Hill High students end up comatose in the hospital, Batman's subsequent investigation leads him to Spellbinder, who is getting teenagers addicted to virtual reality fantasies and forcing them to steal for him.
- 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 Big Time.
- To get to the bottom of the problem facing the Justice League, Batman must face off against his own teammates—including Superman himself. He must seek the help from Bruce who knew of an old enemy of theirs, Starro. Though he defeats it and a grateful Superman offers him to join the Justice League, Batman refuses understanding why the original didn't joins the League full-time in the first place.
- A new vigilante who calls himself Payback begins taking revenge on the tormentors of several troubled teenagers, all of whom are in the same therapy group. When Terry goes undercover in the group to find the culprit, he begins to suspect the doctor running the sessions, but Payback's real identity proves to be someone nobody would have expected.
- Willie Watt, a high school nerd who has been picked on one too many times, steals a construction robot from his father to scare his chief tormentor, Nelson Nash. But when Batman tries to stop the robot, it becomes bonded to Willie mentally, giving him more power than he ever dreamed of.
- Superman drafts Batman into the Justice League when he suspects there is a traitor among them. Despite Bruce's warning not to join, Terry goes against it and soon discovers a conspiracy against the League.
- Derek Powers hires Shriek, a former sound engineer-turned-supervillain, as part of an elaborate scheme to run Bruce Wayne out of his shared control over Wayne-Powers.
- 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. This episode makes reference to Catwoman when Bruce says to Terry, "Let me tell you about a woman named Selina Kyle."
- Shriek traps Batman in the abandoned tunnels beneath Neo-Gotham intent on revenge, and Bruce must ally with Max to find him.
- "Slappers", illegal steroid patches containing the Venom, are all the rage with Hill High School's athletes, and Bruce suspects that one of his old enemies, Bane, may have a hand in their production. However Terry finds that Bane has become a withered old man due to his constant use of the poisonous drug and a caretaker scientist named Chapel is using the drug to his own needs. Chapel douses himself with the Venom, but he is exposed to too much of the toxin leaves him halfway dead and crushed by the broken debris.
- When a friend from Terry's troubled past, Charlie "Big Time" Bigelow, returns, Terry tries to stop him from repeating his mistakes and going back to jail. But when Charlie ends up helping a gang of crooks rob a Wayne-Powers research lab, he is exposed to a dangerous experimental chemical and mutates into a monstrous giant.
- Terry must fight the Batsuit when it is taken over by the virtual soul of a dead communications tycoon, a man who has literally become a 'ghost in the machine'. Without the aid of the suit, he must save the man's grandson from becoming a vessel for his virtual brain.
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