Former robot assassin Zeta meets teenage Ro, who is also on the run and having troiuble with a gang that wants her to shoplift. He helps her and then she distracts the NSA for 500 creds from Zeta's unlimited account. Ro gets tagged by the NSA as being Zeta's "accomplice" so she stays with him. They set out to locate the scientist who originally created Zeta, in hope of proving to the government that Zeta is peaceful at heart and should not be destroyed.
Zeta goes after one of his creators but Bennett finds out about it and tries to capture him but his creator helps him escape and tells him the guy to clear his name - Selig, the head of the Zeta project.
Ro and Zee encounter Bucky, a brilliant but bratty kid genius, while looking for Dr. Sellig at at science competition. Bucky's supervisor Dr. Tannor steals his invention, a remote that can control any mechanical device. When he offers it up at the competition as his own creation, Bucky takes control of Zee and sets him after his Tannor for revenge.
Zee and Ro track Selig to a museum in Grandview, but get waylaid when a little girl becomes trapped in a fusion power chamber. Zee reveals himself and fights to save her life, while the NSA closes in.
Zee and Roe head down south to intercept a drug lord, unaware that the government has sent a new, improved model of the Zeta robot project on their trail. Bucky gets hold of the info as well, and goes to meet them. Zeta's efforts to stop the drug lord are complicated by the killer robot on his trail, which possesses all of his abilities and superior strength as well. At the end Zeta manages to seemingly destroy it, but as they head back to the States, the tracking robot begins to repair itself.
Zeta and Roe flee on a train to avoid pursuit, and only Agent West manages to get on the train with them. Their efforts to avoid him are complicated by the fact that as the monorail train passes through certain electrical barriers, Zeta's hologram projectors go out of control, forcing the robot to change into different people at random. Despite this, the pair manage to escape and save the train after West's shots endanger it.
Ro returns to visit her first foster family, the Morgans, in hopes of digging up information on her biological family. Determined to show them she wasn't a failure, she creates a rich girl persona via Zee's unlimited charge-card, but Zee goes overboard when he holograms as a famous vidstar. Things get dangerous when he's revealed as a robot, but before the pair escape Ro discovers evidence that she has a brother.
Infiltration Unit Seven returns, and a brutal battle errupts in a mall. Ro is hurt and taken to hospital, and Batman picks up on it from Bruce Wayne. Vid records make it look like Zee is solely responsible and Batman vows to take him down before he can hurt anybody. Meanwhile, Zee contemplates abandoning Ro so she will not be put at risk anymore. IU7, Zee, and Batman duke it out in an explosive hospital battle.
While enjoying a day on the beach, Zee and Roe intervene when a child is set upon by a local gang. The child, Wade, is actually a rich snob who mistreats his robots. He invites the duo to his home, and introduces them to his bodyguard Sven and his robot servants. When Wade is later kidnapped, Roe and Zee are implicated in the crime. They confront the gang they met earlier, who reveal they were hired by Sven. Going out to Wade's family's yacht, they find that Sven is holding him there for ransom. Zee and Roe manage to free the kid and beat Sven, and Wade has a new appreciation of robots.
Fleeing from Agents West and Lee, Zeta and Roe are lured to an abandoned candy factory by Knick, a bounty hunter. Knick plans to collect the reward by any means, using first Roe and then Lee as hostages to gain Zeta's surrender. Using the factory's automated "Cody Koala" robots, Zeta manages to rescue them. Agent West tries to shoot Zeta, but Lee "accidentally" stops him, as she begins to realize that Zeta is in fact acting of his own free will and out of concern for human beings.
Ro takes a chance and appears on a Jenny Jones/Oprah like show because they claim to be able to reunite her with her brother.
Zee and Roe are riding through the desert on a hoverbike when it is taken over by boy-genius Bucky and brought to his home. His parents are missing, and are working with Bucky's nemesis Dr. Tanner on some kind of youth-restoration project. Bucky wants the duo to help him. They go to Tanner's spa and discover that the youth-project has gone awry. Bucky's parents, and most of the customers, have become children, while other customers have become devolved apemen. Tanner' knocks out Zeta and forces Bucky to work for him to try and reverse the process. Bucky and Roe manage to escape, as does Zeta. An explosion triggers the nearby mud-geysers, destroying the complex. Zeta downloaded the schematics so they can restore Bucky's parents to his normal age, while an escaping Tanner is stuck with the rest of the "children".
Zeta breaks into a security base to steal a database containing retinal IDs, then breaks into Cyrobin disguised as a Dr. Wilhelm. His creator, Dr. Selig, is working at Cyrobin. Things go amiss when the real Dr. Wilhelm shows up before Zeta can communicate with his creator and prove his innocence. Selig is caught in a cyrogenic freeze unit when a stray shot shatters the control. With the lab in lockdown, Zeta is forced to remain hooked up to Selig's suspension unit and maintain his life. The authorities are breaking in, so Zeta takes a risk and tries to go into the unit, using his internal heaters to revive Selig. At the risk to his own ""life"", Zeta succeeds, but is forced to flee before Selig regains consciousness. Meanwhile, Agent Bennett is being shut out of the investigation by a mysterious Colonel Lomak, and Agent Lee resigns after giving away Bennett's plans to Lomak.
Zeta and Roe are rescued from Bennett by three hackers who claim to be Internet hacker types who want to free technology for the people. They're sort of right: however, they plan to dissect Zeta to find out how he ticks, while one of their members, obsessed fan Buss, keeps Roe prisoner. Roe and Zeta both manage to escape, but Bennett arrives. In the subsequent pursuit, Buss rescues Roe but Zeta is captured and taken in by Bennett in preparation for a complete CPU wipe. (to be continued)
Agent Bennett still believes that the captured Zeta has been programmed to believe he is acting of his own volition, a suspicion that seems to be borne out when the research team discovers a previously unknown chip in Zeta's head. Roe plans a rescue but it goes amiss when Zeta protects his memories from removal by transferring them from sector to sector. This results in the activation of his old killer-type programming. He goes on a rampage but Roe manages to get through to him and they manage to escape the NSA compound.
The parts from the IR hunter unit, that were destroyed by Zeta in a hospital, find their way into the hands of a young boy who likes to build things. The boy, Jace, accidentally activates the primary chip and the IR unit proceeds to rebuild itself from scratch. Zeta gets wind of the unit's activation when he notices the shipment of parts under the unit's ID. Tracking it to Jace's house, Zeta and Roe end up fighting the unit, and with Jace's help Zeta removes the primary chip and deactivates the unit.
Zeta and Roe are on the trail of one of Selig's associates, who is in a business/administrative area, the Hub. However, it's a trap set by Dr. Boyle, who attached a credit-nullifier to Zeta. In return for removing it, the two must steal items for Boyle for his research. Further complicating matters are Agents West and Rush trying to track them down. Eventually Zeta and Roe manage to lose the agents and set up Boyle to remove the nullifier and then be spotted by the NSA agents, while making their escape.
A mysterious organization of super-powered adults kidnap Ro, believing she has super powers.
Zeta malfunctions and recovers his memory of the moment he decided not to hurt people, when he is ordered to impersonate Eugene Dolan but instead gets close to him and his family.
Forced to take refuge from a tornado, Ro and Zeta meet two brothers, Dex and Carl, who are using an experimental process to disrupt tornados. They partially succeed, and the two fugitives join up with to get moving when their car is destroyed. With Zeta's input Carl the smart one manages to come up with a complete process, but pilot Dex gets the glory. Carl goes off on his own to take on another tornado and gets in over his head. With Zeta and Ro's help Dex rescues his brother and the two settle their differences.
Bennett tracks Selig via highly secure files to a research base where Selig was studying aquatic regeneration. Ro and Zeta are also there on the trail of Zelig. Bennett takes his son James Jr. along and while Ro, a local boy and James go underwater in a sub, Agent Bennett spots and pursues Zeta. But the kids get in an accident. Zeta reveals himself and volunteers to go down and Agent Bennett goes with him. Zeta has to act as the rudder for the injured sub to get everyone to the surface in time. At the end Bennett has to choose his son over capturing Zeta.
Ro and Zee take refuge at a "Pictocon" - basically a 21st century comicbook con where they take on the role of Owl Man and Squirrel Girl. Bucky contacts them there and puts Ro in contact with her long-lost brother Casey MacCurdy, a reporter. Casey's boss Jenson finds out he is the brother of a renegade and first insists he do a story on it, then alerts Bennett and the NSA. Ro and Zee duck the NSA in San Francisco but Casey sets up another rendezvous on the Golden Gate Bridge. He's persuaded to make it a trap. The NSA close in but Casey sides with his sister and helps them to escape. Casey plants an ad with a secret message for Ro reassuring her, but is under NSA scrutiny so their family reunion is delayed...but Casey starts to get the true story out on Zeta.
The NAS find out about Bucky and make plans to capture him and, through him, Zeta and Ro.
Zeta and Ro are on the run from the NSA when they stumble into a No-Tech community. The group is protected by law so Bennett can't go into their community without a local warrant. Zeta and Ro take refuge there but Zeta's robotic nature is soon discovered by Amy. She advises them to keep Zeta's nature a secret. Zeta predicts the No-Tech's river levee will break during an upcoming storm. Bennett gets his warrant when the No-Techs use a catapult on West. Zeta has to reveal his true nature to save the No-Techs and is damaged. The No-Techs Zeta prisoner and prepare to destroy him but the levee breaks. Zeta rescues the No-Techs and they come to appreciate his non-soulless nature as the two make their escape once more.
Zeta and Ro break into a NSA depot used to store hologram/robots. They spot Professor Zelig, who downloads information and leaves. The two follow him to a steel yard where he is revealed to be Professor Edmunds, who worked on Zeta's hologram projectors. He is being blackmailed by Sweet, the head of Brother's Day, an anti-tech terrorist organization. They get Edmunds to work with them to lead them to Selig, unaware that Brother's Day has followed them to the hologrammatically concealed floating fortress where zeta's creator is workin to creaet semi-organiz synthoids. Sweet plants an explosive as a disguised Zeta confronts his creator who confesses he secretly planted a "conscience chip" in Zeta (which Bennett overhears). Sweet triggers the explosion before Zeta can reveal who he is. Sweet shoots the escape pod with Selig as he escapes and the scientist is believed dead.
Zeta's quest to locate Dr. Selig leads him to another member of the infiltration unit design team, Dr. Myrell. He runs a non-profit organization called the Myrell center, where he constructs and tests new technology to help the handicapped. One of these is a young man named Kevin, who is confined to a wheel chair. The doctor has created a backpack device called a "synaptic amplifier", which allows him to walk normally. Zeta and Ro sneak into the center disguised as Kevin and his backpack, but end up encountering a thief there to steal the real amplifier pack. On a non-handicapped person the pack provides them with fantastic strength and agility. Blake, the thief, escapes, but a security guard who had seen the Zeta/Ro illusion of Kevin there after-hours accuses him of the theft, and he is arrested for it. It's up to Zeta and Ro to find Blake and clear the innocent Kevin.
Terry becomes suspicious when his biology teacher starts acting oddly. The strange behavior culminates in a manic chase and shootout with federal agents after school, leading him to get involved as Batman. When Commissioner Gordon and her men find the teacher gagged and bound in her home, the truth comes out: an intelligent synthoid code-named Zeta is on the loose. Designed for stealth and assassination, it has the ability to disguise itself as any person using a holographic generator. Batman joins in the hunt for Zeta, but when he corners the robot he discovers that Zeta ran away from the federal agency because he doesn't want to kill. Gary Cole makes his first and only appearance as the voice of Zeta, before Diedrich Bader assumed the role for the Zeta Project spin-off series. Joe Spano makes his first appearance as agent Bennet.
Shadows: Infiltration Unit 7 resumes its search for Zeta. After a mall is destroyed in a battle, Batman believes Zeta is responsible. He also mistakenly thinks Zeta is trying to kill Ro and tries to destroy him. Batman eventually realizes IU7 is the real enemy and then helps Zeta in an explosive hospital battle.
Future Shock: Static assists Batman and Robin in stopping a criminal named Timecode. afterwards Static is accidentally sent 40 years into the future, where he has to help the Batman of that era, Terry McGinnis, save a captured SuperHero [Static's future self] from Kobra, a major criminal organization bent on ruling the world in Batman Beyond.
The Once and Future Thing: Weird Western Tales (Part 1): Batman, Wonder Woman, and Green Lantern chase a time-traveling thief Chronos, into the past and team up with some local "SuperHeroes" to deal with an outlaw who has used the thief's futuristic technology to take over an Old West town.
The Once and Future Thing: Time, Warped (Part 2): In pursuit of a time-traveling thief Chronos, Batman, Green Lantern, and Wonder Woman arrive in a futuristic Gotham City. They then must join forces with the future Batman and the Justice League Unlimited to battle with a group of Jokerz.
Epilogue: Sixty-five years in the future of Batman Beyond, the history of the Justice League is the key to Batman's darkest secret...and his final destiny.
