Ace disarms some plane hijackers working for Doc Terror, who is angered by their surrender. Despairing of the failing of humans, Terror blames Amber for selecting the hijackers, and decides to exterminate all of mankind and replace them with robots. Rex Charger is specially recalled from a skiing trip to respond to a distress signal. He discovers that it is Amber, being chased by Hacker and some Strafers. She tells the Centurions that her father intends to destroy all of humanity this time, and that she wants them to stop his mad plan. With her help, the Centurions track him down to a Florida power plant, and discover that Terror intends to use a weather control satellite to create the biggest storm the world has ever seen. With the storm's strength increasing exponentially, it is left to the Centurions to figure out a way of neutralizing it. Science Lesson: Lightning by Jake.

Ace is seriously injured in a battle with Doc Terror's Doom-Drone Strafers and is turned into a cyborg to save his life. Resenting what has happened to him, Ace enters an underground cyborg fighting ring, calling himself Foss. He impresses Viva Vargas, a millionairess, and agrees to journey with her to her Alaskan base, Xanadu. Doc Terror attacks Xanadu, as Vargas has previously refused to work for him. Ace then reveals that he has only been pretending to be a cyborg in order to infiltrate the underground. He and the other Centurions then defend Xanadu against Terror's army. Science Lesson: Lizards regenerating limbs by Jake.

In Dominion, Doc Terror attempts to turn his dog Brutus into a cyborg, but there is a malfunction that halts the mechanisation process while still giving the dog cyborg strength. With this knowledge, Terror creates the Encephalocaster, a device that can control other animals as well as giving them cyborg-enhanced strength. He uses the device on Skyvault and gains control of the space station with the help of Lucy. Once there, he uses the device to control all animals on Earth. As Jake attempts to deal with a Terror-controlled Shadow, Terror and Hacker prevent the other Centurions from beaming to Skyvault. With the Earth under siege by Terror's super-strong animals, the Centurions must figure out a way of getting to Skyvault and evicting Terror as well as shutting his Encephalocaster down. Science Lesson: Animals' super-human abilities by Crystal.

John Thunder informs the Centurions that his old sparring partner Claw is now working for Doc Terror as a cyborg. Meanwhile, Doc Terror succeeds in creating a dimensional neutron vortex in his base, Dominion. Energy from the vortex is detected by Skyvault, where Crystal determines that the laws of reality will soon collapse. With Terror having stealth and scrambler fields all over the Arctic to hide his base, the Centurions lure Hacker into stealing a vital component for the vortex, and John sneaks on board Terror's airship. John makes it to Dominion, where Claw soon senses his presence and alerts Terror, who then gets Hacker to attack the SETI space probe station in the Andes to keep the rest of the Centurions occupied. Claw captures John and attempts to settle old scores with him. The other Centurions are sent to locate Dominion, but are too late, as Terror's dimensional vortex breaks out of control. Science Lesson: Magnets by Ace.

Terror follows the wandering vortex, attempting to bring it back under his control, while John manages to escape from Claw. The other Centurions, still looking for Dominion, come under attack by their own weapon systems, which are transformed into creatures by the vortex's alteration of reality. Crystal beams them to Skyvault, leaving John still on his own in Terror's Arctic base. John finds a transmitter and contacts Skyvault, but the co-ordinates are unstable as the position of Dominion is not stable anymore due to the vortex. Crystal is able to beam the other Centurions to Dominion, where they meet up with John, who tells them that he still has to deal with his old enemy Claw. As John fights Claw to the finish, the remaining Centurions must figure out a way of destroying Terror's vortex before all of reality is destabilized. Science Lesson: Continental drift by Crystal.

A new surface-to-Atlantis rail shuttle is opened by Princess Diana, with the Centurions in attendance. During its inaugural journey, the train comes under attack by Doc Terror's forces and the Centurions engage them in battle. During the fight, Diana's cousin Naro and the evil physicist Phisto escape from Atlantis' prison. Phisto then creates an artificial micro black hole which soon attracts the attention of Doc Terror. After the battle with Terror's borgs, Ace is sent to look for Naro and Phisto whereabouts, but is ambushed by Naro's henchmen and knocked unconscious, now completely at their mercy... Science Lesson: Micro-technology by Crystal.

Rex attempts to locate the missing Ace but only finds his discarded wristcom and soon comes under attack by Terror's forces. Ace is brought in front of Naro, who plans to take over Atlantis once more. Dr. Terror meets with Naro and plots to take control over the black hole. However Phisto can't control the black hole and it's up to the Centurions to fight Terror's cyborgs, evacuate Atlantis and prevent the growth of the ever-expanding black hole.

Dr. Terror and Hacker's robotic halves join together accidentally to become Uniborg. Dr. Terror and Hacker get banned from Dominion by Uniborg and fall in the hands of the Centurions that make them face trial. Uniborg plans world conquer.

Max and Jake are hospitalized after bad injuries battling the forces of Uniborg. Ace is the last Centurion left. Dr. Terror joins forces with Ace in defeating Uniborg and regaining Dominion. Crystal and Ace finally share first kiss.

Doc Terror observes scientist Marina Abbot's ship heading out to sea and sends out sea-borgs to attack it. The Centurions are sent to defend the ship, while Marina summons help from a giant lobster. After the battle, Marina explains to Max that she has taken over her father's research, but wishes to keep it secret. The ship heads to the research base Neptune-1, and the Centurions observe the giant lobster and a giant turtle first hand. Marina tells them that the creatures are to be used by the World Council of Scientists and that each one can be controlled with an implant. She swears not to have her work destroyed by Doc Terror like her father's early research. Ace is later trapped by Marina, who tells him that she wants to lure Terror to the island and take revenge against him for her father. As Terror begins transforming the creatures into cyborgs, the Centurions arrive to defeat them. Science Lesson: Swan ships by Max.

New Centurions are recruited by the team and trained in the Centurion Academy, whilst Sealab develops new weapon systems for the original three. Meanwhile, Doc Terror makes contact with an alien computer called "Gog".

Doc Terror reflects on his past as his partner Hacker while he stows away on board Skyvault and seizes control of the station. Terror boards and begins coordinating his campaign of destruction, ordering Magog to begin full distribution of a vast, unending armada. John Thunder attempts to find a way of saving Crystal and everyone trapped on the station.

Thunder, now a prisoner of Gog and Terror, is rescued by Crystal when she is able to successfully escape and elude Hacker. The two however remain powerless to help the remaining Centurions on the planet fighting to take back New York from Terror's armies. Terror makes a stern demand to the members of the science council that rejected him years ago.

As the Strafers approach the falling space station, Crystal and John risk turning the computer's power back on to destroy them. In order to free Skyvault's computer from Terror's control, Ace uses the Orbital Interceptor to travel up to Skyvault with Dr. Wu's anti-viralizer ray, avoiding the station's self-defenses after being beamed aboard. Meanwhile, at Gog's island cybernetic hive, Terror has taken the World Council of Scientists prisoner, and shows them Gog's new Triad weapon to fight against the Centurions.

Doc Terror and Hacker rebel against Gog, managing to inflict a decisive blow against him. Gog travels to New York City, now inhabiting the Triad, a vessel equipped with incredible firepower. Only all five Centurions can save humanity from the wrath of this terrifying machine.

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Jenny Rivers returns with a scoop on Dr. Terror. She disguises herself as a man and joins one of Terror's training camps, with some help from a former mercenary named Kaska. She and the other recruits stage an attack on the Centurion's testing grounds.

Hacker is spotted near Manhattan, and the Centurions are sent to investigate. He takes a woman, Cassandra Cross, hostage, but she manages to subdue him with her magical powers. After reviewing Hacker's memory, Doc Terror plans to have her power for himself. Meanwhile, Ace has become smitten with Cassandra, and while enjoying a flight with her, they are both kidnapped by Hacker. In Terror's base under Manhattan, Ace discovers that Cassandra comes from a family of witches. Terror wants Cassandra's powers to sink New York, but before he forces her to help him, she frees Ace as the other Centurions arrive. Science Lesson: Earthquakes by Crystal.

A group of Native Americans comes under attack by a giant totem claiming to be a ghost warrior, who tells them to fight against those who have built upon their land. The tribal leaders call in John Thunder, who brings along his fellow Centurions Ace and Jake. While John confers with his people, Ace and Jake are attacked by Hacker. Meanwhile, the giant ghost warrior appears to John and his tribe and brainwashes them into attacking a geological research lab. John tracks down the ghost warrior and finds out that it is really a giant Traumitizer controlled by Doc Terror. Terror traps John, and as his brainwashed victims keep Ace and Jake occupied, Terror attacks the real target: a nearby space port. John must free himself and his people, and assist his Centurion friends. Science Lesson: The Apaches by John.

While conducting a training exercise, the Centurions come under attack from Doc Terror's forces. Ace is rescued by his old acquaintance, Cassandra Cross, the witch. The Centurions decide to attempt to duplicate her powerful abilities by studying her on board Skyvault. But once connected to Skyvault's computers, she turns off the defense systems and introduces herself as Lilith Cross, Cassandra's twin sister. With no defense systems operative, Doc Terror beams on board Skyvault. Ace manages to escape using the magical white rose given to him by Cassandra, and beams to Earth. He finds Cassandra trapped by Lilith's magic, and frees her. Together, they go back to Skyvault, and attempt to free the other Centurions. Science Lesson: Herbal medicine by Crystal.

Doc Terror attacks the Navigation Control Centre for the East European sector in Transylvania, wanting to cause air traffic chaos. The Centurions successfully defend the installation, and manage to down Terror's ship in a mountain range. Doc Terror and Hacker escape the from wreckage of their ship and seek refuge in an old castle. There, they find a sarcophagus of Count Dracula, and free him from suspended animation. Now free, Dracula is told of the Centurions, and attempts to defeat them himself by hypnotising Max and using him against Ace and Jake. The Centurions soon regroup and launch an attack on Dracula's castle.

In Colorado, mercenaries hired by Doc Terror stage a diversion to keep the Centurions busy by attempting to steal a shipment of plutonium. As they battle each other, Terror implements his plan to sink the entire city of Denver into a huge underground cavern and turn all of the city's inhabitants into cyborgs. The Centurions journey underground to get to the captive city and encounter Terror's new cyborg-enhanced mercenaries, who have stolen their exoframes. Weaponless, the Centurions have to figure out a way of saving both themselves and the city of Denver from Doc Terror's forces. Science Lesson: Caves by Jake.

The World President's yacht comes under attack from Doc Terror's Strafers. With Jake on vacation, Ace and Max alone drive off Terror's forces. Meanwhile, Jake discovers that all is not well in a small town, with its inhabitants seemingly acting like zombies. With the President's train passing though the area soon, the Centurions examine the place further. They find that the townspeople are under the control of Zombie Master, who is working for Terror. He intends to turn the World President into a zombie when his train passes through the town, controlling him. Of course, only the Centurions can stop him. Science Lesson: Steam power by Jake.

Ace is asked to pilot a new superjet, the XM-2000, for an air show in Paris. No sooner do the Centurions arrive than Doc Terror and Hacker stage an attack. The cyborgs are defeated, and the Centurions free the officer in charge of the XM 2000 and his assistant. Ace offers to walk the young lady home, and during the walk she reveals herself as Amber and kidnaps Ace. When Ace awakens, he finds himself strapped to a mind exchange machine stolen by Doc Terror. Hacker is on the other side, and Terror flips the switch, imprisoning Ace's mind in Hacker's body. With Hacker's consciousness now in Ace's body, Terror can hijack the XM 2000. Ace has to somehow get free, stop Terror and get his mind back into his own body...without getting killed by his fellow Centurions. Science Lesson: D.N.A. by Crystal.

Jake Rockwell is sent to give a lecture at Sally Ride HS in Los Angeles. One of the students there happens to be a boy named Jimmy, who has ESP and is picked on by the local jocks. After Jake's visit, Wild Weasel is accidentally left behind at the school, and Jimmy uses his powers to merge with the system. For him, Wild Weasel is a way to impress a girl. But Doc Terror sees them, kidnaps the girl and recruits Jimmy to do some of his dirty work. The Centurions save the kids and stop Doc Terror. Science Lesson: E.S.P. by Jake.