Doc Terror sends Mekko to attack Sea Lab, where the Centurions' weapon systems are created. Max and Ace fight against Terror's forces in South Africa while Jake is visiting Sea Lab and gets caught in the assault orchestrated by Mekko.

A meteorite with alien life on its surface falls into the Arctic Ocean. Doc Terror wants it, and sends Mako to retrieve it. Sealab is also interested in the meteorite, and comes into conflict with Terror's forces. The Centurions are sent to diffuse the situation. However, problems later arise when the new Mark-1 A.I. Prototype onboard is infected by an alien virus carried by the meteorite. With every electronic system on board Sealab affected, the Centurions have to neutralise the virus before Doc Terror's approaching forces arrive.

Science Lesson: Arctic Ocean by Max.

Mei Lee and her colleague Jason from Sealab, are exploring a recently-discovered underwater trench, the deepest ever found. Their sea-bubble comes under attack by a giant squid and loses contact with Sealab. Max is sent to rescue them, but he too is attacked and loses contact with Sealab. Ace and Jake are sent to NASA to use an experimental Venus Probe, as only the probe can withstand the pressure at that depth. Meanwhile Max awakens to find himself in the undersea city of Atlantis, ruled by Princess Diana. At NASA, Ace is reunited with his old Air Academy comrade Sean O'Connor, who still holds a grudge against him since they had an argument over a girl. Diana tells Max her civilization has survived for many centuries since the city sank, and that they want no contact with the surface world, so he, Mei Lee and Jason are to remain there forever. Seeking control over Atlantis himself, Diana's cousin Naro attempts to steal the Venus Probe, leaving Ace to defend the ship underwater, where

Jake has Crystal beam Ace back up to Skyvault, freeing him from the squid's clutches. Naro tells Jake and Sean that he intends to use the probe to take over Atlantis, and O'Connor agrees to help him. Meanwhile, Max and the two from Sealab escape from their confinement and look for a transmitter, but are stopped by Diana troops. Ace returns to Sealab, which engages its new force field to descend to Atlantis' depth. Max and the others escape from Atlantis and take Diana with them, but they are soon attacked by Naro's forces. Sean uses the Venus Probe to return to Sealab, where it is soon boarded by Naro and his followers. Jake escapes and beams outside Sealab, where he attempts to get on board. Sean reveals to Ace that he's still really on their side, and together they attempt to regain control of the base. Now working with Diana, Max and the rest of the Centurions try to defeat Naro's forces.

Science Lesson: Uranus by Ace.

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.

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.