Mera's spacecraft splashes down in the ocean and as she swims to the surface she is surrounded by Commandoes. Seeing the craft come down from the island, Brett, Neri and Jason rush out to rescue Mera. Once safely back on Neri's island, Mera tells of the spread of the red virus on the Ocean planet, the rebel's growing power, and their plans to invade the Earth after melting the polar ice caps. Malakat and Shersheba make arrangements to return to Earth while Neri hides the new ankh in the river near the Bates' farm. Winston picks up Praxis radar activity near ORCA. Agent Shelby has monitored Mera's craft as it arrived on Earth and after connecting it with previous activity in the area, he is able to get Project Pheonix reopened. Neri observes Shersheba returning to the pyramid with her commandoes.

Jason and Winston climb the mountain on Neri's island to install surveillance equipment. Making their descent, Winston is bitten by a snake and falls the rest of the way down. Meanwhile back on ORCA, technicians are preparing to upgrade Helen but when they shut her down improperly, the entire station loses power. Neri and Brett trek across the island for a rare flower that can counteract the snake venom while Cass leads the effort to get Helen back online. On the distant Planet of the Oceans, a fast acting virus has ravaged the world's oceans and Malakat, as the leader of the rebel faction, plans an invasion of the Earth. On ORCA, a signal from deep space has been picked up by the receiver on Neri's island—it is Malakat scanning for any signs of the underwater pyramid.

Richter talks Elly Hauser into rejoining agent Shelby on newly a reopened Project Phoenix. Winston, Cass and Brett program Helen to provide 'just the facts' if questioned about pyramids. Louis overhears them trio talking about pyramids and tells Shelby and Hauser what they're doing. After a little prodding by Shelby, Helen reveals the existence of the underwater pyramid to the Praxis agents. Shersheba leads a group of commandos in a search of the nearby islands for Neri and Mera but they are unsuccessful until Brett is observed in a boat heading towards an island, Shersheba informs Malakat of this and plans a search of this island. After showing her around the station, Louis challenges Ilona in a race to the galley.

Vanessa Lane comes to ORCA and ends up in the same class as Jason. Brett, Zoe and Froggy play a trick on Vanessa and she gets back at Brett and leaves him in a broken boat out at sea. A storm comes up, so they can't search for him. He strands on Neri's island and meets Neri, and tells Jason about her when he comes back.

Neri is taken back to Praxis headquarters where she is interrogated. Neri's captures prompts Jason to put the Ankh out of reach of Malakat and Shersheba, he drops it into the deep ocean. Neri's deteriorating condition and Praxis's uncaring treatment of her results in Hauser developing a sympathetic attitude towards Neri. By showing Jason footage of Neri from Praxis's own security cameras, Shersheba convinces Jason that tshe and Malakat have Neri and offers to return her in exchange for the Ankh. Jason and Brett arrive at the transfer location but Shersheba, disguised as Neri, grabs the Ankh and runs back to Malakat, at which time they discover the Ankh to be a copy. Later, Shersheba sneaks back onto ORCA and, with help from Louis, is able to discover the location of the real Ankh. She retrieves it and returns triumphantly to Malakat.

Budds Praxis begins moving their equipment onto ORCA, including several nuclear weapons. Jason and Brett travel to the underwater pyramid to propose a meeting with Malakat of Neri's behalf. Hauser is opposed to Shelby's heavy-handed approach to dealing with the aliens. Neri meets with Malakat on a deserted beach, during their talk, Malakat reveal that he was responsible for her mother's death. Meanwhile, Mera is captured by Shersheba and her commandos, she will only be released in exchange for the ankh. Richter arrives on ORCA and assumes command of the station. Neri is torn over the decision on whether or not to exchange the ankh for her sister, Jason won't help her telling her it is a decision only she can make.

Dianne is at ORCA Pacific headquarters for her interview, she is surprised to discover her exhusband in the role of interviewer and more surprised to learn the job is hers if she wants it. A return visit is made to the pyramid by Neri, Jason, and Brett. Neri finds a way in and the boys follow in the minifin.Exploring the pyramids interior, Neri activates a holographic recording which relays a cryptic message about a quest. A doorway is opened revealing a swirling vortex which pulls the trio in. They reemerge in another pyramid, and upon exiting, discover that they are in Egypt! Agents Shelby and Hauser begin their search for the receivers of the alien transmissions while Malakat and Shersheba continue their own search.1998 AFI award nominee: ""Best Childrens Television Drama"" (Jonathan M. Shiff)

On the Ocean Planet, Mera is pursued by the rebels but is able to reach safety in the Pyramid of the Elders. A group of rebels arrives on Earth. They pursue Neri are driven off by Jason and Brett in the minifin. Shersheba leads an assault on the Pyramid of the Elders. Mera escapes to Earth with a new Golden Ankh moments before the elders trigger the destruction of the pyramid. As the Pyramid of the Elders is destroyed on the Ocean Planet, back on Earth, the underwater pyramid returns.

Dianne Bates and her sons Jason and Bret come to the underwater base ORCA for six months. They meet Winston Seth which is Dianne's assistant. Sher is going to study whales. Brett finds the place cool, but Jason donesn't like it. They also meet commander Lucas. At dinner Brett meets his new friends Zoe and Froggy whos real name is Jake Reilly{}. Dianne, Winstorn, Jason and Brett go out with the boat to put a transmitter on the whale. A girl comes up out of the ocean and stops Jason when he is about to shoot the transmitter on the whale, so Dianne has to do it instead. Nobody believes Jason when he tells them about the mermaid.

Praxis's return to ORCA prompts Cass and Brett to seek Winston's help to delete all of Helen's records of Neri. Louis observes them through the airduct and informs Shelby and Hauser of what is happening but by the time the agents react, all of the records have been erased. Neri and Jason dive to the underwater pyramid, Neri activates the Shalamorn hologram and the pair are told about a rebel faction on the Ocean Planet that is opposed to a peaceful migration to earth. Soon after Malakat and Shersheba arrive and tell Neri and Jason of their own plans, as part of the rebel group, to use the power of the pyramid to melt Earth's polar icecap to prepare the planet for their people's arrival. Malakat also tells Neri that he caused the spacecraft that she and her father were on to crash to earth. Malakat demands the Golden Ankh be tuned over to him, but Neri and Jason escape through the water gate. They emerge in the same cave in the outback that they were in before and find Jakamarra waiting

Shelby requisitions the minifin to get a closer look at the underwater pyramid, Diane assigns a reluctant Jason as his pilot. Near the pyramid, they encounter a group of commandos and come under attack. The minifin loses power and heads to the ocean floor. Jason is able to jump start the minifin using the battery from Shelby's GPS receiver and brings them safely back to ORCA. Shersheba and her commandos search Neri's island, Neri and Mera hide in a cave but when Shersheba closes in, she and her commandos are frightened off by a group of birds. Ilona eavesdrops on Shelby's report to Richter and reports what she's heard back to Malakat. Hauser interrupts Ilona's transmission and begins to grows suspicious of Ilona. The president of the Global union gives Praxis the authority to take over ORCA to use as a base from which to attack the underwater pyramid.

Neri, Jason, and Brett wander into an archeological dig and meet Professor Malakat and Shersheba. Finding the minifin abandoned, Winston tracks the signal from Brett's vid-phone to Egypt, but discounts his findings as a phantom signal. Back in Egypt, Malakat begins to take an interest in the travelers he's taken in, he has Shersheba befriend Jason hoping to find out more about Neri. Jason is able to make a quick phone call to ORCA and tells Cass where they are. Not long after, Malakat is in contact with the boys mother promising to send them back to Australia, he then tells Jason that Neri will have to stay behind due to problems verifying her identity. From an analysis of the material in Neri's clothes, Malakat determines that she is not from Earth and when Shelby and Hauser enter the camp, he directs the agents to the kids. Forced to make a quick escape, Jason commandeers a jeep and the trio drive off, joining a tour group headed back to the ""Pyramid of Mystery."

With the melting of the polar icecaps well under way, Malakat prepares for the invasion of Earth with seeming ambivalence towards the red virus. Shersheba challenges Malakat to create of cure for the virus immediately and using the power of the pyramid he does. Shersheba quickly releases it into the ocean but the red virus begins to mutate and soon grows stronger, surpassing even the pyramid's ability to stop it. Unaware of Malakat's efforts, Neri goes to the pyramid to plead for him to stop the virus. Malakat orders her to be killed but Shersheba intervenes saying that he cannot kill the chosen one—Neri escapes as they argue. As Neri, Mera and Jason walk along the beach pondering their next move, Neri wonders if perhaps Charlie may hold the answer.

Neri brings Jason's attention to a toxic dump in the ocean that is making Charlie sick. When Jason is reprimanded for leaving an important project, it is up to Lee, Brett, Froggy and Zoe to prove to Commander Lucas that the dumping of waste in the ocean is occurring. A barrel is recovered and dramatically revealed during a presentation on ORCA by Zenco, a major sponsor of ORCA research and the company responsible for dumping the waste. Neri once again expresses her desire to see the inside of ORCA.

Jason and Brett are about to force the chamber open when Neri finds the controls that open the chamber and revive it's occupant. He comes to and says his name is Kal. He is shown around the island where he seems to be content to live. Brett and Jason are surprised when Kal says he will take a subordinate role in relation to Neri, as is done on his own planet. Benny covers for a girl caught cheeting on an exam and is also disqualified. Lena Hellegren makes a surprise appearance at UBRI forcing her father to take her home where she convinces him to let her remain instead of being shipped off on vacation by herself.

Praxis closes in and apprehends the kids at the farm. Jason and Brett are returned to ORCA while Neri is transported, by boat, to Praxis headquarters. En route, Charlie jostles the boat allowing Neri to escape and jump overboard.Cass locates the bug Praxis used to follow Jason, Brett, and Neri to the farm—it was hidden in Jason's watch. Jason, Neri and Brett return to the underwater pyramid, placing the Praxis transmitter on Charlie as a decoy. Activating the holographic image of Shalamorn, her message informs Neri of a crisis on the Ocean planet and tells her that she is a princess destined to lead her people. Meanwhile, Malakat and Shersheba have arrived in Australia to begin their search for the underwater pyramid.

Shersheba makes a surprise visit to ORCA and Dianne gives Jason the task of showing her around the station. Louis pesters Winston about the magnetic anomaly and threatens to tell his father, ORCA's second in command, until Cass brings up the matter of Louis' use excessive of his father's ceredit card. Shersheba asks Jason to give her a tour of the reef which he reluctantly agrees to do. While watching Shersheba dive, Jason jumps in after her when she appears to be drowning. Jason is unable to find Shersheba but she is pulled to safety by Neri who Charlie called away from the pyramid to help. Back in the boat, Malakat suddenly appears and Shersheba quickly recovers. A struggle ensues but Jason and Neri are able to push Malakat and Shersheba overboard. As Jason and Neri make their escape, Neri comes to the realization that Malakat and Shersheba are from the Planet of the Oceans. Back in their seaside residence, Malakat is able to discover the location of the underwater pyrramid using inf

Neri is brought back to ORCA but she cannot be revived. Malakat and Shersheba successfully charge the ankh. Praxis destroys all their records of Project Sphinx and agent Hauser hands in her resignation. Louis calls agent Shelby to tell him that Neri was brought back to ORCA, but with the project over Shelby desmisses him. Jason and Brett take Neri back to the underwater pyramid, Malakat and Shersheba arrive soon after to use the charged ankh. As Shersheba is about to place her hand on the sacret stone, Jason places Neri's hand there ahead of her. The pyramid comes to life and Neri is miraculously revived. In anger, Shersheba destroys the ankh bringing about a large seismic event. Jason and Neri escape the pyramid with Neri and they watch as the pyramid slowly sinks into the ocean floor. As Neri is taken back to ORCA for a reunion with Dianne and Winston.

Paul and Brett Bates are given an audience with the Global Union's Madam President to voice their opposition to Praxis's adversarial stand against the aliens, they are granted an immediate suspension of all attack preparations. Malakat tells Shersheba and Mera that he was responsible for the creation and release of the Red Virus on the Ocean Planet. Hauser walks in on one of Ilona's transitions to Malakat thereby discovering that she is a spy from the Ocean Planet herself. Hauser tells Cass and Winston about Ilona and asks for their help in 'understanding' the aliens. Neri brings the ankh back to the island. Mera locates a hidden passage in the pyramid which gives her access to a source of water. Shersheba rebukes Malakat for his arrogance and controlling behavior reminding him that she will be the one in power when the earth is conquered, Malakat in response stops advising her on what actions to take. Feeling the need to do something, Shersheba takes a vial of the Red Virus and releas

Neri goes to ORCA to see how Jason and Brett are going with their search for the Synchronium. Dianne takes the opportunity to ask her to help Winston with his dive test which she agrees to do. When Neri doesn't return to the island on time, Kal takes the opportunity to go back to ORCA. On ORCA, Kal manages to get signed up for Morgan's fitness class (she's very impressed with him) and gets a date with Marika, which Jason is able to speed him through. Neri helps Winston through his test by getting him to believe in himself. After Lena's visit to ORCA, Kellar warns her that her curiosity may reveal things about her father she might not want to know.

With Jason and Brett back on ORCA, agents Shelby and Hauser arrive soon after looking for Neri. Praxis locks down the base hoping to trap Neri inside but Dianne orders an evacuation of the base in order to countermand the lock down order and with the base reopened, Neri is able to escape. She returns to the underwater pyramid and after activating he hologram, learns that the image is that of Shalamorn, her mother. Shelby subjects Jason and Brett to a lie detector test but Winston is able to use Helen to allow the boys to safely deny knowledge of Neri. Jason, Brett and Neri are flown by the boys father to a farm on the mainland for their safety but unbeknownst to them, Praxis, having followed them to the farm, looks on.

Jakamarra takes Jason and Neri to where he has hidden the Golden Ankh. Malakat is able to determine the location of the cave in the outback and informs Praxis of the Neri's whereabouts. Brett interrupts a meeting between Malakat and agents Shelby and Hauser with an anonymous phone call to inform them that Malakat and Shersheba are aliens themselves. Shelby and Hauser track Neri and Jason through the outback, and after being joined by Malakat and Shersheba, they find Jason, Neri and Jakamarra and close in. Agent Hauser pursues the kids up a cliff face but she slips at the top. Neri sees Hauser slip and goes back to rescue her allowing Agent Shelby to close in and apprehend her. Shersheba takes possession of the Ankh but Jakamarra steps in to grab it and tosses it to Jason. Jason's father arrives by helicopter and Neri tells Jason to escape with the Ankh. Reluctantly, Jason boards the helicopter and must watch as Neri is taken away by Praxis.

Jason's frequent use of the boats results in Commander Lucas banning him from using them for a period of one week, effectively cutting him off from Neri. A pair of eager developers arrive on ORCA expressing an interest in a nearby island—Neri's. Jason volunteers to be their guide on their visit to the island and once on the island he and Neri are able to scare off the developers keeping the island safe. When Jodie takes forty dollars from a lost wallet, Vanessa forces her to spy on Jason and Brett in order to keep the theft a secret.

Jason, Brett, Froggy, and Zoe return to the institute to get Mera but Dr. Hellegren arrives there as well wanting to take Mera back to UBRI with him. Fortunately the kids arrive in time to rescue her, convincing her she can trust them by showing her Neri's silver pendant, to which Mera has the matching piece. While the others are off rescueing Mera, Neri helps Dianne and Winston with the survey. Mick asks Vanessa to the dance as a joke but when she finds out, it is Mick who is all wet. Neri is reunited with Mera.

Neri awakes on the island to find Kal missing, he's gone to ORCA. Jason and Brett introduce Kal to Diane and Winston. Shortly after, Neri arrives and tells Diane about UBRI's plans to use explosives on the ocean floor in their construction. Diane is not happy and takes the issue before the tribunal but unfortunately they rule in favour of UBRI and allow the blasting to proceed. Jason and Brett begin searching HELEN for reports of UFOs and meteorite impacts that may help them locate the Synchronium pieces. Neri senses something wrong with the oceans but cannot be more specific. Successful in their search, Jason, Brett, and Neri venture inland to retrieve the first piece of Synchronium. Lena accesses her father's locked computer files. Kal beats Benny, the youth champion, in a game of trigammono.