Brett and Jason are out testing a new diving suit when Jason encounters a strange bright light while under water, the pair quickly leave and head off to see Neri. Back on ORCA, Winston is puzzled by a magnetic anomaly on his scans of the ocean floor, even more strange is that the anomaly is in the shape of a perfect square. Dianne announces that she is going to pursue the vacant position of ORCA Commander. Jason matches the location of Winston's magnetic anomaly to where he saw the strange lights, Neri is also intrigued by the region prompting a closer investigation of the region. Neri swims out to the sight with Jason and Winston following in the minifin, ORCA's new underwater submarine. What they find surprises everyone—a huge underwater pyramid. Meanwhile, at Praxis headquarters (Preventative Response And eXtraterritorial Intelligence Service), agents Jake Shelby and Elly Hauser are dispatched to Egypt where reports suggest signals from outerspace are being received.

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)

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."

From the DNA sample obtained from a strand of Neri's hair, Praxis identifies Neri as an alien and makes her capture their top priority. Wandering in the desert looking for the Pyramid of Mystery, Neri, Jason and Brett get a ride from two Bedouins who take them back to their camp. Worried they've been picked up for the reward, when Neri rescues a young girl from a well, the trio become welcome guests. They are told a story about a Bedouin man who was abducted by people who ""live like fish."" The next morning they are taken back to the well that holds the entrance to the Pyramid of Mystery, they are spotted by Malakat and Shersheba who, after summoning Shelby and Hauser, pursue them into the pyramid.Inside the pyramid, Neri locates a golden ankh and opens the water portal allowing her, Jason and Brett to escape, emerging on the other side, they discover they've been transported to a cave in the outback.

Leaving the cave to find help, Jason is found by Jackhammer who drives him back to the others but won't take them with him citing a legend about a ""whale woman"" who was pursued after leaving the very same cave. Winston locates the group in the outback but Praxis, after intercepting Winston's transmissions to the region, head out to capture the trio. Hauser and Shelby meet up with Jackhammer who leads the agents astray long enough for Jason and Brett's father to arrive in a helicopter to rescue Neri and the boys. Before leaving, Neri gives Jackhammer the golden ankh for safekeeping.

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.

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

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

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.

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.

Malakat and Shersheba attempt to unleash the power of the pyramid by are told by Shalamorn that the Ankh must be prepared first. Praxis resorts to using experimental procedure to keep a deteriorating Neri alive. Paul locates the plans to the Praxis bunker and a rescue plan is devised. Malakat discovers that the secret to charging the ankh lies in the outback cave. Using Helen, the Praxis facility is flooded forcing an evacuation. In the ensuing confusion, agent Hauser helps Neri escape and turns her over to Jason and Brett who entered the bunker through the flooded aqueduct.

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.

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.

Jason and Brett return with Neri to their father's farm for Jason's birthday but soon after arriving Paul is called away on business. While at the farm, Neri has a series of encounters with a strange young girl by the name of Emma. Neri helps her overcome her fears but afterwards, a story told by Paul Bates and a farm hand reveals the girl's true identity. Back on the Ocean Planet, Mera faces an angry crown of people demanding answers to the problems facing their planet. The installation of the new HELEN 6000 computer is completed on ORCA.

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.

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.

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.

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.

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.

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

As the red virus spreads through the ocean, Jason must restrain Neri from going to Charlie's aid. Through the secret passage from her cell, Mera gains access to the central core of the pyramid and uses it's power to send a telepathic message to Neri. Richter, along with Paul and Brett Bates once again are before Madam President of the Global Union but this time, with the red virus unleashed, she grants Praxis the authority to attack the pyramid. Shersheba encounters Neri in the ocean, she demands that Neri hand over the ankh to ensure the safety of both Earth and the Ocean Planet. When Neri goes to ORCA, she is spotted by Louis who quickly informs agent Shelby, but Helen soon erases all traces of Neri's arrival, affectively destroying Louis' credibility with Shelby. Jason goes to the underwater pyramid to deliver the terms under which Neri will hand over the ankh to Malakat.

With an attack against the aliens pending, all non-essential personnel are being evacuated from ORCA. Louis informs agent Shelby that Hauser has kept Ilona of the evacuation list which leads to Praxis discovering that she and her mother are both aliens. Louis also manages to be taken off the list prompting Brett and Cass to stay behind as well. Believing Malakat and his commandos to have evacuated the pyramid as promised, Jason and Neri go to the pyramid but, along with Mera, they are soon captured when Malakat and his commandos reappear from within the pyramid. The impending launch of the nuclear torpedo aimed at the pyramid is detected causing all those within the pyramid to flee. Frantic efforts on ORCA to stop the launch succeed but Helen admits responding not to Dianne but on orders from ""a higher power."" With the launch stopped Shersheba and Malakat return to the pyramid and use the golden ankh to activate it. Malakat's first order is to begin the melting of the polar ice caps.

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.

As Praxis again prepares to launch their nuclear torpedo at the pyramid, commandos storm ORCA allowing Shersheba and Malakat to seize control of the station. Convinced Charlie holds the key to defeating the red virus, Jason and Neri obtain a blood sample from him for testing. Jason returns to ORCA to find Shersheba in command. Suspicious of him, Shersheba asks Ilona to find out what he's up to. With all ORCA personnel confined to their quarters, Cass and Brett sneak through the air ducts to the lab so that they may test Charlie's blood for antibodies to the virus. Ilona overhears their plans and tells Shersheba who burst into the lab and seizes the cure to the red virus. Ilona and Shersheba return to the pyramid to tell Malakat of the cure, crazed with power Malakat reveals his true colours forcing Shersheba to flee with the cure taking it back to the Ocean Planet. Ilona joins Neri and Mera back on the island as Neri is resolved to sacrifice herself in order to destroy the pyramid.

Asleep on her island late at night, Neri has a vision of her mother, she tells Neri that it is ""her time"" but Neri admits that she is afraid of what is to come. On the Ocean Planet, Shersheba is taken prisoner by Garron, on Malakat's order, upon arriving. She tells Garron that she has brought the cure to the virus—but will only release it if she is recognized as their leader. Neri stops at ORCA to discuss with the Bates family her plans to go to the pyramid. Neri asks Helen, who has been in contact with the underwater pyramid, to ask it to allow her to enter the pyramid undetected. Through Helen, the pyramid directs Neri to the ""cave of light"" in the outback. In the underwater pyramid, Malakat orders the pyramid to destroy ORCA, but soon after Neri and Jason arrive and start the process to destroy the pyramid. Just as they are about to finish, Shalamorn enters the central chamber and retakes control of her pyramid.