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.
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.
Neri, Jason, and Brett wander into an archaeological dig and meet Professor Malakat and Shersheba. Finding the minifin abandoned, Winston tracks the signal from Brett's vid-phone to the Middle East, but discounts his findings as a phantom signal.
Leaving the cave to find help, Jason is found by Jakamarra 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.
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.
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.
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.
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.
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.
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.
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.
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.
Mera's spacecraft splashes down in the ocean and as she swims to the surface she is surrounded by Commandos. Seeing the craft come down from the island, Brett, Neri and Jason rush out to rescue Mera.
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.
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.
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.
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.
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 its power to send a telepathic message to Neri.
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.
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.
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.