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.
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 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.
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.
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.