In ORCA's new Minifin submarine JASON and WINSTON follow NERI to the Mako Abyss and discover a huge pyramid underwater. PRAXIS, an organization dedicated to the search for extraterrestrial life, dispatches two young agents JAKE SHELBY and ELLY HAUSER to Egypt, to identify radio signals being directed to outer space. Meanwhile, already In Egypt, "Professor MALAKAT" and his young assistant SHERSHEBA search for a hidden underwater entrance to the ancient Pyramid of Mystery.
NERI finds a way into the Underwater Pyramid. She swims inside with JASON and BRETT following in the minifin. When NERI triggers a device in a Central Chamber of the Pyramid massive stone walls part to reveal a swirling vortex of water. NERI and the boys are sucked into the vortex and transported to the interior of the Pyramid of Mystery - they emerge to find they're in Egypt!
In Egypt MALAKAT and SHERSHEBA offer hospitality to NERI, JASON and BRETT. But later MALAKAT and SHERSHEBA speculate on the true identity of NERI indicating they have another agenda. SHERSHEBA tries to befriend JASON to gain information on NERI. When MALAKAT and SHERSHEBA attempt to turn the children over to JAKE and ELLY, NERI, JASON and BRETT must make a quick getaway.
NERI, JASON and BRETT return to the Pyramid of Mystery but MALAKAT sees them and instructs SHERSHEBA to summon JAKE and ELLY whilst he pursues the children into the Central Chamber. Inside the kids discover a mysterious Golden Ankh but MALAKAT demands they hand it over, NERI, JASON and BRETT once again activate the watergate to escape MALAKAT but are amazed when they arrive in a new destination - a Crystal Cavern in the Australian outback.
JASON searches for help in the outback and stumbles upon JAKAMARRA, a young local Aboriginal who tells them of the Dreamtime legend of the 'Whale Woman'. JAKE and ELLY track the kids to the outback where JAKAMARRA leads them astray whilst NERI, JASON and BRETT are rescued by the boy's father - PAUL who has been appointed Commander in Chief of Orca Pacific. Before leaving NERI gives JAKAMARRA the Golden Ankh for safe keeping.
NERI returns to the Underwater Pyramid and activates a statue which turns into a hologram of her mother SHALAMORN. Fearful NERI runs away. JAKE and ELLY return to ORCA to test JASON and BRETT with a lie detector but the boys fool them with help from WINSTON, CASS and HELEN. NERI and the boys travel to PAUL'S farm but it is revealed that JAKE, ELLY and PRAXIS operatives have followed them.
Whilst escaping from the PRAXIS agents on a waverunner BRETT and NERI hit a submerged 1og and are thrown into the river. NERI is captured and taken to a PRAXIS boat to be interrogated. Whilst on board she calls to CHARLEY who bumps the launch enabling NERI to escape. Now based in Australia, SHERSHEBA instructs MALAKAT to begin searching for the underwater pyramid. Reunited with JASON and BRETT, NERI activates the SHALAMORN hologram and learns that she is to be a leader of her people - she is a princess.
SHERSHEBA surprises JASON by visiting ORCA. Unaware of who she is, DIANNE, insists JASON take SHERSHEBA snorkeling on the coral reef. SHERSHEBA feigns drowning and NERI races to rescue her but MALAKAT suddenly appears and both he and a revived SHERSHEBA attack NERI and JASON. JASON steers the Shark Cat and throws them overboard but NERI now realizes she was set upon by her own Ocean People. SHERSHEBA and MALAKAT discover the location of the Underwater Pyramid.
MALAKAT and SHERSHEBA are advised by GARRON, the rebel leader, of progress in the rebellion on the Ocean Planet. In the Underwater Pyramid the SHALAMORN hologram informs NERI and JASON of the rebel faction. SHERSHEBA and MALAKAT arrive at the Pyramid and confront NERI. SHERSHEA stuns JASON in the arm with a laser-like weapon. Quickly activating the watergate NERI and JASON flee and arrive at the Crystal Cavern where they are surprised to see JAKAMARRA waiting to greet them.
JAKAMARRA leads NERI and JASON on a trek to retrieve the hidden Ankh. MALAKAT triangulates the location of the Crystal Cavern between the two pyramids and advises PRAXIS of NERI's location in the outback. He and SHERSHEBA arrive in the outback to assist JAKE and ELLY and they close in on NERI at a rocky escarpment. ELLY falls and is saved by NERI. JAKAMARRA grabs the Golden Ankh from SHERSHEBA and throws it to JASON who is flown to freedom by PAUL but must watch helplessly as PRAXIS leads NERI away as their prisoner.
NERI is held prisoner at PRAXIS headquarters where she is questioned by an uncaring scientist, DR LAVICHE. BRETT and CASS with WINSTON's help try vainly to discover NERI's whereabouts using HELEN. SHERSHEBA sneaks on board ORCA at night and with LOUIS' help accesses the position of the Golden Ankh previously hidden by JASON. As NERI's health deteriorates at PRAXIS, SHERSHEBA returns to MALAKAT holding the Ankh high.
Still a prisoner of PRAXISD NERI's condition worsens. With the assistance of HELEN, DIANNE, WINSTON and CASS are able to flood the PRAXIS bunker and JASON and BRETT scuba in. ELLY surrenders NERI to the boys. MALAKAT discovers the secret of how to prime the Ankh and tells SHERSHEBA they must return to the Crystal Cavern in the Outback. JASON cradles a weak and dying NERI as they head homeward.
JASON returns NERI's inert figure to the Underwater Pyramid and sadly recalls the good times they shared. But they are interrupted by SHERSHEB and MALAKAT's return. SHERSHEBA inserts the flow charged Ankh and the Pyramid powers up. But NERI is revived and the Pyramid senses countervailing commands shaking with the threat of destruction. NERI and the boys flee as the Pyramid descends into the ocean floor. When the figures of MALAKAT and SHERSHEBA are revealed back in Egypt we realize they are still at large.
WINSTON assists JASON in installing a satellite dish high on a cliff on NERI's island capable of intercepting signals from space. But when he is bitten by a snake he falls and NERI must save him by using a rare flower from the island, meanwhile a deadly red virus is Infecting the Seas of the Ocean Planet. MERA (NERI's sister) holds the position of Regent on the Ocean Planet and plans a peaceful migration to Earth should it become necessary. But MALAKAT and SHERSHEBA have returned and are inciting the populace to rebel, promising an escape from the virus in the form of a massive Invasion of Earth.
Whilst staying at PAUL'S farm NERI encounters EMMA, a strange and frightened young girl. When Shadow, a mare on the farm foals, NERI must rely on EMMA for assistance. EMMA responds to NERI's support and understanding and overcomes her fear. MALAKAT and SHERSHEBA plan a complete overthrow of MERA's government. HELEN is given new advanced technology resulting in her assuming a personality a somewhat humorous one.
NERI is attacked by underwater COMMANDOES but is saved by CHARLEY and JASON and BRETT in the minifin. She and the boys realize they are no longer safe from the reaches of Ocean Planet people who have arrived on Earth. As the Ocean Planet Pyramid is stormed by COMMANDOES, MERA flees, taking with her the only remaining Ankh. NERI senses that the Underwater Pyramid near her island has risen again.
NERI confirms the Underwater Pyramid has returned to the Mako Abyss. MERA, landing in the ocean near NERI's island, is attacked by COMMANDOES but is saved by JASON, BRETT and NERI. MERA's return by spaceship is monitored by JAKE and RICHTER at PRAXIS. NERI sees SHERSHEBA and MALAKAT arrive at the Underwater Pyramid and tells the boys of their return as leaders of the COMMAN DOES. NERI hides the Ankh at PAUL'S farm.
RICHTER reopens Operation Sphinx at PRAXIS and reassigns JAKE and ELLY to the investigation. LOUIS overhears WINSTON, CASS and HELEN discussing Pyramids and informs ELLY and JAKE. The PRAXIS agents access HELEN who reveals the existence of the Underwater Pyramid. BRETT and CASS race to NERI's island to warn NERI and MERA but they are followed by SHERSHEBA and her COMMANDOES.
JASON is ordered to pilot JAKE in the Minifin and take him to the Underwater Pyramid. En route the submarine is fired on by underwater COMMANDOES. RICHTER seeks permission of MADAME PRESIDENT of the Global Union for an attack on the Underwater Pyramid. When SHERSHEBA and her COMMANDOES search NERI's island NERI and MERA are almost discovered but escape when SHERSHEBA is frightened off by birds.
RICHTER takes over command of ORCA from DIANNE bringing nuclear weapons on board. NERI pleads for PRAXIS to be stopped. NERI and JASON meet with MALAKAT and are shocked at his admission he "killed" NERI's mother. COMMANDOES seize MERA and take her prisoner. NERI realizes she must choose between possession of the Ankh and the safety of her sister, knowing that to surrender the Ankh is to condemn Earth.
While MERA is held in a cell in the Underwater Pyramid, MALAKAT boasts to her it was he who let loose the virus on the Ocean Planet. His admission causes an angry SHERSHEBA to release a sample of the red virus in the nearby ocean which poisons CHARLEY. NERI is horrified but must watch powerlessly from the beach for fear of being contaminated by the virus. NERI retrieves the Ankh from the river at PAUL's farm and hides it on her Island.
Aware of the red virus in the earth's oceans MADAME PRESIDENT lifts the hold on hostilities against the aliens. SHERSHEBA informs NERI that she must surrender the Ankh as a cure for the virus can only be obtained with the Pyramid's help. JASON and BRETT arrive at the Underwater Pyramid and advise SHERSHEBA and MALAKAT that if they will vacate their troops from the Pyramid NERI will deliver up the Ankh.
Evacuation begins on Orca as the PRAXIS attack on the Pyramid draws near. Seeing COMMANDOES withdrawing, JASON and NERI enter the Pyramid but realize they have been fooled by hologrammatic images when they are attacked in the Pyramid by MALAKAT, SHERSHEBA and the COMMANDOES. Losing the Ankh to SHERSHEBA, JASON and NERI flee with MERA. PRAXIS fire their nuclear torpedo at the Pyramid but DIANNE, with HELEN's help, deactivates it. NERI is thrilled when CHARLEY suddenly re-appears.
NERI is pleased that CHARLEY has recovered, but fears for the imminent war. SHERSHEBA, now in possession of the Ankh, starts the Pyramid and MALAKAT sets in motion the destruction of the polar ice caps to flood the world. SHERSHEBA disperses MALAKAT's "cure" for the virus in the nearby oceans but is shocked when it falls. NERI arrives in the Underwater Pyramid Pool Chamber, but is fired upon by MALAKAT and must flee.
PRAXIS prepare to fire the torpedoes when COMMANDOES suddenly board Orca, taking both PRAXIS and Orca personnel hostage. NERI believes CHARLEY's immunity to the virus holds the secret of an anti-viral and JASON takes a sample of his blood with which they are able to effect a cure which is seized by SHERSHEBA. SHERSHEBA returns to MALAKAT with the cure but he ignores her and takes control of the Pyramid. SHERSHEBA flees in a spacecraft.
As MALAKAT continues to wreak global destruction NERI tells all she must destroy the Pyramid from within but JASON won't let her do it alone. SHERSHEBA returns to the Ocean Planet and releases a strange figure from a sleep capsule. Just as NERI is about to activate a self-destruct button in the Pyramid a voice commands her to stop - it is her mother, SHALAMORN liberated by SHERSHEBA. MALAKAT is exiled, and the oceans of the two worlds cured using the immunity found in CHARLEY. NERI is crowned Princess of her people.