Welcome to Orca. Dr. Diane Bates accepts a job on a new underwater science labratory called Orca. She is going to study whales as part of her research. Recently divorced she and her two boys Jason and Brett set out to start a new life, what they don't know is that their life is about to change. After boarding Orca they soon discover irregular patterns in the Whale song. As the story unfolds it appears that the whale is communicating with another being -- a girl in fact! This girl not only can talk to whales but breathe underwater as well. The story continues as Neri discovers a sister and her origins -- a far off planet! She is from an advanced civilization "The Planet Of the Oceans" and that she has been sent on a mission to try to save her home as well as earth.
Jason and Brett eagerly await the return of Neri and Charlie–as does UBRI's Dr. Hellegren who wants to study just one of the returning humpback whales, Charlie. Jason and Brett go to Neri's island to prepare for her return and find a silver pendant inside an unusual flower. When Dr. Hellegren's helicopter crashes into the ocean, Charlie calls to Neri who goes to help him but ends up being taken captive. Neri manages to escape, with a little help from Charlie, but she does so only moments before Hellegren is rescued by Captain Sam Phillips, one of the new arrivals on ORCA. Dianne's research contract is extended another six months by ORCA's new commander, her son however soon proves to be a challenge for the others.
Neri makes her first visit to ORCA since her return, and tells her friends that she wants to discover who "her people" were. Jason, Brett and Neri go to her island to look for clues to her identity. Brett gives Neri the pendant he found in the flower and Neri tells him it was her fathers and is a map of the island. Following clues found on the island, a large object is discovered under the island–from what they have learned so far, Jason suspects it to be a spacecraft. Mick locks Rocky in the recompression chamber.
After locating an underwater entrance to the spaceship, Neri and Jason enter the craft where they find some of her father's belongings. Taking the objects back to ORCA, one displays a holographic message from Neri's father that reveals how her people came to Earth – and that she has a sister somewhere on Earth. Kimberly challenges Mick to a race, but when she beats him, he refuses to pay up. Commander Byrne shows Dianne the top secret plans for the construction of ORCA City; she wants Dianne to do the oceanographic surveys.
The search for Neri's sister Mera is underway. Mick asks Froggy to use his computer to change his grades but Froggy won't do it. Commander Byrne isn't pleased with her son's grades but Mick once again charms his way out of trouble. Rocky fixes up an old boat so Jason can leave ORCA as he pleases. Helping Winston with a survey, Joanne falls overboard. She is rescued by Neri, but to keep her a secret, Joanne is lead to believe that it was Winston who saved her. Dianne and Winston discover that Neri's presence enhances their scans of the seafloor. Dr. Hellegren discovers Neri is the creature that accompanies Charlie. An old newspaper article leads Jason and the others to the man who found Mera.
The kids locate Mera. Her adopted name is Jane Seaforth, and after being bounced from foster family to foster family, she is now living at an institute for gifted children. Dr. Hellegren has also found Mera and wants to take her to UBRI where he can study her. Dianne and Winston ask Neri to help with their survey while the others go ashore to find Mera. At the institute, Jason and Vanessa talk to Mera and she promises to go with them if they prove she can trust them.
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 rescuing 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.
Mera is having a difficult time adjusting to living on the island and Neri leaves her alone while she goes to help with the survey again. Mick gets Froggy to use HELEN to spy on Vanessa's counseling session. The kids on ORCA throw a surprise birthday party for Vanessa but Mick's practical joke results in a dangerous chemical spill and fire. Jason and Brett lead a successful rescue through the air ducts. In the aftermath, it is revealed that Mick has a reading disability. Commander Byrne assigns Mick to Dianne's survey crew. Jason is not happy about his mother's developing relationship with Sam. Dr. Hellegren connects Mera's escape to ORCA.
Suspecting a connection between Neri and Jane Seaforth, Dr. Hellegren sends UBRI agents Forsyth and Liselle to ORCA to learn as much as they can about the two girls. Mick is assigned to Dianne's mission to map the ocean floor and an effort must be made to keep him from finding out about Neri who is still assisting Dianne. Mera dislikes living on Neri's island, but after Neri shows her around she begins to like the place. Sam volunteers to process the survey results for Dianne and in doing so locates a large and valuable titanium deposit.
Neri returns to help Dianne with her oceanographic survey leaving Mera alone on the island to face a UBRI search party that has come to the island looking for them. Mick catches a glimpse of Neri and Mera on a monitor but everyone tries to make him think that he is just seeing things. He persists in his claim of having seen two girls but only Liselle, who is working as an UBRI spy, takes any interest. His story eventually gets back to UBRI where Dr. Hellegren plans to step up his search for the girls. When Dianne learns that Sam has been keeping his discovery of the titanium deposit a secret with hopes of cashing in on the discovery, Dianne asks him not to pursue it.
Prior to leaving on the final survey mission, Dianne learns Commander Byrne has assigned Froggy, Zoe, Joanne, Rocky and Kimberly to her crew. Forsyth hides a transmitter on the boat to allow UBRI to follow it. UBRI divers are dispatched to apprehend Neri and Mera and in their struggle with the UBRI divers, Neri and Mera are caught by the boat's cameras for all to see, revealing their existence to everybody on board. Responding to Mera's call for help, Charley intervenes allowing the girls to escape, it's the first time Mera has been able to talk to Charlie. After being told about Neri and her sister, the kids all agree to keep the secret, except for Mick who just says that he'll "think about it."
Jason takes Neri and Mera swimming off the ORCA platform. Mick finds out and heads out on a jetski, he falls off and must be rescued by the girls.
Neri helps Mick with his reading, he in turn joins the others in keeping Neri and Mera a secret. Forsythe tries to get access to Dianne's research and cripples HELEN in the process, in the confusion Lyselle sees Mera in the corridor and reports back to Dr. Hellegren that Neri and Mera are on ORCA.
Winston, receiving strange signals from Neri's island, goes to investigate and meets two strangers, but back on ORCA he says his trip was uneventful.
Neri leaves ORCA intending to save Mera and Charlie by giving herself up to UBRI. Brett chases after her, gets into an accident with a UBRI boat and is saved by Neri. Sam destroys his remaining records of the titanium deposit. Winston continues to secretly meet with the two strangers. Unable to bring the girls back to the island, Winston takes the two strangers to ORCA where they tell Neri and Mera that they have come to take them back to the Ocean Planet, their home. Vanessa helps Mick with his reading and defends him when Commander Byrne accuses him of slacking off.
Neri and Mera make the decision to return to the Ocean Planet and convince Diane that her research must continue. Froggy fixes HELEN, with a little help from Damien.
Commander Byrne has Forsythe arrested when HELEN identifies him as the saboteur.
The kids take care of Liselle, keeping her from contacting UBRI. Neri and Mera are taken back to the island, with Winston, Mick and Zoey acting as decoys to keep UBRI away.
Final goodbyes are said as the girls board the spacecraft for home but after the ship leaves, one person has stayed behind. Neri says she must stay to "finish father's work."