After a violent storm at sea, the inert body of a man is found on the beach near the Naval Undersea Center. Equipped with webbed hands and gills instead of lungs, he can breathe underwater, swim faster than a dolphin and dive to depths of at least seven miles. He is nursed back to health by Doctor Elizabeth Merrill and given the name of Mark Harris. In return, Mark agrees to help the United States Navy recover a lost missing submarine carrying top military officials.

Mark investigates the disappearance of three scuba divers, two of whom are 'replaced' by waterbourne aliens (Tiffany Bolling as Lioa / Dilly and Burr DeBenning as Xos / Chazz). The aliens assignment is to scout Earth and check its defense capabilities. They also give the impression that Mark may also be one of them, specially bred for Earth infiltration, but this is not specifically confirmed.

When a space capsule crashes in the ocean near the Cetacean, Mark and Elizabeth agree to investigate. When they arrive, Mark is rendered unconscious by a screeching sound. They discover hundreds of strange, blue, intelligent spores that have taken over Mark's body, attempting to find a way back into space. However, they do not know that Mark will die if he does not return to water within a few hours.

Elizabeth is kidnapped, one of dozens of scientists held prisoner on the island of Felicitos, controlled by special mineral springs that render their victims completely happy and compliant. Dr. Smith is using them to build a rocket to take her away from our troubled planet in search of some better world, and Mark must find a way to counter the brain-washing and free the captives.

Schubert threatens to cause worldwide flooding by using powerful microwaves to melt Earth's polar ice caps, unless the government turns Mark Harris over to him.

When a multimillion-dollar underwater probe malfunctions and begins attacking any ship that travels near it, Mark must reason with its highly advanced brain and convince it to stop.

Mark, investigating a power outage, discovers a centuries-old hawk statue from the legendary civilization of Mu. The statue, when used properly, can remove the power from a large area. Schubert discovers the power of the hawk statue and Mark must prevent him from taking it.

The oceans are leaking through a fissure in the ocean floor. A con-man named Muldoon agrees to guide Mark through the fissure to investigate. However, Mark is unaware either that giants inhabit the other side of the fissure or that Muldoon has already stolen gold from one of them.

Using his genetic scientists, Schubert produces a giant jellyfish which he intends to release unless his extortion demands are met.

Mark is somehow linked with a man named Billy, existing in a wild west town, who appears to be his twin. Investigating, Mark arrives in the town and discovers that Billy once had the same webbing as Mark, but also that he has had it removed.

Schubert attempts to make a satellite weapon to knock out Earth's communications. However, to power the weapon, he needs the energy crystals protected by a force field under the ocean. The crystals actually power the force field that protects an underwater world inhabited by a humanoid society.

An underwater landslide transports Mark to Verona, Italy...in the days of Romeo and Juliet.

C. W. develops a Jekyll-and-Hyde personality after swallowing a mysterious liquid.

Mark re-encounters Muldoon, his nemesis from "Giant," who is using a sea monster to make island natives sacrifice young girls to him.

An impish little man enters an underwater station and causes the crew to become irrational simply by touching them. After three crewmen die, the F.F.O.R. hears Duke, the last crewman, talking over the radio in a childish manner and investigates. Mark swims over and brings Duke over to the Cetacean, not knowing the imp has stowed aboard.

While investigating the mysterious loss of three ships in one part of the ocean, Mark and the crew of the Cetacean encounter a submarine operated by a modern-day pirate. The pirate has captured a mermaid that can produce a hypnotic siren song, which mesmerizes anyone who hears it, even Mark.

Mark goes undercover to investigate members of a carnival planning to break into a museum. The only way to break into the museum is through an underwater tunnel, through which only Mark can swim. When he is approached, he refuses. The owner of the carnival is then kidnapped and threatened unless Mark helps.