Mark Harris is the lone survivor of the legendary sunken continent of Atlantis. Having adapted to life underwater, Mark possesses webbed hands, light-sensitive eyes, and the ability to swim at low depths in the sea for long periods. He draws strength from water and can overpower most ordinary men. Mark assists an institute for undersea research operated by his human friends, Dr. Elizabeth Merrill and C.W. Crawford, and joins Dr. Merrill in several exploratory missions aboard a high-tech submarine. They encounter several bizarre phenomena, including portals leading to other dimensions, a substance capable of altering personalities, an impish creature whose touch causes a mental return to childhood, and the scheme of a portly millionaire, Mr. Schubert, to melt the polar icecaps.
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 take over Mark's body attempting to find a way back into space. However they don't know Mark will die if he does not return to water within a few hours.
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.
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 of which only Mark can swim. When he is approached, he refuses. The owner of the carnival is then kidnapped and threatened unless Mark helps.