The Cetacean is called upon to recover a space probe that crashes in the sea, and Mark soon learns that the probe is covered with thousands of tiny alien beings. They intend to learn all they can about the human race by invading host bodies and controlling them. Mark must return them to space before they destroy all humanity.
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.
Water levels are rising all over the Earth. Mr. Schubert offers to stop the disaster in exchange for Mark Harris, but it's the villain himself who is melting the world's ice caps with microwaves. Schubert agrees to stop the melt down if Mark will stay on of his own free will as a test subject, though his true plan is to flood the world and repopulate it with a new species of water-breathing men.
Ships are being damaged by an unknown agent hidden at a depth impossible for the Navy to reach, where the Cetacean finds an automated robot, the Mud Worm. It is programmed to crawl along the sea bottom collecting mineral samples, but was damaged, and now resists all efforts to approach it with deadly force. Mark manages to shut down the robot and haul it inside the Cetacean, but when it reactivates, it will destroy everything in its path in an effort to escape.
Schubert's tracking of a mysterious power source causes a blackout, at the center of which, Mark discovers an ancient statue of a hawk. When he rescues Schubert's daughter Juliette from drowning, the villain learns of the hawk and steals it to discover the secret of its power.
Strapped for cash from his many expensive bids for world domination, Schubert breeds an aggressive genetically-altered jellyfish ten feet across named Poobah, and uses it for blackmail purposes. When the creature attacks a swim meet, Mark must battle the jellyfish.
While investigating an underwater volcano, Mark is stricken with sudden pain in the shoulder. This is not the first time he's felt pain for no reason, and his instincts lead him to a deserted beach and, inexplicably, to a frontier town of the old west called Land's End. There he meets his identical twin, Billy, another water-breather who washed up on a beach with no knowledge of his true identity. Billy takes Mark's place aboard the Cetacean, leaving the Man from Atlantis to face the villains of Land's End.
The Cetacean finds an underwater forcefield, which shelters a race of air-breathers with a strange clicking language. Mr. Schubert forces the Clicks to mine crystals for him, but taking the crystals will cause the field to collapse and kill them all unless Mark can intervene.
An enzyme from a rock fossil Mark finds on the sea floor with the properties of changing people's personalities gets into C.W's coffee while Mark and Elizabeth are sent to recover a lost survey probe with a deadly self destruct booby trap.
When a man who works in a carnival dies from drowning, Mark is sent to investigate. He learns that two men who work at the carnival are planning something that requires a someone who can hold their breath under water.