The Seaview is sent to stop an active volcano from erupting and causing a catastrophe. Accompanying them is Dr. Turner who's suppose to help them. But it turns out he has a different plan and that is to make the volcano erupt so he can acquire something that will make him immortal.
A puppeteer comes on board to entertain the crew. But it is later revealed that his puppets are alive and they plan to take over the sub. That's when they replace the crew members with duplicates. Only Nelson and Crane are left to try and stop them.
When four capital ships vanish, Admiral Nelson and Commander Van Wyck are sent to investigate. They find an island where Nelson removes a dagger from a skeleton which happens to be the captain of the Amsterdammer, the Flying Dutchman, and is then cursed. Van Wyck is in reality the first mate who killed the Captain. His plan is to kill Nelson with the dagger so that he can be free and Nelson will take his place.
Aliens from the planet Centaur bring a capsule containing Commander Morton to Venus. They want to keep earth from invading their planet and kidnap Captain Crane in an attempt to bring the Seaview to their planet.
When a top secret Neutron Bomb begins leaking radiation, Seaview crew men begin disappearing and those who haven't begin seeing things. The Seaview is racing the clock to fire or disarm the missile before it explodes.
Admiral Nelson and Captain Crane are shocked to see a scientist shot to death during a live televised news conference viewed from the Nelson Institute. Especially shocking is that the killer appears to be Admiral Nelson. Both Nelson and Crane are eventually able to overcome efforts to stop them from boarding the Seaview. The submarine races to stop an earth-threatening project set in motion by the radical scientist, who may not really be dead after all. In the meantime, a very dangerous master of disguise causes mayhem and confusion as he tries to stop the Seaview ...
A scientist friend of Nelson has developed a device to control a rare white ape. The scientist's jealous assistant causes the beast to kill the scientist and the ape runs wild after being brought aboard Seaview causing destruction.
A man named Alpha from 2823 sends 2 Collectors to bring Nelson to his time to add the Admiral to his collection of military officers. Chief Sharkey goes to the future to help while the Collectors wreak havoc on the Seaview.
The original Blackbeard takes over some of the Seaview crew including Kowalski to blow up a ship carrying King Solomon's Golden Throne. The remaining crew try to find a way to disable Blackbeard's power source.
The Seaview rescues two scientist from a climate control project at the South Pole but something else is on the ship on a killing spree. The Seaview has to shut down the project before the world's climates change.
The Seaview and an intelligence expert who is more than he seems, try to find a group that is blackmailing the world's nations for gold bullion. The submarine encounters gigantic creatures during their search.
The Seaview investigates why part of the Italian coast has become overrun with jungle growth. Meanwhile new crewman Keeler has 3 miniature silver faced men grow to human size and causes jungle growth to spawn all through the submarine.
Investigating why the world's oceans are rising, the Seaview finds a race of Frost Men at the Polar Cap who are increasing the temperature and they want the submarines' reactor to help them leave the earth.