Mr.Pem returns to help Admiral Nelson prevent the Seaview from exploding. Pem transports the submarine to 1780 where they encounter General Benedict Arnold and Major Andre.

Corpsman Mallory's 4th Dimension Machine causes Captain Crane to kill Admiral Nelson, but did he really? A hunted Crane tries to prevent the event from happening.

Nelson is told the Seaview could be destroyed while carrying a top secret defense weapon but he has to determine if Captain Crane is an impostor.

While investigating the destruction of the fleet by a flying saucer, Nelson and Kowalski are captured by aliens. One of the aliens offers help to the Seaview crew to stop his people.

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.

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.

When Crane tests a new atmosphere to deal with extreme pressures, he turns into a Man Beast. Nelson races the clock to find a cure for Crane.

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 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.

Crane receives a Mayday from the Seaview and finds no one on board except a UFO expert. The crew re-appears and announces they are going to fire nuclear missiles at Washington D.C.

A lobster man arrives in a space craft claiming to be a friend but in reality he wants one of the nuclear rods to cause an explosion thus paving the way for an invasion.

The Seaview is sent to stop a warhead on the ocean floor from detonating. But a leprechaun wants it to go off. So he tries to stop them. But his good twin brother tries to help them stop him.

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.

While trying to find the cause of some underwater pressure blasts, the Seaview encounters a race of Amphibians and Kowalski is transformed into one of them.

While trying to stop a leaking nuclear missile, Nelson undergoes a personality change which endangers not only the Seaview, but the 11th Fleet.

The crew of the Seaview encounter Mr. Pem who can control time. Pem sends Nelson back in time to force the Admiral to let Pem use the reactor to power his device.

An alien plant takes over Admiral Nelson in a plan to turn the Seaview into a giant greenhouse where it can take over the world.

Captain Crane is attacked in the Flying Sub while looking for a mysterious sub pen. The Seaview's rescue attempts are hampered by a spy pretending to be one of the crew men.

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.

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.

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. 

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.

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 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.

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.

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.