In a penal colony, Nemo plans an escape on the submarine he designed. When ordered to move early, he leaves with few prisoners as crew, on their way, they collide with a ship.

When some of the crew try to leave the Nautilus and swim to shore, they are discovered by the company's emissaries and forced back. Now the Nautilus must go out to sea to avoid capture.

Captain Nemo and his crew are forced to make a stop on the island of Karajan for water and supplies. Nemo discovers a shocking truth and Humility and the crew find out who Nemo really is.

Captain Nemo and his starving crew go ashore on a seemingly deserted island in search of food. When Blaster goes missing, Nemo and Humility embark on a daring rescue mission but soon encounter a giant electric eel.

When an eerie red glow appears, the giant eel suddenly releases the Nautilus, it turns out to be a chain of underwater volcanoes. Without steering power, the Nautilus continues to sink towards the dangerous lava.

The underwater volcanoes turn out to reveal a clue to the legendary underwater city of Atlantis. A small group goes exploring and finds what appears to be an ancient outpost of the lost civilisation.