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 civilization.

A daring battle between the Company ships Dreadnought and Nautilus leaves both stranded in the Arctic ice, leading to an uneasy truce. Nemo reunites with a friend from his past and is shaken by more revelations about his father.

When it is revealed that Nemo has been too daring and put the crew in danger, they lock him in his cabin and Boniface takes command instead. At the magnetic north pole, the problems pile up. Nemo must unite his divided crew.

When Nautilus finally arrives at the treasure, they realize that it has not been forgotten at all, on the contrary, it is guarded by wild warriors. Nemo feels that he has led his crew to the end of the world - for nothing.

With the new goal - to overthrow the Company - the crew spreads rumors that the company is about to go under. The share price drops sharply and the Company calls all owners to a meeting.