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 Company troopers find the Nautilus, Nemo must motivate the team to work with each other so they can get to the open seas before they're exhausted.

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

The starving crew venture onto a seemingly deserted island in search of food, but Blaster is kidnapped by the survivors of a Company shipwreck. Nemo and Humility attempt a daring rescue mission but end up disturbing a giant electric eel.

The Nautilus is helplessly dragged into the volcanic Ring of Fire by a giant electric eel. The crew begin to drift off into hallucinogenic stupors caused by mysterious spores. Humility must summon courage to save the Nautilus and its crew.

The Ring of Fire reveals a clue to the fabled underwater city of Atlantis; a small party ventures out to discover what seems to be an ancient outpost of the mythical lost civilization.