Jean, Nadia, Marie, and King are taken aboard the Nautilus with their new enemies-turned allies, Grandis, Sanson, and Hanson. Technophiles Jean and Hanson are thrilled to be aboard the Nautilus. Grandis becomes dangerously smitten with Captain Nemo, much to Sanson's consternation. Nadia, meanwhile, is very suspicious about the submarine and its crew, particularly Nemo, who reacts with surprise upon seeing her for the first time....

Marie and Nadia become sick from a dangerously fatal tropical fever. To save them from death, Nemo charts course for an underground reef, where he takes Jean, Sanson, and Hanson on a quest to find the cure. Coming back, however, they have to deal with a territorial, eel-like Dinicthys....

En route to Captain Nemo's home base of Antarctica, the Nautilus finds itself attacked by a territorial Nautilus shellfish.

Now that they are settled into their new island home (which they dub "Lincoln Island", Jean uses his knowledge and technology to bring a little civilization. Nadia, on the other hand, wants to live with nature... only to discover that doing so is a lot harder than she ever dreamed of.

A violent row between Sanson and Hanson turns into a race between two mechanical lions resembling King(!).

Gargoyle takes Nadia before the puppet leader of Neo-Atlantis, Emperor Neo, who reveals that he has a strong connection with both Nadia and Nemo. Eight time zones away, Nemo and the others plan to fight Gargoyle in a final duel. Throughout, both Jean and Nadia learn about the origins of the Atlanteans.