Jean, Nadia, and King are shot down over a strange island where they find themselves outrunning a squadron of sinister masked soldiers. In their struggle to survive, they find an orphan girl, Marie, who lost her parents to the soldiers.

Marie and King are captured by the soldiers, so Jean and Nadia set off to a forbidding looking area to save them. Their rescue mission leads the pair to the base of the soldiers, who call themselves Neo-Atlantis, and their evil commander, Gargoyle, wants Nadia and her Blue Water at all costs.

In a surprising turn of events, Grandis and her boys join forces with Jean to save Nadia, Marie, and King from Gargoyle. Their escape attempt nearly backfires, until the Nautilus shows up to save them....

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....

Jean is tired of being treated like a child by the Nautilus crew. Hoping to cheer him up, Nadia suggests Jean to build another aircraft. Inspired, he sets off to do just that. At first he is determined to construct the new helicopter by himself, but then realizes he still needs the support of some grown-ups. With Hanson's help, Jean completes the craft and takes Nadia on a very delightful test flight. While airborne, Jean promises that he will one day take Nadia to Africa....

Nemo takes Jean and Nadia on a tour of his secret base, where he introduces the children to his closest friend, a talking whale named Irion, who hints at Nadia's responsibility to hold the Blue Water.

Jean, Nadia, Marie, and King are shipwrecked on a deserted island. They decide to make it their home for a while.

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.

After surviving a typhoon, Jean, Nadia, Marie, and King discover another island drifting mysteriously toward them. Exploring it, the children find Ayerton, a flaky scientist who they met on the battleship in Episode 3.

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

Having escaped their former island home, our pals crash-land into an African tribal village, where they are instantly captured... until one of its citizens recognizes Nadia.

Jean writes a song for Nadia. Actually, our pals burst out into song while various clips from the show play out.

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.