Jean, a 14-year-old orphan, sailing into Paris to help his uncle design an airplane for the Paris Exposition's flight competition meets a pretty young girl named Nadia and her pet lion cub, King. He ends up rescuing her from a woman named Grandis who is trying to get Nadia's jewel, the Blue Water. Nadia leaves the only home she ever knew - a circus - as Jean has offered to help her search for her place of origin, starting with the random choice of Africa...

Jean, Nadia, and King are rescued by another vessel--an impressive and mysterious submarine known as the Nautilus (and yes, the captain's name is Nemo). Here, they learn from Nemo's pretty first officer, a young woman named Electra, that the vessel is in pursuit of a sinister enemy. After an unsuccessful attack against the deadly submarine Garfish, the Nautilus repairs Jean's sea plane, and the children take off for another adventure.

Imprisoned by the wicked Gargoyle, Nadia is forced to admit that she gave her Blue Water to Jean before turning herself in (to save Marie and King from a horrible fate). As the search for Jean is on, the boy desperately tries to find her. Simultaneously, Grandis, Sanson, and Hanson, who have also been imprisoned by the soldiers, break out of their prison cell and attempt to escape. While Gargoyle tours Nadia around his base, he showcases Neo-Atlantis's secret weapon, a tower known as Babel with the power to obliterate an entire island!

In pursuit of Gargoyle, the Nautilus becomes trapped in a dangerous underwater mine field. Sanson and Hanson jump aboard the Gratan to clear the mines before they detonate. Jean sneaks on to help the two men....

When the Nautilus docks on an island to reestablish supplies, Nadia bonds with Grandis when the latter tells her how the first man she fell in love with turned out to be a treacherous cad.

Captain Nemo's vessel falls into yet another deadly trap set by Gargoyle--one which involves the Garfish and a surprise attack from American battleships. The subsequent damage costs the lives of several sailors--including a friendly young engineer named Ensign Fait. Jean, who had become friends with Fait, is horrified and devastated to witness someone being killed by the technology he had so strongly idealized with.

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....

After relocating Jean, Nadia, Marie, and King to his personal quarters (which he will later jettison from the doomed Nautilus), Nemo finds Electra holding a gun on him. In an extended flashback sequence, Electra reveals her tormented past, her complicated feelings for the captain... and a horrifying connection between Nadia and Nemo.

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.

All the pieces fall into place for the final stage of Jean and Nadia's journey around the world, Nemo and Gargoyle's long-standing feud, and the secret behind Nadia's Blue Water pendant.

I won't tell you how it ends....