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 an American battleship in pursuit of sea monsters, who have apparently been responsible for sinking ships. That night, the battleship is attacked, and Jean, Nadia, and King are thrown overboard....

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....

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.

The victims of Gargoyle's latest attack are taken to the long-forgotten underworld of Atlantis to be buried. While there, Jean discovers that his father's ship was sunk by the Garfish. Nadia also learns that she must keep the Blue Water at all costs, no matter what pain or damage it may cause.

Jean's latest invention goes disastrously wrong and accidentally alerts the Garfish to attention. Nadia's detestation of Nemo and jealousy of Jean's friendship with Electra dangerously intensifies--until she finally learns that the Nautilus is merely fighting to destroy Gargoyle and that Electra poses no threat to Nadia's relationship with Jean. During all this, Gargoyle is informed of the Nautilus's prescence and devises to set yet another deadly trap....

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.