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....

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.

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....

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.

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....

The Nautilus is ensnared by Gargoyle's super powerful SeaNet magnet. In the fight that follows, Grandis, Sanson and Hanson escape on the Gratan (to help free Nemo and the others from Gargoyle's battleship). The battle culminates with the badly damaged Nautilus plummeting into the sea....

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.

Four months afterward, the Gratan is nearly repaired, and soon our pals will set off for Africa. But first Jean and Nadia go off on a hike which leads them to a mysterious underground cavern that turns out to be more than they suspected. The exploration culminates when Nadia falls into a trance and vanishes behind a wall, leaving her clothes in Jean's arms! During all this, Ayerton tries to make his move on Grandis.

Finally, our pals arrive at Nadia's real homeland--Tartessos. As they tour through its long forgotten ruins, our heroine finally reveals her darkest secrets... including who she is. How will all this affect her relationships with everyone, especially Jean?

The New Nautilus and Gargoyle, now aboard Red Noah, face off in a spectacular duel of pyrotechnics, lasers, and, ultimately, wills. Midway through, both crafts head into outer space. After finally breaking in, Nemo, Jean, and Electra confront Gargoyle, who now has Nadia under his control.