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...

With Grandis and her two accomplices, Sanson and Hanson, in pursuit, Jean takes Nadia back to his home in LeHarve. His grumpy aunt refuses to take Nadia in, but Jean lets Nadia stay at his own house. The following day, Jean and Nadia set off for Africa in one of his aeroplanes. They do not get far, however, when Jean's invention fails and falls into the sea....

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.

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.

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 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....

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....

Nemo and Electra appoint Jean, Nadia, and the others to new positions on the Nautilus. Jean is permitted access to Electra's library of books so that he can learn how to use the knowledge for mankind's benefit; simultaneously, he, Sanson, and Hanson are given a tour of the Nautilus. Marie and King, meanwhile, are reduced to schooling from Electra, much to their dismay. Grandis and Nadia are assigned to cook in the kitchen. An intense rivalry is ignited between Electra and Grandis as they compete over Nemo's love. Finally, Jean discovers the source of the Nautilus's power, and is quite disturbed when Nemo tells him that the vessel is a killing machine....

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.

Marie and King run off to explore the island, when they find themselves both lost and pursued by Gargoyle's soldiers. Sanson comes to their rescue.

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....

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.

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 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....

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

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'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.

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.

As a result of Nadia's foolishness, the children only have meat for food. This infuriates Nadia so much that she declares to starve... until she becomes desperate to eat a can of rotten spinach, getting sick. Jean sets off to find a cure, only to become intoxicated by hallucinogetic mushrooms(!). Overwhelmingly grateful, and stupidly unaware that Jean is not himself, she gives him his first real kiss....