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....

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 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....

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.

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.