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....