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....

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.

King gets jealous of Jean and Nadia becoming more intimate and runs away. Jean sets off to find him... but not before Nadia goes ballastic upon realizing that he does not remember the kiss she gave him (he had been stoned from the hallucinogetic mushrooms).

Trapped inside a mysterious chamber, Nadia learns from a disembodied voice that their island home is actually a space satellite, Red Noah--and that she is the heir to the throne of Atlantis as well as not human! Tremors engulf the island as Grandis and the others prepare to set off, but Jean returns to save Nadia.

Gargoyle's battleships appear over Tartessos. To save Jean and the others, Nadia surrenders herself... but not before Jean swears to save her. Forced to flee from Gargoyle's battleships, our pals run into Captain Nemo and his crew, who have survived... and now operate a superpowerful battleship called the New Nautilus.

Gargoyle takes Nadia before the puppet leader of Neo-Atlantis, Emperor Neo, who reveals that he has a strong connection with both Nadia and Nemo. Eight time zones away, Nemo and the others plan to fight Gargoyle in a final duel. Throughout, both Jean and Nadia learn about the origins of the Atlanteans.