The series centers around Nadia, a young girl of unknown origins, and Jean, a young French inventor. Early in the story, the two protagonists are chased by Grandis Granva, Sanson, and Hanson, a group of jewel thieves who pursue Nadia for the blue jeweled pendant she possesses. After being rescued by Captain Nemo and his submarine, the Super Sea Cruiser Nautilus, the jewel thieves and the young protagonists join forces and participate in the struggle against the Neo-Atlantean forces, who seek to dominate the world.

In the process, Nadia and Jean save the world from violent domination by the Neo-Atlantean forces led by Gargoyle, explore worldly mysteries and the powers of the blue pendant, uncover Nadia's hidden family ties, and ultimately discover the secret origins of Nadia.