"Nadia - The Secret of Blue Water: The Motion Picture" is a condensed retelling of the 1990 anime series "Nadia: The Secret of Blue Water," reimagined as a feature-length film. The narrative centers on Nadia, a young circus performer of mysterious origins, and Jean, an inventive and optimistic boy. Their paths cross when Nadia is pursued by a group of villains seeking a powerful artifact known as the Blue Water, a gemstone tied to the lost civilization of Atlantis. Together, they embark on a journey to uncover the truth behind the Blue Water while evading the relentless forces of the Neo-Atlantean organization, led by the enigmatic Gargoyle.

The story begins in late 19th-century Paris, where Nadia and Jean meet during the 1889 World's Fair. After a series of events, they escape aboard the advanced submarine Nautilus, commanded by the noble Captain Nemo. The Nautilus becomes a sanctuary and a base of operations as the group travels across the globe, facing threats from Gargoyle's forces, who seek to harness the Blue Water's power to dominate the world. Along the way, Nadia grapples with her identity and her connection to Atlantis, while Jean provides unwavering support and ingenuity.

The film condenses the series' key arcs, focusing on the central conflict between the protagonists and the Neo-Atlanteans. It highlights themes of friendship, resilience, and the consequences of unchecked ambition. The narrative culminates in a climactic confrontation where Nadia and Jean must prevent Gargoyle from using the Blue Water to awaken ancient Atlantean technology capable of catastrophic destruction. The resolution emphasizes the importance of unity and the rejection of destructive power, as Nadia and Jean's bond becomes a symbol of hope and humanity's potential for good.