"Kaitei Daisensō - Ai no 20,000 Miles" is a science fiction anime set in a future where humanity has colonized the ocean floor. The story centers on the conflict between the underwater nation of Atlantis and the surface world, which is on the brink of environmental collapse. The surface world, desperate for resources, seeks to exploit the ocean's depths, leading to escalating tensions with Atlantis. The narrative explores themes of environmental degradation, technological advancement, and the ethical dilemmas of survival.

The protagonist, a young surface-dweller named Kino, becomes entangled in the conflict after discovering a mysterious submarine, the Nautilus, which is piloted by the enigmatic Captain Nemo. Nemo, a former Atlantean scientist, has turned against his homeland due to its oppressive regime and its exploitation of the ocean's resources. Together, Kino and Nemo embark on a journey across the ocean, encountering various factions, including rogue pirates, Atlantean military forces, and surface-world envoys. Their mission is to prevent an all-out war while uncovering the truth about Atlantis's hidden agenda.

Key characters include Kino, who serves as the audience's entry point into the story, representing the surface world's naivety and eventual growth in understanding the ocean's plight. Captain Nemo is a morally complex figure, driven by a desire for justice but haunted by his past. Princess Lana, an Atlantean royal, provides insight into the underwater nation's perspective, torn between loyalty to her people and the realization of their destructive policies. The antagonist, Admiral Gargoyle, represents the militaristic and authoritarian side of Atlantis, determined to maintain control over the ocean at any cost.

The plot unfolds through a series of episodic adventures as the Nautilus travels through various underwater regions, each highlighting different aspects of the ocean's ecosystem and the consequences of human interference. The story builds toward a climactic confrontation between Atlantis and the surface world, with Kino and Nemo striving to broker peace. The resolution emphasizes the importance of coexistence and the need to protect the planet's fragile ecosystems. The series blends action, political intrigue, and environmental commentary, creating a thought-provoking narrative that resonates with contemporary concerns about sustainability and humanity's relationship with nature.