Hiroshi Umino lives in a future dominated by vast ocean cities, whose expansion severely damages marine environments. He survives a catastrophe when an assailant destroys an unfinished city structure he was visiting with his friend Yamamori, plunging them into the ocean. Rescued by Nami Shimaoka, they awaken in a hospital with no memory of the incident.

Upon returning home, Hiroshi finds a note explaining Nami's sudden departure before police arrest him for interrogation. Authorities question him about an unknown battleship, which he denies knowledge of. Government surveillance tracks Hiroshi as he travels by train, indicating ongoing interest.

Seeking answers, Hiroshi travels to a tropical island and meets the elderly couple who raised Nami. They reveal her origin: discovered as an infant in a storm-wrecked ship, placed there by humanoid sea creatures. Hiroshi later finds Nami on the beach, only for military forces to arrive and attempt her capture. Green aliens emerge from the sea to protect her, revealing her connection and leaving Hiroshi bewildered.

Hiroshi is later captured by these green sea people and taken to an underwater Atlantean city. He observes marine snow—decaying organic matter from the surface—covering the seabed and debris, a severe problem for the civilization. He meets Izanami, a blue alien, who informs him Nami is safe and now commands ancient alien forces against humanity. Hiroshi witnesses Nami leading battles against human military forces.

During Doctor Zelvado's critical attack on the undersea civilization, Hiroshi attempts to intervene but is restrained and sedated. He returns home only to be abducted again by the sea people and returned underwater. As Zelvado launches destructive missiles, parts of the city detach and ascend. Hiroshi escapes in a pod, witnessing the city's destruction and Zelvado's death at the hands of the alien Zeina, who also perishes. Surviving fragments of the undersea civilization rise into space, and Hiroshi surfaces to bid farewell to the departing aliens.