Yousuke Obata, a twelve-year-old boy, lives on Fiji's Pagopago Island with his father, Tetsuo Obata, an oceanographic biology specialist. His routine involves school and typical island pursuits like operating a Jet Ski. After a major storm, Yousuke finds a peculiar infant creature in the lagoon and takes it to his father's lab for care.

Naming the creature Coo, Yousuke becomes responsible for its well-being. Coo matures swiftly, identified as a marine reptile akin to a plesiosaur, a species extinct for roughly 65 million years. A powerful bond forms between Yousuke and Coo, driving Yousuke's active involvement in its care and protection, especially as Coo draws dangerous attention.

French secret service agents, protecting France's nuclear interests in the region, target Coo as an object of significant value. Yousuke finds himself embroiled in efforts to protect Coo from capture and exploitation by these forces. The conflict intensifies, transforming Yousuke's role from simple caregiving into active protection against organized threats aiming to control or eliminate Coo for their own ends. This struggle to safeguard Coo defines Yousuke's experience.