The story is set in a village in the southern Japanese prefecture of Kōchi during World War II. Even in this remote mountainous area, the perception of American and British people as "brutes" has taken root, due to the deaths and injuries among the villagers' relatives. A elementary schoolgirl named Eiko transfers from the city of Yokohama to this village. Eiko happens to have blue eyes from her American father, and her classmates make no attempt to rein in their bullying. Other than Eiko's homeroom teacher Akiko, even the teachers view Eiko the same way that the children do. However, a boy named Kenta views Eiko more with curiosity than with hostility. The children's lives change as the injured father of one of Kenta's classmates returns from the battlefield and news of more casualties arrives in the village.
In the future, the oceans have risen to flood all the continents due to humanity's negligence of the environment. Only a few bits of land have been spared, and one of those is the city-island where Elfie lives with her grandfather. One day, due to an underwater incident, she discovers that she can breathe underwater. Her grandfather reveals that in truth she is one of the mythical sea-people. Using the city folk's xenophobia, local politicians spark a war with this hidden people to distract people from their current resource problems, and Elfie is caught in the middle of it.