When Ruka was younger, she saw a ghost in the water at the aquarium where her dad works. Now she feels drawn toward the aquarium and the two mysterious boys she meets there, Umi and Sora. They were raised by dugongs and hear the same strange calls from the sea as she does.

Umi and Sora are not alone in their strange connection to the sea. Forty years ago, Jim met another young boy with the same powers. As penance for letting the boy die, Jim has been searching the world for other children with those same ties to the ocean.

Anglade, a wunderkind who was once Jim's research partner, lures Sora away with the promise of answers. This leaves Umi severely depressed, and it is up to Ruka to help her new friend find his brother. But time is quickly running out...