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.

Ruka is traumatized when Sora disappears into the night sea right in front of her. But although she refuses to speak of the incident, the meteorite Sora made her swallow is not so silent. It whispers to her from inside her body, and with its guidance she leads Umi and Anglade into the open ocean in search of answers.

Surrounded by the sea, Ruka starts to see glimpses of the past that help her understand how Umi, Sora, Jim and Anglade all came to be connected.