The story is set on the remote island of Iwado in Okinawa, which has seen a rise in an independence movement. Ao Fukai, a twelve-year-old whose father is missing, lives on the island with Toshio, an elderly physician. Ao is getting ready to begin middle school. His mother disappeared ten years ago at the hands of unknown attackers. Naru Arata, a childhood friend of Ao's and the protagonist of the story, is also twelve years old and lives with her father, grandmother, and elder sister. Naru's "Yuta" ability was activated when she was young, and she can now control it. Suddenly, a strange force attacks the Scub Coral organism on the island, and a mysterious figure known as "Secret" appears. Ao sets out on a military mission aboard "Nirvash" to protect his home, enlisting the aid of a Japanese military carrier.