The story is set on Okinawa's isolated island of Iwado, which has seen a growing movement advocating a return to an autonomous government. Fukai Ao, a 13-year-old boy with a missing father, lives on the island with an old doctor named Toshio and is about to enter middle school. Ao's mother was taken away a decade ago by unknown individuals. Arata Naru, Ao's 13-year-old childhood friend and the story's heroine, lives with her father, older sister, and grandmother. She has a Yuta power awakened within her due to an incident when she was young.

A mysterious entity called Secret suddenly appears and launches an attack on the Scub Coral lifeform on the island. In his fervent desire to protect the island, Ao launches a certain military FP called Nirvash aboard a Japanese military transport.