The story is set on Okinawa's isolated island of Iwado, which has seen a growing movement advocating a return to an autonomous government. Ao Fukai, 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. Naru Arata, 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.
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"I'd like to share a revelation I've had during my time here. It came to me when I tried to classify your species. I realized that you're not actually mammals. Every mammal on this planet instinctively develops a natural equilibrium with their surrounding environment, but you humans do not. You move to another area, and you multiply, and you multiply, until every natural resource is consumed. The only way you can survive is to spread to another area. There is another organism on this planet that follows the same pattern. Do you know what it is? A virus. Human beings are a disease, a cancer of this planet. You are a plague, and we are the cure." - Agent Smith