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. Ao launches a certain military FP called "Nirvash" aboard a Japanese military transport in his fervent desire to protect the island.
Sequel to Eureka Seven. The year is 2025. Earth is engulfed in the crossfire between massive warring alien life forms that leave annihilation in their wake. While searching for clues about his past, Ao is caught in an attack and forced to fly a giant humanoid fighter craft to save himself and his island. Fragments of the teenager's origin come to light when a hostile shape-shifter seeking revenge on Ao's missing mother - who vanished two years after his birth - targets him instead....