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 12-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 12-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.

Eureka Seven AO premiered with the launch of the new digital over-the-air television system NOTTV on April 1. It finished airing in its time slot with episode 22 on September 28, 2012. Episodes 23 and 24 were aired together on November 20, 2012.