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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. (Source: FUNimation)

The virtual world inside the scub coral (intelligent coral-like lifeforms) created by Eureka... The people from that virtual world appeared on Earth ten years ago when it collapsed. Since this large-scale amalgamation, the humans from the virtual world call themselves "Green Earth" and the original Earth humans call themselves "Blue Earth," and they've come to cause various conflicts with each other repeatedly below the surface. Eventually, Dewey Novak, a senior officer in the Green Earth Armed Forces, rises together with his comrades and finally sets a large-scale terrorism plan into action in order to protect their own dignity. Meanwhile, Eureka, who is detested by the world as the main cause of the chaos, has become a high-grade combatant with the UN's A.C.I.D. unit. Live in order to keep this world at peace... This was the path of atonement she chose. One day, she receives an order to protect a girl named Iris, a new "Eureka" who has the ability to control scab coral. They fight a lot at first but gradually come to understand each other through their lonely escape. Soon the world faces a crisis, and when that happens, Eureka draws on every last ounce of her strength as she fights. "I want to protect Iris and this world." What future awaits her at the end of that wish of hers?

It all begins with the story that was left untold—the earth-shattering incident where Renton's father disappeared. With the mysterious pilot Eureka by his side, only Adroc Thurston could undo his own mistake, sparking the event that changed everything and earned him the title of a hero. Now, ten years later, Eureka lies in critical condition as Renton leaves the crew of the Gekko. But when he finds himself in the care of his father's old friends, he has a choice to make. Either stay with the loving family he's always wanted, or earn the love he seeks.

An original video anime, released on Blu-ray in a combined Hybrid Disc that also hold an Eureka Seven AO game for the PlayStation 3. The OVA is set between episodes eight and nine of the series.

Renton, son of scientists, and Eureka, a girl who can't live under the sun, are raised together when very young and become very attached to each other. One day, Eureka is taken away. Powerless at the time, Renton vows to rescue her. He enters the military and is soon is assigned to the Independent Youths Unit 303 of the First Mobile Forces thanks to his exceptional performance alongside his Nirvash, a bio-mechanical armor/control system. Unknown to Renton, lies a plot to extinguish the alien invasion that is currently happening involving not only him, but Eureka too.