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?

Three years into the war, Mahito Maki loses his mother in a tragic fire at the hospital. Shortly thereafter, his father marries Natsuko, the younger sister of Mahito's mother. They take Mahito out of Tokyo to seek refuge in his late mother's rural family home. There, Mahito is constantly taunted by a strange gray heron, who seems to have taken an interest in him. Unable to come to terms with his loss and struggling to adjust to a new life in an unfamiliar place, the boy is shocked to discover that Natsuko is pregnant. To make matters worse, the pesky heron can speak—and claims that Mahito's mother is still alive. Luring him into a mysterious tower near the residence, the heron says that Mahito can save her from death, but the boy is not easily swayed. When Natsuko disappears one day, however, Mahito watches her walk into the tower and becomes compelled to venture in to rescue her. He soon finds himself falling into another world below his, where life and death seem to be entwined. As he navigates through this foreign realm to find Natsuko, Mahito must understand what it means to live if he wants to safely return home.

Mio has feelings for her childhood friend Arata, but can't convey her feelings. One day, as they continue their delicate relationship, the two fight over something trivial. After letting tensions settle, Mio goes to make up with him in the pouring rain. While on her way, she gets into a traffic accident. When she regains consciousness, a mysterious and unfamiliar world appears before her eyes.