After the virtual world housed within the intelligent, coral-like Scub Coral collapsed, its inhabitants merged with Earth, splitting humanity into "Green Earth" and "Blue Earth." This division fuels rising tensions that lead to ongoing underwater battles. In the middle of this conflict, Dewey Novak, a high-ranking officer in the Green Earth military, works with his allies to plan a major terrorist attack meant to defend their people's honor.
Eureka, blamed for the collapse of the virtual realm, now works as a high-ranking operative in the UN's A.C.I.D. unit, seeking redemption through her efforts to maintain peace. When she is assigned to protect a girl named Iris, who shares her ability to manipulate Scub Coral, their early meetings are marked by friction. But as they face danger together, they slowly develop a deeper mutual understanding. With a global crisis approaching, Eureka gathers all her strength to protect both Iris and the world. Her wish to shield them remains uncertain; what fate lies ahead for her?