In the year 2035, a biological research project intended to create an Artificial and Intelligent Cellular Organism (A.I.C.O.) goes awry, which leads to an incident known as the Burst. The Burst causes Kurobe Gorge to become infested with synthetic organisms known as Matter and cordoned off by the government. Two years later, high school student Aiko Tachibana -- who lost her family in the Burst -- learns from fellow student Yuya Kanzaki that a secret is hidden within her body and the answer to the puzzle lies at the center of the Burst, Primary Point. Aiko vows to gain access to the restricted area, with a team of divers and Yuya guiding her, to discover the secret.