In 2035, a biological research project to create an Artificial and Intelligent Cellular Organism (A.I.C.O.) went awry, resulting in an incident called the "Burst" which transformed Kurobe Gorge into a quarantine area infested by a rampant growth of synthetic organisms called Matter. Two years later, high school student Aiko Tachibana finds that she may be the duplicate of a girl trapped within the Matter whose family disappeared in the Burst. An enigmatic fellow student Yuya Kanzaki offers to solve the mystery by taking her with a group of professional Divers to the Primary Point which was the center of the Burst.