In 2035, an incident called “The Burst” takes place at a Japanese research facility, spawning the rapidly expanding, consuming, and self-replicating "Matter." Winding through the ruins of dams and military installations in the Kurobe Gorge, the hostile Matter is besieged by task forces attempting to stop it from reaching the ocean and mercenaries hunting for the truth behind its existence. Aiko Tachibana lives under constant medical surveillance after being rescued from the Matter. She passes her days waiting for recovery by folding paper planes. Soon, her routine school life is disrupted by the arrival of transfer student Yuuya Kanzaki, who points out several inconsistencies regarding her body. Why is she never injured, and why does she no longer need her wheelchair? He claims that her existence is more complex than she has been led to believe, and that she alone holds the key to ending The Burst. With numerous factions now interested in Aiko, she and Yuuya must gather allies and embark on a dangerous pilgrimage into the heart of the infested gorge before the net closes around them. To escape the conspiracy moving against them, the pair must confront the Matter—an enemy that flows like water.