In Japan in the year 2035, an accident known as the "Burst" occurs during a research project, spawning an out-of-control artificial life form called "Matter" that has spread throughout the Kurobe Gorge. The research city that was once hailed as the hope for humanity is cordoned off by the government. Two years later, 15-year-old Aiko Tachibana, who lost her family in the Burst, learns something unbelievable from Yuya Kanzaki, a new student at her school. A secret is hidden within her body, and the answer to the puzzle lies at the "Primary Point" that was the center of the Burst. Aiko resolves to infiltrate the restricted area, escorted by a team of divers and with Yuya as her guide. When boy meets girl with the fate of humanity in their hands, what new truth will come to light?
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Two years after the mysterious Burst that killed her family, Aiko has nearly learned to walk again.But a transfer student's arrival upends her life.
Kanzaki takes Aiko to the Town, where her father's old colleague Kurose tells her the unbelievable: Her brain was transplanted into an artificial body.
The CAAC detains Aiko and Yuya, but the Divers manage to break them out. Though the Matter is active again, the group plans to head to Primary Point.
The group clears the Gate just as the government orders an evacuation. Their first target is the Guillotine Shutter at K1, but the Matter is active.
Inside the Area, the group rests and resupplies at the camp. Nanbara gets a ride from Kurose, but she and Isazu appear to have their own plans.
Kaede's showing off delays the group's progress to point K2, which they must reach before sunrise to enter Area Three. Isazu tells Kurose what he did.
The CAAC Special Forces intercept the group to try to take Aiko back. Kurose realizes that Isazu's daughter Yuzuha is connected to the Matter.
The Divers confront Aiko and Kanzaki, but they agree to continue with the mission. Isazu becomes lab director and learns about Unit One.
The team reaches the biotech research facility at Primary Point, but Isazu manages to patch in a video feed to confront Kanzaki about his intentions.
Aiko has the chance to speak to her other self inside the Malignant Matter. Meanwhile, the human form Matter engulfs Yura, revealing Yuzuha.
Isazu establishes a link to the Matter so he can interrogate Yura. The JSDF prepares to incinerate the entire Area despite Nanbara's objections.
At the surgical site, Yura admits his intentions changed with Aiko's decision. Kurose tries to sever the link between Yuzuha and her duplicates.