A school trip back to Tokyo turns into a nightmare when a catastrophic earthquake derails the train inside a long mountain tunnel. High school student Teru Aoki regains consciousness to find the wreckage filled with the bodies of his classmates and teachers. Trapped under tons of rubble with no hope of immediate rescue, he discovers two other survivors: Ako Seto, a severely injured girl, and Nobuo Takahashi, a deeply disturbed boy who had been a target of bullying. As days pass in the lightless, corpse-filled tunnel, the group's fragile sanity begins to crack. Nobuo descends into a savage, paranoid madness, declaring himself the king of the wreck and eventually attempting to assault Ako. Teru fights off Nobuo, and just as volcanic lava begins to seep into the tunnel, he and Ako escape through a ventilation shaft, leaving the deranged Nobuo behind in the darkness.

Emerging from the tunnel, Teru and Ako find a world irrevocably transformed. The landscape is buried under a thick, choking blanket of volcanic ash, the sun is a dim memory, and society has completely collapsed. After a harrowing journey through the ashen wasteland, they encounter a military helicopter crew led by the volatile and unprofessional Captain Nimura. A tense and violent confrontation with the soldiers ends in tragedy when Teru, pushed to his breaking point, accidentally kills one of them with a Molotov cocktail. A raging firestorm engulfs the town where they are hiding, forcing the unlikely group of Teru, Ako, Nimura, and the pilot Iwada to flee together in the helicopter.

Seeking fuel and medical supplies for Teru, who is suffering from tetanus, the group lands on the Izu Peninsula, now an island cut off by a tsunami. There they discover a town populated by a cult-like group of survivors driven to homicidal madness by isolation and starvation. After being captured, Ako and Nimura fight their way through the crazed townspeople with the help of a mysterious, scarred boy named Kikuchi, who seems incapable of feeling pain. Kikuchi cryptically refers to a painting and calls himself the Dragon Head. The group narrowly escapes a mass suicide pyre set by the townspeople as a massive ash cloud engulfs the peninsula, leaving Kikuchi behind, standing calmly as he is consumed by fire.

The survivors finally find temporary refuge with an elderly woman who warns them that the greatest danger is giving in to fear itself. Determined to find their families in Tokyo, Teru and Ako lead the group in their damaged helicopter toward the capital. Flying through the apocalyptic sky, they make a devastating discovery where Mount Fuji once stood: a gigantic, smoking crater. The scale of the catastrophe becomes horrifyingly clear, leaving the small group to contemplate their place in a dead and broken world as they fly on, searching for any sign of life.