A light sweeps across the world, turning every person to stone, but high school friends Senku and Taiju remain conscious and emerge from their confinement 3,700 years later; Senku combines his brains with Taiju's brawn to craft a cure for the others.

An emergency forces Senku and Taiju to revive a brutish schoolmate named Tsukasa Shishio whose attitude and traumatic past clashes with Senku's plans for a new society.

Tsukasa reveals his murderous intentions, and Senku must devise an ingenious plan to stop him in his tracks.

Three millennia after a mysterious phenomenon turns every person on Earth into stone, two best friends, a science genius and a passionate strongman, discover a way to reverse the effects and fight a rival clan of survivors to rebuild civilisation.

As Taiju and Yuriha escape from Tsukasa with Senku, it is revealed how Senku survived after being released from petrifaction.

Taiju and Yuzuriha figure out the secret to reviving someone and wake Senku, but now that he is back, they must deal with Tsukasa.