Several thousand years after a mysterious phenomenon turns all of humanity to stone, the extraordinarily intelligent, science-driven boy, Senku Ishigami, awakens from petrification. Facing a world of stone and the total collapse of civilization, Senku makes up his mind to use science to rebuild the world. Starting with his super strong childhood friend Taiju Oki, who awakened at the same time, they will begin to rebuild civilization from nothing. Depicting two million years of scientific history from the Stone Age to present day, the unprecedented crafting adventure story is about to begin.

Facing immediate danger from wild animals Senku and Taiju are forced to revive Tsukasa Shishio "The Strongest High School Primate". Although Tsukasa has tremendous fighting ability and provides abundant food as their hunter, their new ally harbors an opposing view on restoring humanity.

Senku does not trust the motivation of Shishio, so he will try to hide his plans from a new and unforeseen enemy for his plan to revive civilization.