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.

Senku has the idea of ​​creating gunpowder to have a way to balance the scale and have a chance to defeat Shishio. The production of gunpowder causes a fire. Shortly thereafter, Senku and the others discover smoke signals on the horizon. An accident? Hardly likely. Apparently there are other people in the stone world ...

Shishio is determined to end Senku's life if he does not promise at that moment that he will abandon his idea of ​​recovering civilization as it was before the incident.

Senku continues in trying to advance the Stone World, this time he makes "space food", it is in actuality cup noodles. After Senku finishes his project, Gen has an epiphany and devises a plan to take down Tsukasa's army without violence.

While continuing to use the hot air balloon to search for the oil, it's decided that Ishigami Village needs to take up agriculture to prevent future food shortages, as well as to produce preserved food for their upcoming sea voyage.

Amaryllis, Ginro and Kohaku are chosen to join the inner palace. The science team will need a way to communicate with them in secret, and, eventually, a way for them with the science team.