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.

After a successful test of their new cell phone, Senku learns of a mysterious tale about a bee named Speaker who can play the voices of the dead.

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.

Amaryllis explains how she evaded petrification and how she came to her decision to sneak into the inner palace.