In 2019, a mysterious flash suddenly petrifies ostensibly all humans. The human race is frozen in stone for 3,700 years until in April 5738, when You, a 16-year-old prodigy is suddenly revived to find yourself in a world where all traces of human civilization have been eroded by time. You set up a base camp and begins to study the petrified humans in order to determine the cause of the event, as well as a cure. Over the next six months, your friend Taiju Oki wakes up and Senku learns their revival was made possible with nitric acid. With this discovery, they develop a compound that will allow them to instantly revive others. They begin by reviving a famous high school martial artist named Tsukasa Shishio and their classmate Yuzuriha Ogawa with the goal of rebuilding civilization with a focus on science.

Tsukasa ultimately reveals that he opposes your idea of forming a new scientific civilization, believing the old world was tainted and should not be restored. Instead, he desires to establish a new world order based on power and strength, going so far as to destroy any petrified adults he encounters in order to prevent them from interfering with his goals. After extorting the formula for the revival compound from you, Tsukasa attempts to murder you when he realized that you knows how to create weapons that he cannot defend against. Believing he successfully killed you, Tsukasa leaves to begin establishing his own faction in the Stone World. After recovering from his near death experience, you discovers a tribe of people already living on the planet and sees this as an opportunity to create your Kingdom of Science.