Beginning in April 5738 AD, it has been over 3,700 years since a mysterious flash petrified nearly all human life. A 15-year-old genius named Senku Ishigami is suddenly revived to find himself in a world where all traces of human civilization have been eroded by time. Senku sets 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 6 months, Senku’s 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 martial artist named Tsukasa Shishiō and their classmate (and Taiju’s crush) Yuzuriha Ogawa with the goal of rebuilding civilization with a focus on science.
Tsukasa ultimately reveals that he opposes Senku’s 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 Senku, Tsukasa attempts to murder him when he realized that Senku knows how to create weapons that he cannot defend against. Believing he successfully killed Senku, Tsukasa leaves to begin establishing his own faction in the Stone World.
After recovering from his near death experience, Senku discovers a tribe of people already living on the planet and sees this as an opportunity to create his Kingdom of Science. These people are originally hesitant, but eventually learn the benefits that science can bring to their survival. Over time, Senku becomes more trusted by the tribe, eventually being taught of their past where he discovers that the village was started by his adoptive father Byakuya, along with five other astronauts, who were unaffected due to being in the International Space Station at the time of the petrification event.
Together with his new allies and friends, Senku’s Kingdom of Science engages in a war with the Tsukasa Empire, ultimately emerging victorious and affirming themselves as a force to be reckoned with.
After the victory, they discover that Senku’s adopted father had left precious metals which can be used as catalysts to mass-produce revival fluid in the nearby island which is now inhabited by a tribe known as the Petrification Kingdom, who possess the device used to petrify the world so long ago.