In April 5738 AD all humans were petrified by a mysterious flash of light. After 3700 years a 16-year old named Senku Ishigami is revived suddenly to find himself where all human civilization has been eroded by time. Senku was a genius whose dream was to become a scientist and using his knowledge of science he begins to study the petrified humans to determine the cause of the event and to find a cure. He sets up a base camp for his research for the next six months and discovers that the cause for his revival was due to nitric acid.
With this discovery, he develops a compound that can revive others instantly but he cannot produce it in mass production due to lack of raw materials. Using this compound he first revives his friend Taiju Oki, their classmate Yuzuriha Ogawa and a famous martial artist Tsukasa Shishio. They revive Tsukasa by chance when they were attacked by lions since only humans were petrified and they need someone strong to help them. Senku’s goal was to rebuild the civilization with a focus on science.
Later Tsukasa reveals that he is against the idea of reviving the other humans believing the old world was tainted and should not be restored. He also opposes Senku’s idea of new scientific civilization as he desires to establish a new world order based on power and strength. He also destroys any petrified any adults he encountered in order to prevent them from interfering with his goals. Tsukasa extorts the formula for the revival compound from Senku. Senku also has the knowledge for making weapons which he cannot defend against. So he attempts to kill Senku.
Believing he successfully killed Senku, Tsukasa begins to establish his own faction in the petrified world. Tsukasa’s attempt fails and Senku recovers from his near death experience and finds a tribe of people already living on the planet. Seeing this as an opportunity to create his Kingdom of Science. But the people of the tribe was hesitant. Eventually the people learns the benefits of science which can help in their survival and over time Senku becomes more and more trusted by the tribe, eventually being taught of their past.
From the stories heard from the tribe, he discovers that the village was started by his father along with five other astronauts. These astronauts were unaffected by the petrification due to being in space at the time of the event. Later he was given the title of the chief of the village. During the time in the village Tsukasa’s people came to attack the village and also discovers that Senku is alive and declares war against them. So together with Senku’s new allies and friends he creates his kingdom of Science and prepares for the war against Tsukasa’s group.