"Dr. Stone" is set in a world where humanity is suddenly petrified by a mysterious flash of light, turning every human into stone statues. Thousands of years later, high school student Senku Ishigami awakens to find civilization in ruins, with nature reclaiming the planet. Senku, a scientific genius, begins rebuilding society using his knowledge of science. He revives his friend Taiju Oki and later Yuzuriha Ogawa, but their reunion is complicated by the emergence of Tsukasa Shishio, a physically powerful classmate who believes only the young and pure should be revived, aiming to create a new world order free from the corruption of the old world.

Senku and Tsukasa’s ideologies clash, leading to a conflict between Senku’s Kingdom of Science and Tsukasa’s Empire of Might. Senku’s goal is to revive all of humanity and restore civilization through science, while Tsukasa seeks to prevent the revival of adults, whom he views as responsible for societal decay. Senku gathers allies, including the skilled craftsman Chrome and the village chief Kohaku, who belong to a small community of humans that survived the petrification event. Together, they work to develop advanced technologies from scratch, such as electricity, medicine, and communication tools, to counter Tsukasa’s growing influence.

As the story progresses, Senku uncovers the origins of the petrification event, linking it to a mysterious substance called the "Petri-Device." The narrative expands to include global stakes, with Senku and his allies facing new challenges, including rival factions and the race to uncover the truth behind the petrification. The series emphasizes the importance of scientific discovery, innovation, and collaboration, blending adventure, humor, and educational elements as Senku and his team strive to rebuild a world where science reigns supreme.