In the town of Kamisu 66, 12-year-old Saki Watanabe has just awakened to her psychic powers and is relieved to rejoin her friends—the mischievous Satoru Asahina, the shy Mamoru Itou, the cheerful Maria Akizuki, and Shun Aonuma, a mysterious boy whom Saki admires—at Sage Academy, a special school for psychics. However, unease looms as Saki begins to question the fate of those unable to awaken to their powers, and the children begin to get involved with secretive matters such as the rumored Tainted Cats said to abduct children.

Shinsekai yori tells the unique coming-of-age story of Saki and her friends as they journey to grow into their roles in the supposed utopia. Accepting these roles, however, might not come easy when faced with the dark and shocking truths of society, and the impending havoc born from the new world.