Around the year 2011, a segment of humanity began to manifest telekinetic abilities called Cantus. A millennium later, in the village of Kamisu 66, Saki Watanabe is the final member of her cohort to awaken these powers and enter the Sage Academy, an institution dedicated to Cantus users. Despite every student possessing such abilities, true equality remains elusive; shortly after Saki starts her education, a classmate deemed less powerful vanishes without a trace.
While returning home with her companions—Maria Akizuki, who is resolute; Shun Aonuma, recognized for his intellect; Satoru Asahina, keen and perceptive; and the shy Mamoru Itou—Saki encounters two strange creatures known as Monster Rats. These mole-like entities revere Cantus users as kami. When Saki employs her power to assist one, she is greeted with profound gratitude.
As Saki contemplates the role of Monster Rats in their society, she and her friends uncover yet another disappearance. With each passing day, they delve deeper into the surrounding enigmas, gradually realizing that the seemingly utopian new world hides the grim realities of human history.