In the year 2011, a small percentage of humans began manifesting psychokinetic abilities known as "Cantus." Over a millennium later, in the small town of Kamisu 66, Saki Watanabe is the last of her friends to awaken her powers and join the Sage Academy, a school for psychics like her. Although everyone at the institution has Cantus, they are not all equal; shortly after Saki enrolls, one of her classmates who is regarded as being weaker than the others suddenly disappears.

Walking home one day with her friends—the determined Maria Akizuki, the intelligent Shun Aonuma, the observant Satoru Asahina, and the timid Mamoru Itou—she comes across two unfamiliar creatures known as "Monster Rats." These beings resemble moles and worship those with Cantus as gods. As a result, when Saki uses her abilities to save one from trouble, she is met with exceptional gratitude.

Now unsure about the Monster Rats' place in society, Saki and her friends find out about another disappearance. As time passes, they slowly look for answers to the mysteries that surround them and begin to realize that this seemingly "perfect" new world masks humanity's dark past.