"Shin Sekai Yori" is a science fiction manga adaptation of the novel by Yusuke Kishi, set in a post-apocalyptic future where humanity has developed psychic abilities known as "Cantus." The story unfolds in a seemingly utopian society where humans live in small, isolated communities, governed by strict rules to maintain order and prevent the misuse of Cantus. The narrative centers on Saki Watanabe, a young girl who, along with her friends Satoru Asahina, Maria Akizuki, Mamoru Itou, and Shun Aonuma, grows up in this tightly controlled environment.

As children, Saki and her peers undergo rigorous education and training to master their Cantus. However, their world begins to unravel as they uncover dark secrets about their society. They learn that those who fail to control their powers or exhibit dangerous tendencies are eliminated, often through a process called "extermination." The group also discovers the existence of "Queerats," a subhuman species created through genetic engineering, who serve as laborers and soldiers for humans but harbor their own ambitions and resentments.

The story takes a dramatic turn when Shun, one of Saki's closest friends, begins to exhibit signs of instability due to his powerful Cantus. He is eventually exiled, leaving a profound impact on the group. Years later, as adults, Saki and Satoru investigate the disappearance of Maria and Mamoru, who fled the village after Mamoru was targeted for extermination. Their search leads them to confront the Queerats, who reveal their own plans for rebellion against human dominance. The Queerats' leader, Squealer, orchestrates a war against the humans, exposing the fragility of their society and the moral compromises made to sustain it.

Throughout the narrative, themes of power, control, and the ethical implications of genetic manipulation are explored. The society's reliance on fear and suppression to maintain order is juxtaposed with the Queerats' struggle for autonomy, raising questions about the nature of humanity and the cost of survival. Saki emerges as a central figure, grappling with the weight of her discoveries and the responsibility to protect her community while questioning its foundations.

The manga delves into the psychological and emotional toll of living in a world where trust is scarce, and the line between friend and foe is blurred. The characters' relationships evolve as they navigate betrayal, loss, and the harsh realities of their world. The story culminates in a climactic confrontation that forces Saki to make difficult choices, ultimately shaping the future of her society and the fate of both humans and Queerats.