"Boku no Tonari ni Ankoku Hakaishin ga Imasu" centers around Seri Koyuki, a high school student who prides himself on his intelligence and rational thinking. His life takes an unexpected turn when he discovers that his seemingly ordinary classmate, Sadako Kurusu, is actually the reincarnation of the Dark Destruction God, Ankoku. Sadako, despite her divine origins, is clumsy, socially awkward, and struggles with everyday tasks, which contrasts sharply with her immense destructive power. Seri, initially skeptical, is forced to confront the reality of Sadako's divine nature when her powers inadvertently cause chaos in their daily lives.

The narrative explores the dynamic between Seri and Sadako as they navigate the challenges posed by her divine abilities. Seri, who values logic and order, finds himself constantly cleaning up the messes caused by Sadako's uncontrollable powers. Despite her destructive tendencies, Sadako is kind-hearted and genuinely wants to help others, though her efforts often backfire. The story balances comedic elements with moments of tension, as Seri and Sadako encounter various supernatural beings and situations that test their growing friendship.

Supporting characters include other deities and supernatural entities who interact with Sadako and Seri, often adding layers of complexity to the plot. These interactions reveal more about Sadako's past as a god and the responsibilities that come with her powers. The series delves into themes of identity, responsibility, and the clash between the mundane and the extraordinary, all while maintaining a lighthearted tone.

As the story progresses, Seri and Sadako's relationship evolves, with Seri gradually accepting his role as Sadako's confidant and protector. The manga blends humor, action, and emotional moments, creating a narrative that is both entertaining and thought-provoking. The interplay between the ordinary and the divine serves as the core of the story, driving the plot forward and shaping the characters' development.