Whispers among students at Shinyo Academy speak of an urban legend: Boogiepop, a shinigami who appears to release people from suffering. The truth is both stranger and more specific. Boogiepop is a guardian entity that resides within a seemingly ordinary high school girl named Touka Miyashita, emerging only when the world faces a supernatural threat.

The story unfolds in an unnamed Japanese city, where a rash of female student disappearances is initially dismissed as runaways. Nagi Kirima, a fellow student known as the Fire Witch who spends her time investigating mysteries, suspects something far more sinister. Her instincts prove correct when an alien being named Echoes arrives on Earth to judge humanity's capacity for kindness. Captured and experimented upon by the Towa Organization, a shadowy group dedicated to shaping human evolution, Echoes is cloned. The clone, a man-eating creature called Manticore, escapes and begins preying on young girls, taking the form of its victims.

The series is structured as an anthology of four interconnected story arcs based on the original light novels. The first arc, Boogiepop and Others, follows the battle against Manticore, who gains an eager human accomplice in the form of the student Masami Saotome. As the creature consumes and impersonates students, its trail of destruction forces Boogiepop to act, aided by a network of students including Nagi, the archer Shiro Tanaka, and the discipline committee president Kei Niitoki.

The second arc, VS Imaginator, shifts focus to a new antagonist known as the Imaginator. This entity plans to standardize the human psyche to eliminate all misunderstanding and conflict, a goal that brings it into direct opposition with Boogiepop and the Towa Organization. The third arc, Boogiepop at Dawn, serves as a prequel, delving into the tragic origin of both Boogiepop and Nagi Kirima. It reveals the events of five years prior involving a serial killer doctor, a stolen experimental drug, and the birth of the guardian persona within the young Touka Miyashita. The final arc, Overdrive: The King of Distortion, returns to secondary characters from the first story, trapping them in a tower where a bizarre phenomenon manifests as an alternate personality born from their own guilt.

Told through a non-linear narrative that presents events from multiple perspectives, Boogiepop and Others explores themes of identity, free will, and the often blurry line between normalcy and monstrosity, as an ensemble of students and supernatural beings collide in a struggle for the future of humanity.