The story follows Koyomi Araragi, a high school boy who retains vampiric healing abilities after a spring break incident, and his companion Shinobu Oshino, a former legendary vampire now bound to his shadow. The narrative picks up immediately after the events of Kabukimonogatari. While walking with the lost snail ghost Mayoi Hachikuji, Koyomi encounters a mysterious and terrifying entity that appears as a formless, all-consuming darkness. This entity, which Shinobu identifies from an encounter four hundred years prior, is not a traditional aberration but an agent of natural law that enforces the proper order of the world by erasing aberrations that have strayed from their purpose.

As the darkness pursues the group, they are rescued by the doll-like shikigami Yotsugi Ononoki and seek refuge in the ruins of an old cram school. There, Shinobu recounts her arrival in Japan centuries ago, the creation of her first vampire servant, and how she first drew the attention of this merciless executioner. The true nature of the threat is revealed by the enigmatic specialist Izuko Gaen, who explains that the darkness is not targeting Shinobu or Koyomi, but Mayoi Hachikuji.

Having been helped by Koyomi to reconcile with her past, Mayoi has resolved the circumstances that bound her as a wandering spirit. She has effectively become a harmless ghost who no longer makes people lost, thus ceasing to function as the aberration "Mayoi the Snail." By abandoning her role, she has violated the natural law of aberrations, marking her for erasure by the darkness. Faced with this inevitable outcome, Mayoi chooses a bittersweet resolution. To protect Koyomi and Shinobu from being consumed alongside her, she finally accepts her fate and passes on to the afterlife, officially becoming a ghost no more. Her departure leaves a profound and sorrowful impact on Koyomi, who is forced to confront a loss he cannot undo.