Shinomonogatari unfolds across two volumes as part of the larger Monogatari series, presenting parallel narratives that delve into the origins of vampires and the consequences of past sins. The story opens with a dire situation: human society has fallen into disorder while a virus that infects only aberrations begins wiping out vampires. In response, the former vampire knight Shinobu Oshino and her companion Koyomi Araragi journey to her homeland, the Kingdom of Acerola, to seek out her original master, Deathtopia Virtuoso Suicide-Master. The first volume, subtitled Shinobu Suicide, follows their expedition to a place where the line between life and death is razor-thin. Upon finding Deathtopia, Shinobu must confront the weight of her own immortal history and the fate of her entire species. Araragi, meanwhile, finds himself entangled in a crisis where the rules of oddities are being rewritten by a plague that targets their very existence.

The second volume, Nadeko Around, shifts perspective to a different group of characters. As part of her training to become an oddity specialist, Nadeko Sengoku travels to Iriomote Island alongside the doll-like servant Yotsugi Ononoki and the deceptive con artist Deishuu Kaiki. Their mission is to confront Uroko Around, a snake charmer who is revealed to be the biological daughter of the all-knowing specialist Izuko Gaen. Nadeko, who previously struggled with her own transformation into a serpent deity, must now face the source of many of the series' underlying conflicts. The narrative describes their encounter as a deathmatch, forcing Nadeko to test her newfound resolve and abilities against an opponent who represents the root of much evil in the world. Through these two interwoven arcs, Shinomonogatari explores themes of mortality, legacy, and the enduring consequences of choices made across centuries.