1883, the sixteenth year of the Meiji era, Tokei (Tokyo).
Shizume Kurahashi, a "worshipper" of the scientific method, suffers from a peculiar problem: when her heartbeat becomes irregular, she falls into a sleep full of nightmares, while an arachnid-like creature appears from her chest. Can this be explained with scientific reasoning? Shizume believes that the answer is yes, and she will do anything to prove it.
Meanwhile, her father, the diviner Hikofumi Kurahashi, has mysteriously disappeared, and the intrepid secret agent Kogenta Inui is searching for him in an uncertainty-filled, Lovecraftian context.
Strange events happen around this capital city of a country growing closer to the Western world. Science, superstition, mysterious diseases and hidden sects start to be tied together by a unique common denominator that people call Tsukumo:
九十九 (9-10-9 in Japanese characters, meaning 9 tens plus 9, or in English, 99).