When widespread supernatural incidents involving youkai occur in Gensokyo, the shrine maiden Reimu Hakurei typically resolves the situation by directly confronting the perpetrator. However, cases that target specific individuals and involve hidden identities are often too delicate for such straightforward methods. This is where Satori Komeiji, the mistress of the Palace of Earth Spirits, proves essential. As a satori youkai, Satori possesses a third eye that grants her the power to read minds, making her capable of detecting any criminal regardless of the lies they might tell. Despite her extraordinary aptitude as a detective, she does not always wish to leave her mansion.

The story follows Satori and her assistant and investigator, Rin Kaenbyou, as they work to solve mysteries across Gensokyo. The first major case involves an attack on Patchouli Knowledge, the youkai magician living in the Scarlet Devil Mansion. Patchouli is not killed but is left in a comatose state. Rin interviews the residents of the Scarlet Devil Mansion and other individuals who might have a motive, including Reimu Hakurei herself. The case expands as additional victims emerge. The narrative progresses roughly in order of the Touhou Project games, incorporating encounters with many characters from the series.

The setting spans Gensokyo, the fantasy realm where humans and youkai coexist, with significant events taking place at locations such as the Scarlet Devil Mansion and the Hakurei Shrine. A later narrative arc involves vengeful spirits that had engulfed Gensokyo finally being settled and managed at the Hakurei Shrine. Conflicting motives arise among those who want to return the vengeful spirits to the underworld, those who wish to help them find peace, and those who seek to use them for their own purposes, leading to further trouble. The series experienced a hiatus following the February 2021 release due to the health concerns of the original artist Ginmokusei, and it resumed serialization in October 2021 with Yuu Akimaki as the new artist. A related manga adaptation titled Samsara Edition launched in October 2025.