The narrative of Touhou Chireikiden: Hansoku Tantei Satori Meikyū-hen, also known as the Labyrinth Arc, follows the aftermath of a massive escape of vengeful spirits from the Palace of the Earth Spirits in Former Hell. This incident directly threatens the delicate balance of Gensokyo, as these spirits possess the bodies of various youkai and humans, draining their life force and leaving them in a comatose state. The protagonist is Satori Komeiji, the mistress of the Palace of the Earth Spirits and a satori youkai capable of reading minds with her third eye. Her unique ability makes her an ideal detective to uncover the culprit hiding among the innocent, though she is reluctant to leave her home. She is accompanied by her loyal animal companion, Rin Kaenbyou, a nekomata who serves as her assistant. The main antagonist is an unnamed and powerful vengeful spirit, later implied to be a separate entity from Mizuchi Miyadeguchi, who seeks to avoid detection and cause widespread chaos.

The story is set across various iconic locations in Gensokyo, beginning at the Scarlet Devil Mansion before moving to the Netherworld, Eientei, the Moriya Shrine, the Myouren Temple, and ultimately deep underground. Unlike a typical mystery of the week format, the plot quickly evolves into a serialized thriller. The initial case, involving an attack on Patchouli Knowledge, is solved by Satori, but the true culprit escapes, revealing a larger conspiracy. As Satori and Rin investigate, the vengeful spirit hops between bodies, framing innocent characters like Mizuchi Miyadeguchi and leaving a trail of victims, including Yoshika Miyako and Satori herself. The narrative shifts focus to Reimu Hakurei, the shrine maiden of the Hakurei Shrine, who becomes the primary force confronting the spirit directly. The arc is notable for its high-stakes action, breaking the traditional spell card rules, as characters like Kanako Yasaka resort to lethal force to protect their shrines. A significant subplot involves a complex gambit orchestrated by Yukari Yakumo and Satori to trap the spirit, which includes recruiting Flandre Scarlet to lay siege to the Myouren Temple and transporting the entire building to Former Hell. This arc concludes with the vengeful spirit temporarily escaping to the Shining Needle Castle, setting the stage for further confrontations.