Yatsuki Nishizuru, a part-time worker in Akihabara, has the unique ability to see and interact with spirits— youkai—who inhabit the area. Despite this, Yatsuki tries to ignore them, living a normal life by working, taking care of his younger sister Nanao, and visiting a local maid cafe. However, Yatsuki's life suddenly becomes much more complicated after a strange girl falls out of a tree and onto his face. This girl, Rokka Ayatsuji, quickly becomes friends with Yatsuki and Nanao, until they discover that she is actually a Rokurokubi, a soul-eating youkai who can stretch her neck to incredible lengths! At the same time, Yatsuki reveals his sister's body and spirit are separate—Nanao is a ghost.

At the same time, one of the cafe maids, Momo Chitoseya, becomes possessed by a dark spirit. Yatsuki and Rokka's exorcising it draws the attention of Momo's sister Nagi, a professional medium, who enlists them for youkai extermination. In exchange for Yatsuki defeating the more dangerous youkai in Akihabara, Nagi will look for a way to return Nanao's spirit to her body. No longer able to ignore the secret world around him, Yatsuki must begin his quest and continuously risk his life in order to return his sister's.