"Dusk Maiden of Amnesia" is a supernatural romance manga set in Seikyou Private Academy, where rumors of paranormal activity abound. The story centers on Yuuko Kanoe, a ghost who haunts the school, and Teiichi Niiya, a first-year student who becomes the only person able to see her. Yuuko has no memory of her past or the circumstances of her death, and she enlists Teiichi's help to uncover the truth. Together, they form the Paranormal Investigation Club to explore the mysteries surrounding her existence.

As the narrative progresses, Teiichi and Yuuko delve into the school's dark history, uncovering clues about Yuuko's life and death. Their investigation reveals that Yuuko died decades ago under mysterious circumstances, and her spirit has lingered in the school ever since. The bond between Teiichi and Yuuko deepens as they work together, blending elements of mystery, horror, and romance. Their relationship is complicated by Yuuko's ghostly nature, as she struggles with her inability to fully interact with the living world and the emotional toll of her unresolved past.

Supporting characters include Kirie Kanoe, Yuuko's living descendant, who harbors mixed feelings about her ancestor's ghostly presence, and Momoe Okonogi, a classmate who joins the Paranormal Investigation Club and becomes involved in their adventures. The story explores themes of love, loss, and the passage of time, as Yuuko's memories gradually resurface, revealing the tragic events that led to her death.

The manga balances eerie supernatural elements with heartfelt moments, creating a narrative that is both suspenseful and emotionally resonant. The resolution of Yuuko's mystery ties together the threads of her past and present, offering closure to her story while leaving room for reflection on the enduring nature of love and memory.