60 years ago, a young woman was left to die in the abandoned school building behind the exclusive Seikyou Academy. Perhaps it’s not so surprising then, that among Seikyou’s many school clubs is one for students interested in “paranormal investigations.” Unable to remember how she died and trapped in the grey land between life and death, the ghost girl Yuko latches onto Teiichi Niiya, a freshman who can inexplicably see her, and together they and the other unsuspecting members of the club begin to unravel the many dark mysteries that surround Seikyou. In a tomb of silent classrooms, the answers await in Dusk maiden of Amnesia.
The Paranormal Investigation Club is tasked with looking into the strange incidents that go on around campus. Lately, an old dumbwaiter has been causing a stir, behaving strangely and moving on its own.
Seikyou Academy is known for having vacant classrooms, stairs that no one climbs, and hallways that end with no warning. Teiichi becomes lost in the labyrinth of buildings one night, in the older section of the school.
It looks like Teiichi is not the only one who can see ghosts. A mysterious letter arrives, warning him that he is in danger of being haunted.
The Paranormal Investigation Club is holding a training camp. Yuuko appears unexpectedly, but Teiichi pays her no mind. That night she takes him into a forgotten part of the school.
The school festival has arrived, and the Paranormal Activities Club has opened a haunted house: those unlucky few who enter are confronted with their greatest fear!
There is a strange rumor going around about a monster. The rumor mill is blowing it out of proportion and a martial law-like atmosphere has taken over, leaving Paranormal club members in danger.
Teiichi notices Yuuko has been acting strange, as she unknowingly keeps lashing out everytime he spends time with Momoe. He confides this with Kirie, who tells him she saw the shadow ghost again and concludes the shadow ghost is actually the darker half of Yuuko's split personality.
Yuuko tells Teiichi to leave her alone, believing she has forgotten him for causing her painful memories. Kirie concludes every time Yuuko experiences a painful memory, she has it removed from her mind and into her shadow.
Yuuko has recovered her memories and is exhibiting emotions she has never before shown. Subsequently, Shadow Yuuko begins to lash out irrationally.
Teiichi is trapped inside Yuuko’s memories. As he relives her last days as a human, he feels everything she felt. As Yuuko dies, Teiichi feels something darker being born.
Yuuko and Teiichi are unable to see or hear each other. When he tries to reach her, it causes him pain.
With all the mysteries surrounding her life and death solved, Yuuko is finally whole. For the first time, everything is copacetic. With no regrets, Yuuko now questions if she can remain a ghost or if she will finally cross over.