As a child Sakura Mamiya mysteriously disappeared in the woods behind her grandma's home. She returned whole and healthy, but since then she has had the power to see ghosts. Now a teenager, she just wishes the ghosts would leave her alone! At school, the desk next to Sakura's has been empty since the start of the school year, then one day her always-absent classmate shows up, and he's far more than what he seems!

When he was a child, Murakami was friends with a girl he called Kuroneko. One day, while trying to prove the existence of aliens to Murakami, she is killed in an accident that he barely survives. Guilty of his role in the accident, Murokami decides to dedicate his life to proving that aliens exist. Then, one day, a new student with mysterious powers transfers into his class who not only looks a lot like Kuroneko, but is named Kuroha, Neko.