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 Rinne Rokudo shows up, and he's far more than what he seems. After school one day, Rinne helps Sakura deal with the ghost of a boy who has a crush on her. Rinne it seems, knows just how to handle such ghosts, and has the skills and tools to properly dispatch them to the aftelife.

Sakura starts to learn more about her mysterious classmate, and her curiosity about Rinne draws her deeper into the amazing world between life and death.