Oga Tatsumi is a first year student in Ishiyama High, a notorious school for delinquents. One day he sees a man floating by, and the man suddenly splits in half to reveal a baby boy inside!.

Shiki Tohno is a boy who, after an accident as a child, is able to see strange lines coming from objects and people. He has to wear special glasses to stop seeing them. If he cuts some of these lines, he destroys people connected to them. One day he meets a woman called Arcueid and together they start a journey that's going to reveal some secrets of his past.