The story follows Tohno Shiki, a teenage boy who, after a near-fatal accident in his childhood, gained the mysterious power to perceive lines covering everything around him. When he cuts along these lines, whatever it was immediately falls apart with a clean cut; in other words, killing it. He would have quickly gone insane from living in a world that could fall apart so easily, had it not been for a wandering self-proclaimed magician who gave him a pair of glasses that blocked his unnatural perception when worn.

Soon afterwards, he was disinherited from his family and sent to live with some relatives. For eight years he lived a normal life, hiding his special eyes, until one day he receives a letter inviting him to come back home. Shiki suddenly becomes caught up in strange and life-threatening series of events, ones that are somehow linked to his childhood accident and a forgotten past...

Aya and Hiromi are students at the same nursing school. Aya has known from a young age that she is a lesbian, and when she falls for Hiromi, the two of them end up becoming a couple. Thanks to Aya's influence, Hiromi begins to come out of her shell and stand up to her strict, controlling parents. However, her newfound rebellious streak could spell disaster for their relationship...