Seven years ago, Kakeru Satsuki lost his only family left after witnessing his sister's suicide, and ended up at an orphanage. Now in high school, everything seems to be going well for Kakeru. Until one day, during an outing with his best friend Yuka Minase, the sky suddenly turns red and everyone besides them disappears. As monsters start chasing them, death seems imminent—but the world inexplicably turns back to normal just in time.

The very next day, the same nightmarish event dubbed as the Red Night takes place, but Kakeru and Yuka are saved by their senior, Misuzu Kusakabe. The trio soon discovers that a girl imprisoned in a crystal is seemingly behind it all. Moreover, more people from their school are involved, each with their own struggles. To protect Yuka, Kakeru must get stronger and join forces his peers to end the Red Night for good.

11eyes is an adaptation of the visual novel 11eyes: Tsumi to Batsu to Aganai no Shoujo, developed and published by Lass.