11eyes begins with Satsuki Kakeru and his best friend Yuka Hasebe being thrown into the Red Night, a strange and hostile parallel world where the sky turns red, the moon turns black, and monsters roam empty streets. Cut off from everyone else and given no clear explanation for why they have been taken there, the two struggle to survive while trying to understand the rules of this unsettling place. When the nightmare briefly ends, Kakeru and Yuka are left wondering whether it was all a dream—until the Red Night returns and leaves them trapped in a far more dangerous situation.
As the threat closes in, they meet four others caught in the same predicament: Kusakabe Misuzu, an expert swordswoman; Tachibana Kukuri, a quiet mute girl who looks uncannily like Kakeru's deceased sister; Hirohara Yukiko, a lively young girl whose personality reverts to that of a cold killer when her glasses are removed; and Tajima Takahisa, a young pyrokineticist. Forced to rely on one another, the six band together in search of answers, only to discover that the shadows watching them are as dangerous as the world itself.