Suddenly one day the sky turns red and the moon turns black. Everyone around Kakeru and Yuka disappear and monsters start roaming the streets. They are only able to run away and hide and after a while, the world returns to normal. But just when they thought this world was a dream, the Red Night occurs again.
Kakeru and Yuka manage to find four other humans involved in this mysterious phenomenon: Misuzu Kusakabe, a red-haired onmyouji swordswoman, Kukuri Tachibana, a strange mute girl who looks like Kakeru's deceased sister, Yukiko Hirohara, a lively young girl who reverts to the personality of a cold killer when her glasses are removed, and Takahisa Tajima, a young pyrokineticist with a heated attitude to boot.
They get together and try to survive, but six shadows suddenly appear in front of them....
These six shadows call themselves the Black Knights, and for an unknown reason wish to kill Kakeru and friends. The teenagers wind up coming across a girl with flowing silver hair wearing a white dress, trapped in a red crystal. Her name is Lisette. She claims that she is being held captive and asks for their help. The Black Knights prevent them from doing anything and begin referring to Kakeru's friends as fragments and to Kakeru as "the bearer of the Eye of Aeon". As they go on trying to survive, the six teenagers gradually form bonds and begin to work together in order to defeat the Black Knights, in the hopes that this will end the Red Night (phenomenon) once and for all.