After losing his sister seven years ago, Satsuki Kakeru led a vacant life, only able to return to his normal days with help from his childhood friend Minase Yuka and other friends at school.
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: Kusakabe Misuzu, a red-haired onmyouji swordswoman, Tachibana Kukuri, a strange mute girl who looks like Kakeru's deceased sister, Hirohara Yukiko, a lively young girl who reverts to the personality of a cold killer when her glasses are removed, and Tajima Takahisa, a young pyrokinetictist 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 once and for all.
Along the way, Kakeru receives a strange note saying "You are the reason the demon has awakened." This note and "the demon" does not come up again until much later in the series.
They manage to defeat four of the six Black Knights, while revealing their pasts.
Takahisa was abandoned by his parents because of his abilities as a pyrokineticist, and the school nurse (Saiko) took him in. the Kusakabe are a clan of magic users and sword fighters; Misuzu is both of which. Yukiko was raised to be a human weapon from her earliest years so that she could fight in a war in a far off country until her grandfather in Japan took her in, and she falls in love with Takahisa. Its revealed that Kukuri has no memories of her past. Kakeru's other eye is revealed to be the fabled Eye of Aeon, able to see into the future for instants.
A history of the Eye of Aeon is also revealed. It once belonged to an ancient Drasuvanian king, Velad. According to legend, Velad was tricked by a witch; at this statement the girl in the crystal is instantly mentioned by one of the characters.
A black knight known as Superbia is later revealed to have once been a woman named Misao; an exiled member of the Kusakabe clan, and a transfer student turns out to be a member of a society of mages, and a fragment as well.
After Takahisa is tragically killed (this happening after he nearly destroys the city in a mad rage, caused by Saiko's being killed by Superbia the black knight) by Yukiko because he lost control of his powers, the reason for everyone's being referred to as "fragments" and the reason for the girl in the white dress's imprisonment is revealed. Their powers come from fragments located inside them. These are the fragments of the Voidstone; the lost source of power for the captured witch. The captured witch is also the witch said to have tricked Velad; Liselotte. But in truth, she was in love with Velad, and their kingdom was at war. Seeing the carnage, Velad (whom is also the original owner of the Eye of Aeon) felt that the world was a pointless void of chaos, and said that it should just be destroyed. Liselotte responded by saying that the entire world could come to an end, so long as she had Velad.
Later on, Velad was assassinated, and the blame was pinned on Liselotte. In rage and anguish, she dedicated her life to causing the "Hellfall" and ending the world. She is also the source of all of the major eras of turmoil in history. The society of mages fought her time and again, until six mages used forbidden magic to strip her of her magic and memories while sealing away what was left (Lisette) in another world. The reason the magic was forbidden in the first place was the terrible cost: the spell casters would be forced to take on hideous forms. The six spell casters then became the Black Knights.
Unaware of her past and in a world where she wouldn't age, Lisette bided her time until the fragments were gathered in one place, and she could bring them into the parallel world that was created in the spell: the Red Night. The Black Knights quickly came to the conclusion that killing the fragments would stop any chances of Lisette escaping forever, and took on the initiative to kill them.
Now Kakeru and his few remaining friends must find a way to stop Liselotte's resurrection that doesn't involve them getting killed.