Five supernatural factions have been fighting against each other for who knows how many centuries, with the beginning of Aquarian Age always in mind. Kyouta, soon begins to see visions of mystical girls fighting, except they do exist. Soon he and his girlfriend Yoriko become involved and the battle for Earth and Aquarian Age lies in their hands.

Life could be better for shy, anxious university student Rin. The apartment she has rented is hardly the sunny palace the rental listings suggested. The housing complex is rundown, grim and haunted by troubled souls lurking in dark corners. Ghastly crimes are occurring in the vicinity. And a grinning stranger makes his unsettling presence known. Beyond all this, Rin is coming to realize that something even more sinister is manifesting itself, something at the cursed crossroads of mythology, monstrosity and medical science. Determined to find out more, Rin visits the library, where she meets a sympathetic young staffer. But what she learns does not begin to put her mind at ease.

Based on the RPG game of the same name. Aurica Nestmile is a young Reyvateil, or "singing maiden" who feels her song magic is not of much use to anyone. From high up on the tower Ar Tonelico comes Lyner Barsett, whose airship is totaled upon impact with the ground. These two meet up, and in the search for someone who can repair the ship, end up helping both each other and themselves.