In 1895 Austria, a princess named Aurora is born to a Duke, who rules over a kingdom of five hills, and his beautiful, yet mysterious wife. After Aurora's mother apparently died, her father eventually remarried. On Easter Eve, Aurora falls mysteriously ill, her body freezes, and she seemingly dies in her sleep. As a result the Duke becomes bedridden, overcome with despair.
The player first takes control of Aurora after she awakens on an altar in the land of Lemuria. She meets and befriends a firefly named Igniculus, who leads her to a sword that she uses to arm herself, and eventually a chamber where the Lady of the Forest is imprisoned. Upon freeing the Lady, Aurora is told of the history of Lemuria. Lemuria was once ruled by the Queen of Light until one night when she mysteriously vanished. From the darkness rose Umbra, Queen of the Night, who sent her daughters to steal Lemuria's light — the sun, the stars, and the moon. The Lady further reveals to Aurora that the two worlds are connected by a mirror that was stolen by Umbra. To be able to use the mirror to go home, Aurora must recover Lemuria's light. The Lady then gives Aurora advice, a flute, and the stars which she had, granting Aurora the ability to fly.
Along Aurora's quest, she is joined by Rubella, an Aerostati jester with a slight word pronunciation problem, who is searching for her brother Tristis; Finn, a young, rather timid Capilli sorcerer whose village is beset by a curse cast by Umbra; Norah, Aurora's stepsister, who was pulled through the mirror to Lemuria; Robert, a Populi trader and skilled in archery; and Rubella's brother Tristis. She further learns through a series of visions that her father's health is declining and a nearby dam has burst, flooding the area. The people of his kingdom seek his leadership to resolve the crisis, but his combined despair and failing health render him unable to guide them.
The party eventually locates the mirror back to Aurora's world at the Temple of the Moon. Upon crossing, Aurora is immediately confronted by her stepmother and other stepsister Cordelia. Norah reveals that she led Aurora into a trap; her mother and Aurora's stepmother is in fact Umbra herself, and Norah and Cordelia are Nox and Crepusculum, the daughters Umbra sent to steal Lemuria's sun and moon. Aurora further learns that Umbra's arch-enemy, the Queen of Light, is in fact Aurora's mother. Umbra attempts to kill Aurora, but Aurora's false crown—a gift from her father—shields her from harm. Aurora is thrown into prison and left to die.
While imprisoned, Aurora has a vision of her mother, who is revealed to have transported her to Lemuria in order to protect her from Umbra. Upon awakening she is joined by Óengus, a Kategida who was exiled when he pledged himself to Umbra in exchange for his clan's lives. The two free the party, but upon leaving the tower they are confronted by Crepusculum; Aurora defeats her and retrieves the moon, causing her to change from a child into a grown woman. She and her friends head to the Cynbel Sea seeking the sun. They are joined by Genovefa, a young sorceress of the Piscean Village, and one of the last of her kind.
After making her way through the Palace of the Sun, Aurora confronts and defeats Nox, regaining the sun. Umbra promptly arrives, enraged at the death of her daughters, but offers Aurora the chance to reunite with her father in exchange for the moon and the stars. Unable to abandon the Lemurians to their fate, Aurora reluctantly tells her father through the portal that she cannot return to him, leading to his death. With the Duke dead, the fake crown protecting Aurora disappears, leaving her vulnerable to Umbra's magic. Severely injured from the attacks, Aurora crawls her way to escape with the sun.
Igniculus, with the help of his firefly friends, carries Aurora to the altar where she first woke in Lemuria. Beside the altar is the Lady of the Forest, who reveals herself to be the Queen of Light. She revives Aurora with the aid of all the Lemurians Aurora helped throughout her journey. With Aurora's renewed powers, she quickly flies the party up into the sky to Umbra's castle, and together, they defeat Umbra.
Through one last vision, Aurora learns that the flood is worsening. With the help of all of her Lemurian friends, she goes through the mirror to her world, arriving on Easter Sunday, and rescues all of the people of the Duke's kingdom from the flood by leading them back through the mirror to Lemuria.