Once upon a time, there existed a giant tree that was the source of mana. A war, however, caused this tree to wither away, and a hero's life was sacrificed in order to take its place. Grieving over the loss, the goddess disappeared unto the heavens. The goddess left the angels with this edict: "You must wake me, for if I should sleep, the world shall be destroyed." The angels bore the Chosen One, who headed towards the tower that reached up unto the heavens. And that marked the beginning of the regeneration of the world.

Colette is the next Chosen of Mana to undertake the Journey of Regeneration in order to regenerate the dying world of Sylvarant. On the Day of Prophecy, Colette receives the oracle at the Martel Temple and thus began her journey to heaven. Together with her two childhood friends Lloyd and Genis, her teacher Raine and the mercenary Kratos hired to protect her, they set off on a journey to regenerate the world.