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.

Nina, a wyndian princess, and her guardian Cray are searching everywhere for Nina's missing elder sister, Elina. While traveling to her last known whereabouts they suffer an accident. On her way to a nearby town, Nina meets Ryu, a seemingly amnesiac young man. This meeting triggers a series of events that will involve them with the godly race known as The Endless, immortal dragons with the power to shape the world itself.

Closely follows the storyline of the original game.

From Bliss:

One day, Kunisada Haruichi who is specializing in Japanese dance in his high-school dance department, meets Yuri Arbatov, a famous and young ballet dancer who comes for a short-term study abroad. However when he gets a hold of Haruichi's weakness, Haruichi is forced to crossdress on stage...