17-year-old Lloyd is a young man who has lost his mother and father at an early age and was raised by a dwarf who adopted him. Together with his childhood friends, Colette and Genis, he sets out on a journey to their world of Sylvarant, which is on the verge of destruction, and restores it to the lush and peaceful world it was centuries ago.

Colette is a member of the Mana Lineage, and holds the key to regenerating the world. Believing that their world will be saved once Colette transforms into an angel, Lloyd and the others surmount countless obstacles. However, Lloyd begins to have concerns about this process as the true nature of their world slowly becomes clear. The regeneration of the world of Sylvarant actually equates to the decline of another world, Tethe'alla, as their fates are intrinsically linked—for one to flourish, the other must be sacrificed. But can this somehow be avoided...?

As Colette gradually loses her humanity and begins to transform into an angel, these sorts of questions become more and more urgent...