Four thousand years ago, a great war raged. In time, it became known as the Kharlan War, and it caused the Kharlan Tree, the source of mana, to wither and die, limiting the amount of mana in the world. The fighting stopped when the hero, Mithos, sacrificed himself upon the spot where the tree once stood, bringing about a peace to the two warring factions. A great tower was built upon Mithos' grave by the angels, and the Goddess, Martel, became distraught at the death of Mithos. She left the angels with a message: "You must wake me, for if I should sleep, the world shall be destroyed." The angels bore the Chosen One, who climbed the Tower of Salvation in hopes of waking the Goddess. This is the first World Regeneration, as passed down through the generation.
Colette Brunel, the current Chosen of Regeneration, embarks on a journey, leaving a will-like letter behind for her life-long friend Lloyd Irving. He and Genis Sage, another friend and an elf, track her down and join her after being banished from their village. Little did they know that, by doing so, they would change the course of the world as they knew it… After learning the truth of the Regeneration journey, Lloyd and the others with him learn of another world parallel to theirs that fights with Sylvarant for mana, known as Tethe'alla. They travel to Tethe'alla and, after a series of discoveries that astound them, learn that the two worlds were once one, and the legend that they all took as truth… was anything but…
