Two worlds exist, unaware of the other`s existence. These worlds survive by competing for the use of mana. The most important beings in these worlds are known as the "chosens". These chosens must go on a journey to awaken the sleeping Summon Spirits, defeating the Desians, and restoring mana. Lloyd Irving and his friends Colette Brunel, the Chosen of Sylvarant, and Genis Sage, the smartest kid in Iselia set off on a journey with Kratos, a mysterious mercenary and Raine, Genis` sister. Along the way, they make more friends and discover the truth behind the World Regeneration. Based on the video game of the same name.
After a big war of that time, much of the mana that keeps the world alive has been exhausted. The world Sylvarant is nearing destruction and can only be saved by the Chosen One, Colette. She then sets off with her teacher Raine and swordsman Kratos on their way to their holy exams in order to help regenerate the world.
On the way to the first seal, Kratos hears suspicious noises one night and is immediately on alert. It turns out they are not attackers, just Lloyd and Genis, who could not afford to leave their friend alone. So they make their way to the first exam, which brings some difficulties.
Lloyd and the others learn from the Renegades that Colette is said to be in the "Nest of Dragons". The "Nest of the Dragons" is a fortress surrounded by storm clouds, which can be approached only with kites or Rheairds. Sheena tries to make a pact with elementalist Volt before the group has a chance against their overpowering opponents.
Lloyd and his companions set out to attack the "Nest of Dragons" and free Colette. However, the fight is harder than expected and the opponents seem to be overpowering. Will they be able to save Colette?
A group of Desians attacks a small village. Sheena tries to reach the attackers, but fails. When Lloyd and the others find them, they forge out a plan to try and fight against the Desians. Then, they come across an unbelievable secret...
The transformation of Colette into an angel progresses piece by piece. Unfortunately, not without consequential damages. Colette suffers more from exam to exam. Slowly, Lloyd, Genis and Raine doubt whether it was right to sacrifice Colette for the benefit of Sylvarant. They decide to save Colette and end up meeting a group that wants to help them.
Sheena tells the group that the medical development in Tethe'alla is more advanced than in Sylvarant, so they may be able to help Colette. Therefore, the group sets out together to Tethe'alla, Sheena's home, to meet the Chosen of Tethe'alla. But there are already new enemies waiting for them. To make matters worse, Colette is also kidnapped...
The group meets a blacksmith and a young girl named Presea. The blacksmith forges special versions of the exspheres, thus bringing them under control. However, the blacksmith is too old to do his job, yet agrees to teach Lloyd. One night, however, a prisoner is handcuffed in front of the house.
Lloyd and his companions can only see one chance to save both the Sylvarant and Tethe'alla: they must unite both worlds and their mana. The group has also gained a little boy named Mithos. Genis makes friends with him and they feel a strong connection. However, Mithos seems to have a dark secret.
Colette was kidnapped by Mithos to retrieve his deceased sister Martell. He plans on using her as an empty vessel for Martell's return. Lloyd and the others want to prevent this at all costs, and to do this they have to fight their opponents at the Tower of Salvation. However, the clock is ticking...
When Mithos realizes that his beloved sister does not want to return, he gets angry and wants to fight again. Lloyd, on the other hand, not only has to face his opponents but also deal with his past. Can the two worlds really be saved from destruction?