A long time ago in the world of Sol Ciel, a great disaster occurred. Because of that disaster now the sky is covered by a shell of plasma called "Blastline", while the land are destroyed and no longer habitable. Those who survived the disaster with the power of the magical tower "Ar Tonelico", create a new place to live. Now Sol Ciel has been reborn as a floating island with the tower of Ar Tonelico in the center of it. However, another disaster occurred as a new hostile creature that are called "Virus" appeared and attack the resident of Sol Ciel. But with the joined forces of human and "reyvateil", a new artificial race with the ability to connect their souls to Ar Tonelico and use "song magic". The virus are defeated and Sol Ciel are saved once again. In order to prevent and prepare for another disaster, a group of elite knights called "The Apostle of Elemia" is formed. Now as a new disaster about to happen again. Lyner Barsett, a young Apostle of Elemia is about to embark on a journey to save the world of Sol Ciel with the help of his friends and the three reyvateils: Aurica Nestmile, Misha Arsellec Lune, and Shurelia. Let the journey begins.