Ar Tonelico takes place in the world of Sol Ciel, a small world consisting of nothing more than a tower and a floating continent. This small world is isolated by the Sea of Death below and a deadly sea of plasma above. The game also features a rare group of people called the Reyvateil, which, through the power of Songs, can converse with the world and cast powerful magic. However, in order to cast more powerful magic, they have to take a harmful material called Grathnode into their bodies, through an act called Install. Since the Install is a very painful experience for the Reyvateils, they only let people that they really trust to do it. The story centers on Lyner Barsett, an eighteen-year-old whose father governs Platina, a town located in the top floors of the tower. Lyner is uninterested in politics, and instead seeks adventure in the army. However, when a strange virus appears and they can't defeat it, Lyner is assigned the task to go down to the floating continent and retrieve a mystical artifact to defeat the virus.
A mysterious epidemic called Infa Pira Dependency (IPD) has been driving Reyvateils insane and killing them at the floating island of Metafalss. Croix, a young knight from the Church of Pastalia, is sent to contain the epidemic. However, many more challenges await, which lead him to unravelling the mysteries of the planet Ar Ciel and seek the legend handed down by the people of Metafalss: the lost Song of Metafalica.