Ar tonelico takes in the region of Sol Ciel, upon a huge tower that rises above a sea of deadly plasma that swallowed the surface world in a disaster centuries past. This is where the series gets its name: Ar tonelico is the name of that tower. As well as humans, the tower is home to a race of human-like artificial beings named Reyvateils, who can communicate with the tower by singing songs to cast magic.
The story starts in the city of Platina, during an outbreak of enemy creatures called Viruses. The protagonist, a Knight of Elemia named Lyner Barsett, goes to investigate with fellow knight Ayatane, and the tower administrator, Shurelia. Unfortunately, they rapidly discover that the Viruses are able to turn intangible, rendering normal defeat impossible. Shurelia therefore sends Lyner on a quest for the only thing that can help them: the Hymn Crystal Purger. Taking an airship, he travels down to the Wings of Horus, the floating continent that surrounds the tower. More accurately, he crashes thanks to an attack from a dragon, which complicates matters extremely.
In the process of searching for the crystal and a way to repair his airship, he meets and teams up with a number of people, including two Reyvateils. First is the shy Aurica, who healed his injuries after his crash. Second is the more outspoken Misha, actually his forgotten childhood friend. But there’s one problem – Misha looks much younger than she should be. Aside from those two are the wanderer Jack, the local church knight Radolf, and the airship grathmelder Krusche. As the story progresses, Lyner and his comrades not only try to find the Hymn Crystal and fix Lyner’s airship, but discover the reason for Misha’s youthful appearance, and the source of the recent Virus outbreak.