The region of Metafalss surrounds the second Tower of Ar tonelico, which is said to represent the Goddess Frelia of the Trio of Elemia. Reyvateil in this region have been succumbing to a raging Reyvateil-exclusive epidemic called the Infel Pira Dependency (I.P.D.). Croix, a Knight under the Grand Bell Church of Pastalia, is sent to find the source of the problem and contain the epidemic. There is more transpiring in this region than just the epidemic, however, and one mission will throw him into an adventure to unravel the mysteries of the planet Ar Ciel and seek out a legend handed down by the people of Metafalss: the lost Hymn of Metafalica.

A mysterious disease is spreading amongst the reyvateils, causing them to go berserk. The key to stopping them lies in the hands of Espada Reid. The only problem is: he hates reyvateils. Will he be able to overcome his feelings and stop the reveris illness?