Ar tonelico Qoga: Knell of Ar Ciel is set two years after the happenings of Ar tonelico II: Melody of Metafalica and takes place in the Sol Cluster. The player controls Aoto who witnesses the murder of an old man by Clustanian soldiers, the faction in power of the region. A girl named Saki survives the assault and turns out to be a Reyvateil, basically the game's version of magically gifted persons. Now Aoto takes care of her, flees from the hostile soldiers and tries to find out the reasons for their hostility.