Ar Tonelico 3's story unfolds on another tower located in the same world as Ar Tonelico and Metafalss, the towers that provided the settings of the two prequels. On the third tower, Sol Cluster, a ruling regime of Reyvateils oppresses humans as lower-class citizens. The protagonist is a young construction worker by the name of Aoto. He has never liked the Reyvateil nation of Clusternia, and when he encounters an amnesiac Reyvateil named Saki who is being pursued by them, this animosity turns into outright hostility. The two are joined in their escape by another Reyvateil, Finnel, who possesses a secret and accompanies them for reasons of her own.