In the world of Sol Ciel, there is only a lone Tower and a small floating island. Between the Sea of Death below and the Blastline above, this small world in the sky is isolated by poisonous clouds and deadly plasma. Thanks to the Tower of Ar tonelico, a legacy left behind by an ancient civilization, life was peaceful. Long ago, when this world still had its land and skies, people built a great civilization with the help of their goddesses, the Trio of Elemia.

But now, two forces are striving to fulfil their goals, the Elemia Church, who want to rebuild the utopia by resurrecting the Trio of Elemia, and Tenba, a conglomerate who plans to use advanced technology to revive the lost civilization, and its secrets.

The player takes the role of a young adventurer who dislikes his fathers politics and instead seeks to serve in the world as a Knight.