The story of Atelier Iris 2: The Azoth of Destiny follows Viese and Felt, two orphans from the land of Eden. At the beginning of the story an earthquake has caused vast portions of the land to disappear. Viese and Felt have volunteered to find out what has happened and to prevent the world of Eden from being destroyed completely. With the aid of a magical sword called the Azure Azoth, Felt sets off through a gate to another world called Belkhyde to search for the answer to their trouble while Viesa remains in Eden to take care of things there.