In the continent of Polyphonica, spirits materialize in the world, surviving on the music that is played by humans, and live together with them. While the spirits don't appear often, some spirits have enough power to materialize in human or animal forms and live together with humans.Dantists, who play special music called "Commandia," are widely respected in this world. They are usually in contract with powerful spirits. The story of Shinkyoku Sōkai Polyphonica revolves around the new Dantist, Phoron Tatara, the spirit that he made contract with, Corticarte Apa Lagranges, and their friends, in their daily life and work. It also revolves around the feelings of the protagonist (Phoron Tatara) and his contract spirit (Corticarte Apa Lagranges).