Persona -trinity soul- takes place ten years after the end of Persona 3. It is set in Ayanagi City, a city located near the Sea of Japan, and its police force begins to investigate several cases involving a mysterious illness called the Apathy Syndrome.

In the midst of the crisis, two brothers named Shin and Jun Kanzato move back to Ayanagi to see their elder brother Ryō, who is now the Superintendent of the Ayanagi City Police. It has been ten years since the three siblings last met with each other.