The story begins when the protagonist, a high school student, is transferred to Tokyo after a false accusation of assault. During his probation period at Shujin Academy, he discovers the Metaverse, an alternate world that reflects the twisted desires of people. Along with other students who have been wronged, he forms the group Phantom Thieves of Hearts, aiming to change the hearts of corrupt adults through raids on “Palaces” — psychological versions of reality.

The Royal edition adds Kasumi Yoshizawa, a new character with her own story and Persona, as well as the mysterious advisor Takuto Maruki. It also includes an additional third semester, new dungeons, gameplay improvements, and more social activities. The game combines JRPG battles, social simulation, and psychological storytelling, exploring themes such as freedom, oppression, and personal growth. It is considered one of the most complete and beloved games in the Persona series.