The story is a continuation of the events depicted in the game Persona 4 Arena and begins the day after it concludes. The Midnight Channel is back on the air and once again broadcasts a strange advertisement for another fighting tournament christened P-1 Climax, that shows members of the Investigation Team and the Shadow Operatives in combat. Just moments after this, Inaba is subject to a power outage and is engulfed by a bizarre red fog.

Ren Amamiya is about to enter his second year after transferring to Shujin Academy in Tokyo. Following a particular incident, his Persona awakens, and together with his friends they form the “Phantom Thieves of Hearts” to reform hearts of corrupt adults by stealing the source of their distorted desires. Meanwhile, bizarre and inexplicable crimes have been popping up one after another…