Framed for assault a young Ren Amamiya is on probation and exiled to a caretaker in modern-day Tokyo. On probation for a year to ensure his freedom, the pressure is on for Ren to keep a clean record. This all goes south pretty quickly and by his first day of school Ren and local degenerate Ryuji Sakamoto as they get transported to an alternative world where all peoples prevented desires come to fruition.
In this place they are held captive by a corrupted version of the schools Gym teacher who has a sordid past and present. Upon the teacher beating on Ryuji, Ren unleashes his inner power, known in this world as a Persona and takes the name of Joker. He then uses this power to get Ryuji out of there and is aided by the mysterious cat known as Morgana.
Morgana tells Ren about his Persona and that Ryuji has similar power, Ryuji unlocks his Persona when he sees members of his old track team and volleyball team being regularly abused. Morgana tells the pair that the only way for the teacher to repent is to steal their treasure, where the corrupted souls will be purified and will be made to repent.
From there, the Phantom Thieves are formed and venture towards justice.