While under arrest, Ren Amamiya aka Joker, the leader of the Phantom Thieves recalls recent events, starting with his arrival in Tokyo and a fateful encounter with his new PE teacher.

After escaping Shadow Kamoshida, Ren returns to school and learns that Kamoshida is abusing students. Later, he and Ryuji return to the Palace, where they meet.

Ann joins the team after her friend Shiho jumps from the school roof as a result of Kamoshida's abuse. In an attempt to expose Kamoshida's Treasure, the Phantom Thieves leave.

The gang confront Shadow Kamoshida, who transforms into a powerful monster hell-bent on protecting his Treasure. To steal it and expose his crimes, Ren creates a new Persona.

Set on changing more twisted hearts, the Phantom Thieves enter Mementos, a Palace for the general public that Morgana has a mysterious connection to.

Yusuke, a student mentored by renowned painter Madarame, asks Ann to pose for a piece. Later, the Thieves learn Madarame is plagiarising work.