The Phantoms break into Madarame's palace to steal his treasure, only to find it is a trap. Revealing the treasure is the original "Sayuri" painted by Yusuke's mother, Madarame is defeated by the Phantoms and admits his crimes in the real world, increasing the thieves' reputation.

The gang infiltrate Kunikazu's Palace and discover that Morgana has teamed up with a girl calling herself Beauty Thief, who Makoto identifies as Kunikazu's daughter, Haru Okumura. Haru explains that she became a phantom thief and teamed up with Morgana in order to find out the truth behind her father. As Morgana remains defiant about rejoining the others, he gets injured while trying to protect Haru from her abusive fiancee, Sugimura, prompting the others to come to their aid. As Morgana becoming honest about his feelings of wanting to stay with everyone, Haru learns that Kunikazu has decided to speed up her engagement to Sugimura.

The students of Shujin High unanimously vote for Akechi to appear as a guest speaker at the culture festival. Despite the clear danger to this, Makoto follows through with it to gain more information. On the day of the festival, Akechi reveals that he knows of the Phantom Thieves' identities, explaining that he awakened his own Persona while up against the man in the black mask. Offering to help clear their names, Akechi asks for the gang's help in triggering a change in Sae's heart with the group to disband afterwards.

Following a reunion with Arsene, who urges him to remember everything, Ren is captured by the police, leading to his present day interrogation by Sae. As the interrogation draws close to an end, Ren, recalling an important discussion with Morgana and Futaba, asks Sae to show his phone to Akechi as he makes his way towards the interrogation room. After running into Sae and being shown the phone, Akechi reveals his true intentions and shoots Ren, making it look like a suicide.

As news spreads of Ren's alleged suicide, Sae brings a very much still alive Ren back to the LeBlanc to hide. Upon reuniting with Ren, the gang explain that they took advantage of Sae's cognitive world, which had an interrogation room identical to the one in reality.

The politician who was the mastermind behind all of the cases has been successfully reformed by the Phantom Thieves. However, the public’s reaction was not as expected. In order to eliminate the world’s distortion and enforce the justice he believes in, Ren proceeds towards the final battle along with the Phantom Thieves of Hearts.