During a class excursion to a television station, the gang spectate an interview with police detective Goro Akechi, who claims that the Phantom Thieves' ability to change hearts could be used for evil. Later, Makoto learns of the Phantom Thieves' identities and blackmails them with a recording, stating she will only delete it if they can change the heart of a crime sindicate boss who has involving students. Meeting up with reporter Ichika Ohya, Ren learns the boss' name, Junya Kaneshiro, which leads the gang to his Palace; a bank flying above Shibuya.

As the thieves find they cannot get into the Palace while it's in midair, Makoto, wanting to prove herself useful, uses herself as bait in order to lead the gang to Kaneshiro, who blackmails them with an incriminating photo. Now considered a customer in Kaneshiro's bank, Makoto accompanies the others to Kaneshiro's Palace where she awakens her Persona, Johanna.

While making steady progress through Kaneshiro's Palace, Makoto manages to become closer with the rest of the team. With the route to the Treasure secured, the Phantoms confront Kaneshiro's Shadow, taking advantage of his weakness of money in order to defeat him. Before the Palace is destroyed, Kaneshiro informs the Phantoms about a man in a black mask who is able to enter Palaces.

Finding himself in an art slump, Yusuke asks Ren to be his bodyguard while he draws inspiration from Mementos, only to receive harsh criticism on his piece. Meanwhile, Akechi asks for Ren's help in finding evidence against an art dealer named Akio Kawanabe, who he believes is into some shady practices. As Yusuke manages to get out of his slump thanks to encouragement from his friends, Ren discovers that it was Kawanabe's assistant committing crimes, allowing Akechi to arrest him. Receiving praise for his new piece, Yusuke declines Kawanabe's funding in order to pursue his own hope.

While looking around Shinjuku with Ren, Makoto spots a fellow student named Eiko working at a dubious looking café, becoming friends with her due to their similar taste in goods. Worried about Eiko being scammed by her host boyfriend Tsukasa, Makoto tells Ren about her late father, who was a police officer, and asks for his help. Managing to expose Tsukasa's lies to Eiko, the Phantoms defeat his Shadow in the Metaverse, while Makoto aspires to become a police officer like her father.

As a mysterious hacker group known as Medjed issue a public warning to the Phantoms, Ren is contacted by someone known as Alibaba, who threatens to reveal the Phantoms' identities unless they can change the heart of someone named Futaba Sakura. When asked to meet in person, Alibaba suddenly calls off the request and asks the Phantoms not to look into Futaba any further. Learning that Futaba is a relative of Sojiro, who is under pressure from Sae concerning his parental authority of her, the gang, receiving a threat from Medjed that they will attack Japan if their identities are not revealed by 31st July, go to Sojiro's house and come face to face with Futaba.

After Sojiro catches the group sneaking into his home, he explains how Futuba's current situation as a shut-in stems from witnessing her mother Wakaba seemingly commit suicide, and how a few months prior started imagining hallucinations. Although he pleads with them not to involve themselves into Futaba further, the gang decide to help and change her heart after discovering she has a Palace. Visiting Futaba as the school holidays commence, they learn that she sees her home as a tomb and that she will die. The group infiltrates Futaba's Palace and become aware of her deteriorating mental state. After finding their way blocked by the same door to Futaba's room, the group return to reality and convince her to invite them inside. After some more persuasion, Futaba opens up and directly asks the gang to change her heart.

Gaining access to the core of Futaba's Palace, the Phantoms are confronted by a monstrous cognition of Wakaba. As Futaba manages to enter the Palace herself, her Shadow encourages her to remember Wakaba's love for her, leading Futaba to realise that Wakaba's suicide note was faked by people after her research on cognitive psience. Gaining the Persona Necronomicon as a result, Futaba use its supportive abilities to help the Phantoms defeat the monster. After putting a stop to Medjed as promised, Futaba asks for Ren's help in finding out who killed Wakaba and stole her research.

With Futaba now a part of their team, the gang try to help her improve her social skills by taking her to the beach. Futaba then explains what she learned about Wakaba's research on cognitive psience, leading the gang to believe it is related to Palaces, mental shutdown cases, and the man in the black mask. As Mementos expands with the Phantoms' increasing popularity, Morgana becomes uncertain over whether he is really human while Ann is troubled with problems with her model work.

Needing information to help search for the culprit behind the mental shutdowns, the gang ask Makoto to extract data from Sae's laptop. The next day, everyone goes on a school trip to Hawaii, where Ren comes to the aid of shogi player Hifumi Togo. Meanwhile, Shujin High School's principal, Kobayakawa, is killed after suffering a mental shutdown and walking in front of traffic. Sae's investigation data leads the gang towards Kunikazu Okumura, whose company allegedly stood to profit from those who died from mental shutdowns. Despite Kunikazu having a Palace, the group becomes split over whether they should rush into pursuing him. Deciding to infiltrate the Palace on his own only to run into trouble, Morgana is saved by a certain girl.

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.

Wanting to change Kunikazu's heart before she is forced to move in with Sugimaru, Haru decides to help the Phantoms progress further into his Palace, awakening the full power of her Persona, Milady. Upon locating the Treasure, the gang confront Kunikazu's Shadow and defeat his army of robotic employees. After the Phantoms are forced to leave the Palace before it collapses, a mysterious figure kills Kunikazu's Shadow. Unaware of this, the gang become shocked when Kunikazu suddenly dies of a mental shutdown during a press conference.

As public opinion of the Phantoms plummet following Kunikazu's death, Haru learns of a fake calling card placed in Kobayakawa's office, leading the gang to realise that someone set them up. As Sae is put in charge of investigating the Phantoms, Futaba deduces that someone had imitated Medjed and hacked the Phansite to make the Phantom Thieves more popular on purpose. Later, Ann calls Ren to meet up with her and Shiho, who thanks them for saving her life and reminds them of why they became Phantom Thieves in the first place. Afterwards, the gang, upon discovering Mishima has become too obsessed with the fame he received from the Phansite, find his Shadow in Mementos, choosing not to destroy him but instead urge him to think things through for himself, helping the real Mishima find the right path as a result.

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.

As the gang try to figure out a way to reach the top floor of Sae's casino Palace, Soujiro, who discovers a calling card in Futaba's room, is under pressure from Futaba's uncle, who is demanding that he pay him money or else give up custody of her. Ren gets Akechi's help to dig up dirt on the uncle, only for him to accuse Ren of pushing him. When government officials come to question Soujiro, Ren and Futaba manage to assure them that Soujiro is a good guardian, after which they come clean to Soujiro about being Phantom Thieves.

Needing an excessive amount of coins in order to access a bridge to the Treasure, Ren wins the money in a coliseum battle. Sae raises the bridge's fee, but Akechi manages to make use of a loop hole in the casino's charge card system to obtain the full amount and access the bridge. After the gang manage to defeat Sae's Shadow, enemies surround the Palace, prompting the gang to split up and find their way out.

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.