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.

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.

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.

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.