After high school student Ren Amamiya gets in trouble with the police, he’s labeled as a juvenile delinquent. As part of his probation, he is forced to start living with Sojiro Sakura, a stranger who agreed to take him in. While walking to his new school Shujin Academy, Ren becomes lost in another world…

Ren begins his new school life, but it's tough being a transfer student, especially when he comes with seemingly shady baggage. He meets Ryuji, a classmate who's similarly isolated, and they use a mysterious app to enter a world in which their gym teacher, Kamoshida, is a sadistic king.

The members of the volleyball team are terrified of the tyrannical Kamoshida's irrational violence. Meanwhile, Ren's classmate, Ann Takamaki, has been protecting her best friend from being cut as a regular player on the volleyball team, but she's at a loss as to what to do about the persistent approaches of Kamoshida, who lusts for her with his twisted desires.

The first heist of the Phantom Thieves of Hearts is underway, as the group sends Kamoshida a calling card, threatening to steal away is twisted desires. Ren and the gang begin prepping for their dangerous delve into the cognitive world, and encounter a couple potential allies in the process. Will they be successful in taking the terrible King Kamoshida’s precious Treasure?

After safely changing Kamoshida’s heart, Ren and friends decide to continue changing the hearts of selfish, clueless adults. And no sooner are the "Phantom Thieves of Hearts" established than a fan website springs up, soliciting requests from troubled teens who want the heart of an adult in their life changed.

Yusuke Kitagawa, an arts student studying under painter Ichiryusai Madarame, asks Ann to be the model for his next art piece. Meanwhile, student council president Makoto Niijima grows suspicious about Ren's group of friends. Noticing comments on the phansite about Madarame plagiarising artwork from his pupils, the gang go to Madarame's studio to talk with Yusuke, who shows nothing but admiration for him. Initially assuming they were mistaken, the gang discover that Madarame has his own Palace, where they learn he intends to plagiarise Yusuke's work just like his other pupils. While Yusuke claims he is letting Madarame use his work willingly, the gang learn the full extent of Madarame's crimes from one of his former disciples, along with Yusuke's true feelings.

Needing to change Madarame's cognition to further access his Palace, Ann distracts Yusuke while Morgana access Madarame's secret room, exposing his plagiarism of his most known piece, Sayuri. After inadvertenly following the others into the Palace, Yusuke learns that Madarame was responsible for the death of his mother, leading him to awaken his Persona, Goemon.

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.

While waiting for their next target, Ren tries out a dubious-looking maid service, discovering that his homeroom teacher Sadayo Kawakami is secretly working as a maid. Noticing Ryuji being bothered by his former track teammates, Ren asks Kawakami for the details about what happened between him and Kamoshida. Learning that the new track team advisor, Yamauchi, has been manipulating the players by leaking rumors to them, Ryuji learns to control his temper and make peace with the team.

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.