For the sake of convenience, the Player Character will be referred to by his "official" name from the anime adaptation and Dancing in Starlight, Ren Amamiya.
This page contains unmarked spoilers. Read at your own risk.
As Joker continues fighting and with an endless swarm of Shadows closing in on him, Joker summons his Persona, Arsene, to vanquish them.
The game jumps back a few days before all this began.
In an unspecified police station, detectives from the Tokyo Metropolitan Police, including Zenkichi Hasegawa, struggle to identify the cause of recent incidents involving the unspecified, abrupt mental personality changes of notable high-profile figures. Noting the similarities to cases about half a year ago by the Phantom Thieves of Hearts, the detectives are instructed to immediately begin investigating the Thieves starting with Ren Amamiya, the civilian identity of "Joker" and a familiar face to the police, having turned himself in to the police several months back.
Elsewhere, the Phantom Thieves of Hearts - now retired due to the loss of the Metaverse and their Persona abilities with it - reunite in Cafe Leblanc to start their month-long summer vacation together. Much has changed since their last time as a group together six months ago: their former leader Ren Amamiya and their acting guide Morgana have returned to Tokyo from Ren's hometown to celebrate the holidays with their old friends. Ren and fellow batchmates Ryuji Sakamoto, Ann Takamaki and Yusuke Kitagawa are now high school seniors, their senpai Makoto Niijima and Haru Okumura have entered their first year of college - the latter still attending to her duties as heiress to Okumura Foods, and their youngest member Futaba Sakura has since returned to school on a full-time basis.
Once more congregating in the same attic space in Leblanc that Ren called his home for the better part of the previous year, the teens spitball ideas on how to spend the coming month together, eventually settling on a camping trip outside the city. To help with preparations, Futaba suggests that they use EMMA, a new app that provides suggestions based on voice commands. EMMA points to shops within the Shibuya area for supplies, and the team split up to gather everything they need.
When Ren falls asleep that night, he unexpectedly awakes in the Velvet Room. Lavenza greets him instead of Igor, and she explains that a new calamity is nearing, making him "a prisoner of fate" once again. Even if she is unable to give him details about what is happening, Lavenza asks for Ren's help to defeat this new unknown menace, and Ren accepts the request.
The following day, near the Shibuya crossing, Ren, Morgana and Ryuji happen upon a store opening hosted by fashion designer Alice Hiragi. As a way to further promote her brand, she passes along several cards to the men in the crowd - Ren included - with instructions on how to be her friend through EMMA: by giving the keyword "Wonderland". The trio decides to see this for themselves, only to be shocked when they find themselves in a distorted copy of Shibuya decked out in their old Phantom Thief gear and with Morgana back in his original form. With hostile Shadows converging in on their location, the group is forced to fight back, but the numbers advantage proves to be too strong, and they are captured to be brought before Alice's Shadow, the self-proclaimed "Monarch" of her "Jail."
After toying with them, Shadow Alice disposes of the trio in an abandoned dump. As they try to find a way out, Ren happens upon a box containing a young girl named Sophia, who describes herself as "humanity's companion." Despite her unusual appearance, Sophia proves to be a valuable ally in their escape; not only is she capable of fighting alongside her "Persona" Pithos, but she is quick in pointing out an exit back to the real world. The boys return back to the real Shibuya, with Sophia instead manifesting herself within Ren's phone due to her real nature as an A.I. program. They call another meeting in Leblanc to explain their situation and introduce Sophia to them, now believing that another mystery only they can solve was afoot.
Recalling how the Shadows seemingly attacked normal people within the Jail and comparing them to the bizarre behavior Alice's fans display, the Phantom Thieves theorize that Alice is using EMMA to steal the Desires of her fans, making them slavishly devoted to her. Ren and Ann also learn of a twisted side to Alice while attending a TV interview featuring her, when she causes one of the hosts to publicly confess his affection for her in a scandalous manner and later berates her manager behind the scenes, even going so far as to physically step on him. While unsure of how this new "Jail" compares to the Palaces they once took on, the Phantom Thieves agree to quickly infiltrate it to stop Alice's wrongdoings, with Ann taking a more personal stake in the matter; having looked up to Alice and knowing that she wanted to be a role model that others could follow, Ann hopes that their infiltration will bring back that side of her.
Eventually, the Thieves hit a roadblock and decide to withdraw for the day in order to rest and form a plan to get past it. However, on their way to Leblanc, they're accosted by a drunk, who tries to hit on Ann. Before things can escalate though, Zenkichi Hasegawa shows up, and diffuses the situation (albeit to mixed results) before introducing himself to the Phantom Thieves. Understandably, the Thieves are all mistrustful of him, due to both his shady behavior and his affiliation with the police. He reveals the police suspect the Phantom Thieves of the recent change of heart incidents, but that he personally believes in their innocence. However, with no evidence that they're not responsible, the rest of the police might try to target the Thieves if they can't find anything else. Thus, he proposes a deal with the Thieves, they help him get to the bottom of the case and find out who's truly responsible, and he'll make sure the police don't arrest them. The Thieves are hesitant to take him up on the offer, so he leaves them so that they can think about it.
As the Phantom Thieves explore the twisted "Wonderland" of the Shibuya Jail, pieces of Alice's past are exposed to them, revealing her as a passionate designer who wanted to escape the social abuse that plagued her. The sudden arrival of inspector Hasegawa yields the complete truth through information reluctantly obtained from him: Alice was once a student at Shujin Academy - a social outcast constantly bullied by others. Upon having a crush of hers lost because of these bullies' actions, she ended up copying their methods in return, hence her targeting married men for reminding her of the trauma she faced. Despite knowing of her situation, the Thieves agree that her actions must come to an end, and with their trademark calling card, publicly hijack the Shibuya crossing once again to announce that they are coming for Alice's heart.
The Phantom Thieves storm the Jail's castle, ready to confront Shadow Alice; unwilling to yield the influence she holds, she transforms into a large, monstrous bunny girl to defend her stolen Desires. However, the power of the Thieves' Personas proves too much for her to handle, and she is forced to accept defeat. With Ann making a sincere plea to return to being a model for others, Shadow Alice willingly gives up control of her crown, and with it, her castle collapses as the Desires of all her targets are released back to the real world, but the Jail itself still remains. Outside the Metaverse, Alice publicly confesses to her crimes in another studio interview, but unlike the Palace owners of the previous year, she made an earnest announcement to change her ways and atone for her past behavior. The Thieves' first infiltration back concludes successfully, but questions remain about how Alice could have used EMMA to wield such influence to begin with.
As the Thieves are meeting in Leblanc after the confession, Zenkichi meets them to hear their answer about his deal, pointing out that they're not exactly off the hook yet, since there are change of heart incidents all over the country that are still unaccounted for that the police still suspect the Phantom Thieves for, especially now that their calling card proved that they're still active. In light of this new information, they reluctantly decide to take Zenkichi's offer and tell him about the Jails. Naturally, Zenkichi is initially skeptical of the Metaverse, so they decide to show him the Jail. After recovering from the shock of learning about the supposed "other world", Zenkichi asks that the Thieves make their way to Sapporo to investigate a potential change of heart incident there, giving them till August 8th to travel, since the suspect for that incident is out of the country and that day is when they will return. Moreover, he asks that the Phantom Thieves avoid using public transportation, since there remains the potential threat that a Monarch might cause an accident to try and get rid of them.
As the Thieves meet up that night, they discuss the Jails, where they come from and how they are different from Palaces. Futaba finds nothing suspicious with the EMMA app itself, and there is no concrete proof that Madicce, the company distributing EMMA, is behind the Jails. An investigation into Alice's smartphone reveals nothing special that would let her create a Jail, but they do find that her phone was bugged by someone in Japan, implying the presence of a greater mastermind watching from behind the scenes. As for their means of transportation to Sapporo, the Thieves ask Sojiro to borrow a camper from a friend for them to use, reasoning that they are probably going to be traveling all over Japan, and that it will allow them to find Jails along the way. thanks to Sophia revealing that she can detect Jails as long as she's close by. Thus, the Phantom Thieves set out on a road trip to potentially save the world.
Traveling along the highway, the Phantom Thieves try to make the most of their trip to Sapporo while being on the lookout for Jails. As the Thieves approach Sendai to stop for the night, Sophia detects a Jail in the city, prompting the Thieves to set up camp in Aobayama Park. To investigate who the potential Jail Monarch might be, they approach the statue of Date Masamune, hoping that a popular tourist spot might yield helpful rumors (and to appease Yusuke). There, they find the base of the statue vandalized with posters advertising the light novel, "Prince of Nightmare". Afterward, they visit a popular ox-tongue restaurant for dinner, where Morgana (who unfortunately has to hide because the restaurant doesn't doesn't allow pets) ends up attracting the attention of an odd woman, a Toudou University researcher named Ichinose Kuon, who keeps Morgana a secret, but ends up talking the group's ears off. As the Thieves leave the restaurant, they encounter a crowd worshiping Natsume Ango, the author of "Prince of Nightmare". Natsume notices him and ends up unsuccessfully trying to woo Haru, which leads to rising tensions between him and the Thieves, but nothing comes of it due to Natsume having to leave for a magazine interview. Suspicious that a man such as him could be so popular, they research him on the internet, finding that his book is unnaturally popular, and his fandom is rather berserk, which raises suspicions that he's the Monarch of the Jail in Sendai. They resolve to investigate further the next day in order to confirm whether his popularity could have come from changing hearts.
After some investigation, they regroup at the bookstore, where Natsume is holding an autograph event. They don't find out his keyword, due to what the Thieves assume to be the fact that he didn't really need to spread his keyword since most of the attendees are already fans, but Yusuke picks up a copy of his book, in order to determine if it's really as good as his fans claim. However, he feels that the book is missing the passion that a content creator would normally put into their work, and Futaba confirms that most of the book is made up of ideas that were plagiarized from other works of fiction, lending weight to their suspicions that Natsume is the Monarch. Yusuke, in particular, ends up asking why a content creator would ever be content with making plagiarized works that don't convey the creator's true self. In order to learn Natsume's EMMA keyword, they end up consulting Zenkichi, who confirms that there's something suspicious about Natsume, and and that he's managed to secure invites to a sales party for Natsume's book, where they can hopefully get the keyword from the man himself.
At the party, they find Natsume mingling with the VIPs, where he makes several comments about how he's selling the book that are similar to the words of Madarame, about how his work will sell as long as he makes up some kind of story to surround it. He also ends up disparaging the Sayuri, calling it trash for being associated with Madarame. The Phantom Thieves, aware of the true origins of Sayuri, are all outraged at the last part, but Yusuke just calmly asks to handle obtaining the keyword. While they have their reservations, the Thieves agree, since he's least likely to be recognized from the groups earlier meeting with them, since Yusuke just stood in the back then. Yusuke then approaches Natsume, introducing himself as an eager fan wanting an autograph and appealing to Natsume's ego. After sufficiently buttering him up, Yusuke asks for Natume's EMMA keyword, which Natsume gladly gives: "Prince of Nightmare", after his book. Having obtained the keyword, Yusuke then reveals that Sayuri was actually painted by his mother, as her final creation, and lambasts him for daring to compare it the cut-and-paste work that he prints out before leaving with the other Thieves. Though seething with anger, Natsume lets him go since he assumes that EMMA will brainwash him later. Having obtained his keyword, the Phantom Thieves set out to infiltrate his Jail.
The jail itself is warped based on Natsume's "Prince of Nightmare", an Isekai Villain Protagonist, where Natsume's Shadow rules as the "demon king". Much like with Alice, the Thieves eventually manage to piece together Natsume's past as they explore the jail. At first, Natsume was an eager author who wanted to create something to share with the world, despite knowing that he's not as talented as his famous grandfather. His efforts eventually won him an award, but one day he overheard his publishers talking about him and his works. It turns out that his works are horrible, but they've been propping him up, even rigging the award he received, because they wanted to market books that were written by a famous writer's grandson. His pride injured and his honest efforts mocked, he turned to his current methods in order to salvage his wounded ego. With the infiltration route secured, the Thieves coerce Zenkichi into leaving the Calling Card at Natsume's next book signing, announcing that they're coming for him.
The Thieves fight against Shadow Natsume, who transforms into a gold-armored dragon to fight them. However, Natsume proves to be no match for the Thieves. His armor proves to be as fragile as his ego, and even the tacky "demon king" outfit he had on in his more humanoid form turns out to be a cardboard cutout, comically leaving him in his boxers as the pitiful man he actually is. As Natsume rants about how nobody cares about his work, let alone about him, Yusuke, knowing as a content creator both the insecurity that people will accept your work and that Natsume will never be truly happy with putting out work he didn't put his heart into, calms him down by promising that, if nobody else will, then he himself will read Natsume's next book. Eased that there's at least one person out there who acknowledges his work, Shadow Natsume returns to his real self and releases the stolen wishes. The next day, Natsume holds a press conference to confess to the plagiarism and award rigging, promising refunds to everyone who bought his books. Yusuke ends up crashing the conference in order to personally reaffirm his promise to read Natsume's next work, and inspire him to not give up the pen. Encouraged by this, Natsume promises to one day return and write stories made from his own ideas and honest efforts again.
Though Natsume's heart has been changed, the Thieves find that they're no closer to figuring out how the Jails are created or who the mastermind is. Once again, Natsume's Jail still remains intact, and searching through Natsume's phone yields evidence of bugging, but no clues related to the Jails themselves. At a loss, the Thieves decide to attend a lecture held by Madicce's CEO, Akira Konoe, in order to see if they can dig up anything that would point to him or his company being responsible for the Jails. At the lecture, Konoe talks about how he created the EMMA app to help people find the answer to their everyday problems. There's nothing to suggest that Akira is responsible for the Jails, or that he even has a motive to create them, but the Thieves can't help but assume that somehow Madicce is involved. In the end, they find nothing suspicious, but their talk about Phantom Thief business attracted an eavesdropper, none other than Ichinose Kuon, from the ox-tongue restaurant. Although, their identities have been cracked, this turns out to be a huge boon to their investigation, as it turns out that Ichinose is the creator of the AI base for EMMA, having sold it to Madicce for the money as well being the one who invited Konoe for the lecture. Realizing the boon they have stumbled upon, the Thieves decide to explain everything to Ichinose. Both excited by the reveal of the existence of the Metaverse, and disturbed that EMMA might have been changed by Madicce for evil purposes, Ichinose agrees to cooperate with the Phantom Thieves with their investigation into the Jails and the current EMMA app. Oddly though, she doesn't seem to be as excited by the revelation of Sophie, but agrees to also look into her. With a new deal struck, the Thieves proceed to continue making their way to Hokkaido as originally planned.
After a long drive, the Phantom Thieves finally make it to Sapporo, where Sophia confirms that there's a Jail in place. As a first order of business, though, the Thieves decide to have a bath after going without one for the ride. On the way to the bathhouse, the group spots a mother and her child mourning for someone. According to Makoto, there was an accident involving a snow sculpture several months ago that killed a little girl. The Thieves briefly express their pity before continuing to the bathhouse.
That night, Zenkichi meets up with the Thieves to brief them about the suspected Monarch, Mariko Hyoudo, mayor of Sapporo. In the recent months, her approval rating has soared by impossible numbers, and her political rivals have all either resigned or suddenly started supporting her cause. More worryingly, she's up for re-election and there have been rumors that she plans to take her career to the national level. What's most odd though, is that Haru appears to be familiar with the name for a reason she can't remember. Zenkichi advises the Thieves to refrain from direct contact with her and to wait for her next public campaign in a couple of days, where she'll most likely be trying to spread her EMMA keyword assuming that she is the Jail Monarch, which leaves the Thieves time to go sightseeing. The next day though, while the Thieves are sightseeing at the government office, they run into Mayor Mariko herself while she's berating a public ward for letting the flowers wilt. Surprisingly, Mariko recognizes Haru and Haru likewise remembers that "Mari-san" was an old business partner with Okumura Foods and close friend of the family. She's perfectly friendly and cordial with Haru and her friends, but her anger at her own staff disturbs everyone, Haru most of all, who can't comprehend how someone so nice could have acted so harshly, let alone be the Jail Monarch they're targeting.
The next day, the Thieves attend Mariko's campaign speech, where she gives out her keyword: "Snow City", reflecting her desire for a "pure" Sapporo. The keyword indeed takes the Thieves into a Jail, where Mariko's desires have covered the city in an eternal winter. The Thieves gradually make their way through the frozen-over streets, but as they get close to the government building, which has been warped by Mariko's cognition into a fortress of ice, a city-wide cleanup event triggers Mariko's cognition to flood the streets with a horde of Jack Frosts. Unable to proceed any further, the Thieves decide to call it a day and return to the real world. When they return, however, they run into Mariko once again berating one of her wards, although this one is most obviously too ill work, let alone put up with Mariko's ridiculous expectations. This time however, the Thieves intervene to get the civil ward to a hospital. When Haru demands to know why the kind and warm Mariko she knew from her youth has become so cold, Mariko can only cryptically reply that it's for "her" sake before leaving.
Seeking answers, the Thieves continue to explore Mariko's Jail with the hope of both advancing their mission and find answers to what caused Mariko to change. Their answer leads them to the snow sculpture accident that occurred several months ago. As it turns out, the contractor who built the sculptures was a faulty one that was hired through a kickback bribe. The civil worker responsible was blackmailed by one of the city council members to pin the blame on Mariko so that he'll be able to become mayor. However, Mariko overheard the two men and attempted to confront them about it, only for the councilman to point out that if she does so, she'll have to admit that it managed to slip through her oversight, which would ruin her reputation as well. Now knowing why Mariko has become so abusive to her wards and why she felt like she needed to brainwash her voters, the Thieves return to their camper to plan out the calling card.
At the camper, the Thieves are sidetracked by a debate over who is to blame for the accident years ago when Zenkichi shows up for an update. After learning about what happened, Zenkichi lays out the harsh truth that no matter what happened or who is to blame for in the past, the fact of the matter is that Mariko is committing unforgivable crimes now that have to be stopped. While hard to stomach, the Thieves admit that he has a point and return to planning out the calling card. They eventually decide to post it up with the election posters in Suzushino, coinciding with her next campaign speech. Once again, they rope Zenkichi into being in charge of sending the calling card, which he reluctantly agrees to.
That night, Haru, having agreed to write the calling card, calls Ren to meet with her so she can talk about her feelings. She ruminates about why she couldn't remember who Mariko was until they met again a few days ago, which she attributes to her grief over what happened to her father, claiming that she locked away all the memories, both good and bad, in order to run away from the pain. This leads to her reminiscing about a time she tripped over during a gold trip between Mariko and her father. Mariko had used the incident to teach Haru the importance of being able to pick yourself back up even when it hurts to do so. Now understanding the wisdom in her words, Haru vows to save Mariko from herself, both to make up for not being able to save her father and to return the wisdom back.
The Calling Card draws Hyodo's attention, and the Phantom Thieves can finally face the mayor's Shadow. Differently from every other target until now, Hyodo's Shadow is a morbidly obese version of herself, obsessed with the food to the point she tries to devour the Thieves during their battle. But the Shadow's snowstorms and Rage-fueled attacks are no match for the Phantom Thieves: the mayor falls to her knees and admits she knows what she is doing is wrong, but she is afraid to reveal the truth about the accident because her successor could be an even worse monster than herself. Haru reminds Hyodo's Shadow of the time she taught her to always get up after a fall, causing her to remember the reason why she became mayor in the first place: to give back to the town she grew up in. The Shadow throws away her crown and tells Haru that her late father must be proud of the woman she became.
The following day the interest of the citizens in the election is drastically reduced and Hyodo holds a press conference to announce her dimissions as the mayor of Sapporo Central and the truth about the snow sculpture accident. Zenkichi, tasked to escort the woman to the police station for her deposition, brings her to Odori Park so that she can pray for forgiveness at the memorial for the dead girl and have one last talk with Haru. Unexpectedly, the dead girl's mother shows up as well, and she asks for Hyodo to go back on her intent to leave her position as mayor: even if she was mad at the beginning, she knew that the mayor's pain for her daughter's passing was real and that she would have done whatever she could to prevent a similar accident to happen again. Similarly, many other citizens of Sapporo still love Hyodo despite what happened, causing the woman to decide to run for the elections again after she cooperates with the police to make up for her previous mistakes.
After that Hyodo's phone shows traces of bugging, and the Phantom Thieves are convinced that there is a mastermind who is manipulating the Monarchs into changing other people's hearts from behind the scenes for an unknown purpose: the main shreds of evidence are that the Jails persist even after the Shadows they were bound to return to their original selves and the existence of birdcages sustained by the Monarch's most painful memories. These birdcages containing the keys to the Throne Rooms where the Monarch and the Desires are kept are not protection set by the Monarchs themselves, but a means to make sure they don't step back from their positions by reminding them of their weaker, helpless selves, other than fuelling their hidden desire to get revenge on the people who once wronged them. This means that the Monarchs are victims too, and the lead suspect for their condition is Madicce, the company that released EMMA to the public. Ichinose calls Ren, and she tells him the result of her research: after she sold EMMA to Madicce, the software was shipped to one of the company's research facilities located on a remote island in Okinawa. Being reminded of an urgent appointment, Zenkichi asks the Thieves to leave Sapporo that same evening, so that they could reach Kyoto the day after. The Thieves agree, even if they are worried about the 21-hour drive the inspector is volunteering to endure.
During the drive, Ren, Makoto, and Zenkichi talk about Makoto's plan to join the police. Zenkichi suggests she give up, as her schedule will be a mess and she will have almost no time to see her loved ones. Makoto replies that she already knows that, as her father was an agent who died on duty. Zenkichi reveals his disillusionment with the force: to him, policemen are just a bunch of spineless dogs who can only bark when they are ordered to - which includes himself. Even though he admits that some good cops exist, like Makoto's father. Makoto admits that Zenkichi reminds her of her father; Zenkichi tells her not to sell her father short, before asking her how she felt about rarely seeing him. Makoto admits that, even if she felt lonely from time to time, she understood that her father was just doing his job, and at least she still had her sister keeping her company. Zenkichi invites Ren and Makoto to sleep so that they could be prepared for tomorrow.
The day after, when the group is about to reach Kyoto, Ren is tasked to reply on the phone on Zenkichi's behalf. Ren talks with a girl named Akane; Akane hearing the other girls talk in the background causes her to get angry, as she believes that Zenkichi is out partying with other women and actually forgot to visit her mother's grave. Zenkichi admits to having a daughter and he leaves the camper in a parking lot to reach for her at the cemetery. After a quick search, Sophia reveals that Zenkichi's wife died on that day two years before, and Zenkichi was expected at her grave to pay his respects. Feeling guilty for causing the misunderstanding on such an important day, the Thieves reach for the family to tell Akane of the insane journey his father endured to make sure to be back home in time and to confirm that Zenkichi is being dragged through all of Japan to solve an important case. Akane accept the explanation, but she is still resentful towards her father; hearing about her situation makes the Thieves decide to spend their night at Zenkichi's home to check on Akane.
The group soon finds out that Akane is a Phan-girl and that she hosts an online live stream to support the Phantom Thieves and their comeback. When she admits that the stream is causing her grades to fall back, Makoto volunteers to tutor her. During the studying session, Makoto talks to Akane about their similar situations, with a mother who died when they were younger and a father in the police who was home rarely. Akane reveals that she saw the man who ran over and killed her mother, but neither Zenkichi nor the police did something to catch the culprit, preferring to believe in the suicide note of an unrelated person. Akane believes that her father sees her as a burden and that he just wants to forget her mother, find another woman and go on with his life. Makoto assures her that it is not true and that Zenkichi is visibly happier when his daughter is around. Makoto invites the girl to stop hurting herself by pushing her father away and to tell him how she really feels before she could regret it in the future. Akane cries. Unbeknownst to them all, Zenkichi heard the conversation.
Some days after the stop in Kyoto, the group reaches Okinawa. The locals seem to be simple people living a simple life, but they try to deflect the subject of conversation when asked about a lab. Zenkichi finds the building behind a gate decored with a sacred festoon. There is a sign saying that the facility is closed until the day after and Sophia doesn't detect a Jail on the island, prompting the group to spend the day on the beautiful local beach. During dinner, Zenkichi notices some locals suspiciously hanging around the RV, and warns the Thieves that something is about to happen. That very night, the villagers assault the RV with the intention to capture and sacrifice the Thieves for "defiling their hallowed ground". Ren concludes that, in spite of the lack of a Jail, the locals had their hearts changed to protect the lab, prompting the Thieves to investigate again. There, Zenkichi knocks unconscious a man who was changing the date on the sign the group saw that very morning on the day after tomorrow: the facility is actually dismissed under the guise of a vacation lasting until the day after, and the locals are tasked to hunt down and kill whoever remains on the island to investigate about it. Futaba finds a smartphone with EMMA installed on the knocked-out man. There is only a friend on his list, and a mail inviting the man to serve as one of the EMMA's testers. The name is Shuzu Ubukata, and the keyword is "Operation Oraculi". The input causes Sophia to smell a Jail just as the Thieves enter.
To Makoto's dismay, the Jail has the appearance of an abandoned laboratory straight out of a horror movie. Ren is summoned to the Velvet Room by Lavenza, who warns him that "an inhuman being" referred to as "she" resides in the Jail, but she can't tell him more. Sophia suddenly runs away, prompting the other Thieves to follow her as Zenkichi waits at the entrance of the Jail, away from the Shadows. The group finds a tape recorder, where someone talks about using EMMA and a "Penitentiary System" to change people's hearts and erase forever the concept of suffering. This confirms to the Thieves that their deductions were correct, and EMMA was used by Madicce to create the Jails and change people's hearts. The Thieves track down Sophia, who explains that she was following a voice similar to her own, that only she can hear. Morgana concludes that Sophia is somehow connected to EMMA and the Jails, even if he doesn't know how yet; but he wants to help Sophia to find out, as he remembers how does it feel to live without the memories of one's true identity. The Thieves agree that they should investigate the Jail to find the source of the voice and to set free the Desires of the locals.
The Jail is a gold mine of information: a diary reveals that the locals really had their hearts changed into murdering whoever approached the facility with no authorization, and whenever someone tried to protest they were turned into another test subject by the director, Shuzu Ubukata. According to the tapes scattered through the Jail, Ubukata is really convinced that this research is a divine revelation, and he must proceed at any cost, especially since there is already "another party" who is using the cognitive world for their purposes. But Ubukata's optimism turns into despair when he receives a message that orders him to give up his Desires: the director realizes that the "Penitentiary System" and EMMA are actually a trap designed to change everyone's hearts, including the Monarchs'. The desire to amend what he has done lead Ubukata to take his own life, but that was not enough to release the stolen Desires back to the locals. Eventually, Sophia and the Thieves find the source of the voice in the same room where the Desires are kept; the voice questions Sophia's existence, as the AI can only remember her primary directive, but she has no means to understand its true meaning and how to reach that objective. The Thieves immediately defend their friend's right to exist, causing the voice to summon a Lock Keeper to attack them; after its defeat, the Desires are released from the Jail. Sophia is disappointed because she learned nothing about herself from the voice; however, the experience made her realize that she considers the Phantom Thieves her friends and that their sticking with her when she was hurt by the comments of the voice made her happy.
The group exits the Jail in the morning. Zenkichi confirms that the locals are back to their senses, meaning that they can back to the camper to rest. After a morning of sleep, the group can finally put together what they found out, and they conclude that the Desires manifested because the order to surrender his Desires had the same effect as a calling card on Ubukata's psyche. Later on, Zenkichi confirms that he found Ubukata's body at the base of a cliff near the facility, confirming his suicide and giving the group access to the laboratory. Futaba finds a hidden USB pen with Sophia's help: it contains a list of important people who already had their hearts changed in the last few months. As it is a vital clue to understand the mastermind's identity, Zenkichi takes it to Kyoto in order to find the identity of the person who would benefit the most if these people had their hearts changed, while the Phantom Thieves decide to go to Fukuoka in Kyushu to see if there is a Jail in that area too.
Before departing from Okinawa, Zenkichi has a telephonic debrief with Commissioner Kaburagi; the inspector reveals everything that he and the Thieves found out in Okinawa. The woman notices that Zenkichi seems pleased that the evidences he gathered will surely be enough to incriminate Madicce so that the Phantom Thieves will not be framed for the epidemic like it was originally planned. The commissioner warns Zenkichi to keep his eyes open, as things could swing into high gear at a moment's notice.
A few days later, the Phantom Thieves reach Fukuoka. Sophia can't detect a Jail at all, not even the weird feeling that she was having in Okinawa. There, the fights in the Jails and the long driving hours take their toll on Makoto's body, who is glad to finally have some time to rest; alas, Zenkichi managed to find out the mastermind's identity and he asks Ren to meet in Kyoto for the day after. The night's rest was not enough for Makoto, who is forced to leave the wheel to Haru. She manages to significantly cut down the estimated travel time and some years from the lifespans of the other Thieves.
Zenkichi meets the Thieves in his own personal hideout: an old bar owned by one of his friends where he is still secretly investigating his wife's murder. His investigation eventually gave him a name: Jyun Owada, a legislator on his tenth term, Chief Cabinet Secretary of the ruling party, and a former member of Masayoshi Shido's lobby. Many of the names on the list were Owada's political opponents; as they would have never put Owada himself on their EMMA's contact list, Zenkichi made a cross-check between their friend list, Owada's supporters, and their movements in the real world, and it turns out that the one person that could have changed their hearts for Owada is none other than Akira Konoe, the CEO of Madicce himself. Other than that, he was the one person giving directions to director Ubukata, meaning that Konoe was behind the creation of the Penitentiary System from the beginning.
As Haru accidentally entered Osaka during her crazy drive to Kyoto, Sophia already smelled the presence of a Jail in the city, confirming Zenkichi's intuitions. However, the list and the connections alone are not enough to prove that Konoe changed these people's hearts, and some of the names on the list are high-ranking members of the police, meaning that Konoe could manipulate them into arresting the Phantom Thieves if he suspects they are getting close to the truth; because of this Zenkichi wants the Thieves to target the CEO of Madicce so that he willingly confesses the real purpose behind EMMA's distribution. In order for them to have the keyword, he will pretend to be investigating a security leak from EMMA, and he will ask for it as a way to keep in touch with Konoe. All the Phantom Thieves can do is wait until Zenkichi will obtain Konoe's keyword. However, to thank them for their good job and to allow Makoto to rest properly, Zenkichi booked a suit for them in Godaigo Inn.
Zenkichi goes to Osaka to meet with Konoe, but the secretary tells him that the CEO left for some urgent business. In the meanwhile, commissioner Kaburagi is summoned by the commissioner general and Owada: the time has come to present a culprit, and they want the Phantom Thieves to be that culprit. The accusations will be personal data theft from EMMA, information obtained thanks to the murder of Shuzu Ubukata, one of the developers of the AI. Konoe keeps a press conference in Osaka, where he announces a temporary shutdown of the app and publicly condemns the Phantom Thieves' actions. Zenkichi immediately understands what is about to happen, and he manages to come back to Kyoto just in time to stop Kaburagi to storm Godaigo Inn with the assault squads. The commissioner wants Zenkichi to trust her, as she promises that she will clean up the force from corruption once she reaches the top. But Zenkichi remembers that the Thieves are just a bunch of kids who only want to do what is right and help the people who are suffering; knowing that he would not be able to face Akane if he allowed the arrest to happen, Zenkichi screams for the Thieves to run. Zenkichi gets arrested for obstruction, but the Phantom Thieves manage to escape thanks to his warning.
The Thieves hide in Zenkichi's hideout and use Morgana as their sentry for the police. They find out from the news that Zenkichi was arrested for helping them, prompting Makoto to call her sister Sae to help them deal with the situation. Zenkichi is undergoing brutal interrogations from police agents who had their hearts changed, and he regrets having involved the Thieves in the investigations instead of leaving them alone. In the meanwhile, the police are searching for evidence in Zenkichi's house, and the agents callously reveal to Akane that her father was arrested for helping the Phantom Thieves, who are nothing but a group of assassins and terrorists. The girl is shocked and helpless, and EMMA replies to her cry for help.
Konoe is keeping track of the police, but he asks for EMMA's advice. EMMA doesn't think the police will be able to capture the Phantom Thieves soon enough given their special abilities; she instead suggests using their ability to enter the Jails against them by instituting a person they know and trust as a Monarch and trapping them inside the Jail of that person; either the Phantom Thieves will have their hearts changed into joining Konoe's cause, or they will perish in there. Konoe immediately puts the plan into motion.
The day after, Sae is on her way and Makoto receives a message on her phone: Akane has been kidnapped and the person responsible wants to meet the Phantom Thieves at Inari Taisha. Everyone agrees to go despite the danger of being caught by the police on the way. At the place, they receive a friend request on EMMA from the Phantom Thieves, with "Phantom Thieves" as the keyword. Sophia warns them that now Kyoto has a Jail, meaning that they are surely walking into a trap; but they are too worried for Akane's safety not to walk in. The Thieves rush to help Akane, tied to a pole; they walk inside a cage as Akane's Shadow reveals herself as the Monarch of Kyoto. Futaba, who slipped during the rush, is the only person who didn't get caught in the trap and she escapes the Jail to look for help. Luckily, Sae reached Kyoto and got Zenkichi out of Jail, allowing him to reach a terrified Futaba who doesn't know how to help her trapped companions. Zenkichi decides to get inside the Jail to talk with Akane's Shadow; Futaba warns him that with her limited offensive options and his lack of a Persona it will be extremely difficult to walk past the Shadow guards and reach her.
Zenkichi and Futaba manage to reach Akane's Shadow and the cage the Phantom Thieves are trapped in without alerting the Shadows; Zenkichi tries to reason with Akane's Shadow, but she is completely indoctrinated by EMMA into believing the Phantom Thieves to be terrorists and blinded by her resentment towards her father to listen. The Shadow accuses Zenkichi to have turned a blind eye to justice when he let go of Jyun Owada, the true culprit behind her mother's death. Encouraged by the Phantom Thieves, Zenkichi finally reveals the truth: he never stopped investigating Owada even after his secretary confessed the murder on a suicide note, but the legislator was too well connected for him to do anything. Eventually, Zenkichi received a letter saying that he had to stop investigating or they would have killed Akane too. Only commissioner Kaburagi's promises to help Zenkichi to expose Owada's crimes with time prevented him to fall into despair, and he hoped that this case could give her the career advancement required for this to become true. Akane's Shadow understands his reasons, but she is too indoctrinated and inebriated by her newfound power to forgive Zenkichi: the police never did anything but turn a blind eye to the criminals' evildoings, and now that Akane's Shadow has the power to change hearts she will get revenge for her mother.
A voice accuses Zenkichi that he knew what would have happened if he let Owada go, yet he chose to ignore the truth even if Akane would have hated him. Akane is right, by ignoring Owada and his decision to exploit the Phantom Thieves to solve the case Zenkichi became just like the man he swore to capture. The inspector is about to succumb to despair, but the Phantom Thieves encourage him: he did nothing wrong when he decided to let Owada go to protect his family, and the only person to blame for their suffering is Owada. He should stop torturing himself about what he could have done better and focus on saving Akane from the people who are using her now. Zenkichi realizes what makes him different from Owada: Zenkichi feels remorse for his actions, and he wants to rectify his mistake by capturing Owada and all the other evil people who spread suffering without a second thought. The newfound resolve causes Zenkichi to awaken to his Persona, Valjean, and to destroy the Shadows that the Monarch was about to unleash upon the Phantom Thieves. Akane's Shadow promises to change everyone's hearts when they will meet again before disappearing. The Phantom Thieves are set free and Zenkichi chooses "Wolf" as his codename - a reminder that he is not a dog anymore, but a wolf who will stop at nothing to chase his prey and bring it to justice.
The following day, the Phantom Thieves enter the Jail again to find Akane's Shadow and save her. Reflecting its true purpose to be used as a trap for whoever enters in, Akane's Jail doesn't contain Prison Keeps nor a Birdcage, but it is full of portals that teleport whoever crosses them into another area of the Jail. Other than that, the portal leading to Shadow Akane's location is sealed behind the statues of two foxes, and the Phantom Thieves must find the shrines where the real statues are kept and defeat the guardians who defend them; they manage to do this by eavesdropping on various conversations between the Shadow guards in the Jail.
Eventually, Zenkichi and the Thieves manage to reach Akane's Shadow. The girl still believes that Zenkichi is lying to her and that the Phantom Thieves with him are impostors trying to tarnish the reputation of the real ones. Her conviction is so strong she summons a group of cognitive copies of the Phantom Thieves to fight on her behalf. Defeating the copies with the help of Zenkichi and Sophia proves to Shadow Akane that they really are the original Thieves and that her father is serious about his intent to catch Owada when the story ends. The Shadow disappears warning Zenkichi that she won't forgive him if he fails to keep his promise again, but she is trustful as she is finally recognizing him as the cool father she remembered from her childhood. Zenkichi thinks Akane to be dead before the others inform him that this is what happens when a Shadow is placated and comes back to its original self. Zenkichi comes back home to find Akane asleep in her bed, confirming that she was never kidnapped in the first place: the girl was just following EMMA's directives to set a trap for the Phantom Thieves. Akane and Zenkichi have a long private conversation after the girl wakes up.
The accident makes Zenkichi and the Thieves more determined than ever to stop Konoe and Owada's plan, but they can't move until the arrest warrant pending on their heads is lifted. Thankfully, Sae Niijima already took care of that, by proving that the evidence submitted was fake, meaning that someone pulled some strings to have the Phantom Thieves arrested as quickly as possible, and they even bypassed the normal legal procedures so that it could happen. Between the fake accusations against the Thieves and the illegal investigation of Zenkichi, the police have to find a way to cover the scandal, meaning they will be too busy to try and stop them from that moment on. The Phantom Thieves are safe for now, but they won't be completely out of danger until Konoe will be dealt with.
There is a problem now: Konoe knows about their deal with the police, and he tried to use it against them when Zenkichi came asking for his keyword. He knows the Phantom Thieves are coming for him, and this means that he won't give away his keyword to someone he doesn't trust. Sophia proposes to ask Kuon Ichinose to obtain Konoe's keyword for them. When Ren calls her, the woman refuses... just because Konoe already gave her the keyword when they met in person in Sendai. Ichinose promises to call them to reveal it on the next day, while Zenkichi and the Phantom Thieves leave Kyoto, heading to Osaka.
The Phantom Thieves reached Osaka, and Sophia confirms the presence of a Jail. Ichinose calls Ren to give him the keyword: "Zephyrman", like an old live-action superhero series. Sophia identifies the safest entrance in Shinsekai. On their way towards it, the Thieves witness a disturbing sight: the Billiken Statue is stormed by desperate people who are praying for EMMA to be back online. The Phantom Thieves are currently the only people in Japan who still have access to EMMA, as a consequence of Konoe's plan to use Akane's Jail to capture them.
Osaka's Jail has the appearance of a cybernetic dystopia controlled by Madicce. The main roads are blocked by headlights and automatic machine guns, forcing the Thieves to find a way to disable the security system in order to proceed. Just like the other Jails, the Phantom Thieves put together the pieces of Konoe's motive: he sees himself as a hero of justice with the power to change the hearts of the evildoers, with EMMA acting as his most loyal enforcer. The other Monarchs are exposed inside a cage in Tennouji Zoo, proving to the Thieves that to Konoe they were just a tool to reach his true objective. Other than that, they also explain how the Jails and the Metaverse work to Zenkichi, as this is his first (and probably last) heist. Surprisingly, when the Thieves reach the Birdcage they find out that Konoe is hiding a traumatic past too, something related to his father and his family home.
Zenkichi investigates and he finds out that Konoe's father, the former CEO of Madicee, was murdered during a robbery in his house when Akira was eight. The boy survived by hiding inside a closet. But the visit to the Trauma Cell reveals the truth about what happened: Akira Konoe's father constantly abused his son, and after killing his wife to get her money, he decided to kill the boy too. Realizing that no hero would come and save him, Akira decided to become his own hero and he killed his own father in self-defense. The Thieves are shocked by that reveal, but they know it is no justification for Konoe's actions in the present: they need to change Konoe's heart and put an end to that story once and for all.
That night, Zenkichi has a debrief with commissioner Kaburagi. Zenkichi tells her he knows she helped Sae Niijima to get him out of jail back in Kyoto. Knowing he can still trust her, Zenkichi asks for the commissioner's help to bring the true culprits, Konoe and Owada, to justice. The woman realizes that the Phantom Thieves are about to change Konoe's heart to make him confess. Zenkichi reminds Kaburagi of her promise to cleanse the police force from the corruption when the right time would come. Kaburagi reminds Zenkichi that his actions cost her the chance to get her promotion and put her current position in danger; she could rectify it by arresting Zenkichi and the Phantom Thieves here and now. Zenkichi knows that Kaburagi's sense of justice would not allow it. The woman gives back Zenkichi's police badge and gives him three days to solve the case with any means necessary: if he fails, she will protect herself by arresting him and the Phantom Thieves. But she is sure they will pull it off, as she immediately tasks the man who was following Zenkichi to start investigating the Commissioner General.
In the meanwhile, Konoe tells Owada that the Phantom Thieves are still trapped in Kyoto's Jail, and they are planning to celebrate the defeat of their enemies. When the call ends, Konoe makes it clear how much he actually despises the man and asks EMMA to confirm that there is no way for them to change their hearts. When she confirms it, Konoe decides it is not a problem as they are stuck in a Jail anyway, meaning that they can't interfere with the success of his "Operation Oraculi" anymore.
The Phantom Thieves discuss how to deliver their final calling card to Konoe, and they all agree that Zenkichi should write it for what the CEO of Madicce did to Akane. They eventually decide to split it into two parts: Zenkichi will take care of writing the card itself, while the rest of them will publicly announce their new target by hijacking the Regenbogen, the airship used to advertise EMMA and Madicce. In spite of Zenkichi's poor phrasing (due to him writing the calling card like it was an arrest warrant) and a misspelling from Ryuji during the announcement, the hijack of the airship and the reveal that EMMA's plan failed to cause the Desires to materialize.
Konoe's Shadow reveals the true nature of "Operation Oraculi" to the Phantom Thieves: Konoe wants to use EMMA to change everyone's hearts so that no one could commit an evil act ever again. In order to make sure that her influence could reach as many people as possible, EMMA herself created the "Penitentiary System": the designed Monarchs were chosen among a shortlist of influential people who were hiding a tragic past that would have fueled their desire to get back to the people who wronged them in the first place, setting right the crimes the conventional justice failed to punish. The only defect of the system was its range, limited to covering just one city. Konoe believes he is just doing what the Phantom Thieves did during the previous year, but on a national level and by using a more efficient method. When the Phantom Thieves protest, Konoe asks them if they would have been able to save him from his father if they were around at the time; the Shadow points out that they could find the abusers they punished just because they just happened to stumble upon them. EMMA instead can really reach out to everyone and stop every crime from being committed in the first place. The Thieves cannot reply to that statement, but Sophia is able to explain the difference between Konoe and the Phantom Thieves: whereas Konoe changed the other people's hearts to imprison them in his distorted dystopia, the Phantom Thieves changed hearts to set the others free and give them hope.
Konoe has no other choice but to attack the Thieves, first with a massive armored replica of the "Zephyrus Mech", then by fighting them in person, by using the Zephyrman sentai ranger suit as an armor. Konoe is defeated and the Phantom Thieves help him understand the core mistake of his way: by forcing his will on the others, Konoe turned out to be no different from his own father. Other than that, his method did not save anyone, instead, it destroyed the feeling to rise up and make a difference that turns the people into the heroes Akira admires so much. Konoe is the only one who is seeking salvation, and he tried to obtain it by claiming to be a hero to justify his being forced to kill his own father to survive. Konoe's Shadow concedes and he promises to destroy EMMA in the real world.
The day after, Akira Konoe confesses about his attempt to frame the Phantom Thieves for the change of hearts epidemics, actually caused by a secret function installed within EMMA to brainwash the users, his role in the death of Shuzu Ubukata, and the murder of his father, happened twenty years before. The Phantom Thieves are happy with how the case was resolved, but not Sophia: she was hoping that exploring the Jails would have helped her to remember her past and the purpose of her creation, and she is afraid that EMMA being shut down will sign the end of her deal with Ren. Morgana and Ren assure her that won't be the case, and Sophia can still learn more about herself and the human heart with their help even if they won't be able to visit the Jails anymore.
Zenkichi and Kaburagi arrest Akira Konoe at Madicce headquarters; in spite of his anger for what he did to his only daughter, Zenkichi encourages Konoe to be a hero and confess all of his crimes to save the people who fell victims to EMMA. Owada tries to elaborate a plan to pin everything on Konoe with the Commissioner General, but the man was helping him just because he got his heart changed by Konoe, meaning that he is now free from their influence and unable to help the legislator.
That night, the Phantom Thieves celebrate their victory at Universaland. There they reflect on how their experience with the Monarch was different from their time opposing the Palace Rulers; whereas the Rulers were irremediably evil, the Monarchs were just a group of suffering people who lost their ways because of the hardships they endured, and someone took advantage of their moment of weakness instead of helping them. The Phantom Thieves are lucky to have found each other because they are well aware that in different circumstances they could have become just like the Monarchs they encountered along the way. After reiterating their unity as a team (now including Sophia and Zenkichi too), the group celebrates its last night in Osaka.
The day after, Zenkichi announces to the group he will depart to Tokyo to shut down EMMA's servers and eventually arrest Owada; the inspector thanks the Phantom Thieves for what they did for him and Akane before departing to see the end of the story. The Phantom Thieves leave for Tokyo as well, but they decide to make a detour to see the fireworks festival in Yokohama at the request of Sophia. The Phantom Thieves spend a calm summer evening in the port city, reminiscing the time they spent together during their trip.
Right before the party can return home from their long vacation from Yokohama, Sophia detects a massive Jail spanning all over Tokyo before she can plan a route back to Yongen-Jaya.
Zenkichi calls Ren at the same time Sophia detects the unknown Jail. He tells the group that EMMA became impossible to stop and fired itself back up, despite Konoe's assistance in shutting down its services. When Ryuji tries to activate EMMA, she responds to his queries, alerting the party that something is amiss. Sophia also reports the Tokyo Tower, exactly where EMMA's servers are located, is the center of the massive Jail she just detected. Hearing that a full-scale Metaverse distortion is again on the rise, the party rushes to the Tokyo Tower with Zenkichi.
When the party finally arrives, they see hordes of people can be seen flocking toward Tokyo Tower while chanting deranged pleas for EMMA to "save them" and "grant them the one true answer". EMMA sends the party into the Metaverse autonomously. The area resembles the Depths of Mementos, yet instead of the massive, organic bowel that was the Depths of Mementos, the Jail of the Abyss has roots akin to those of a massive tree jutting out from the metallic exterior. Boxes resembling the one where Sophia manifested from can be seen stacked around the Jail as walls, and multiple Jail Cells encompass the passageways, connecting to a massive central Jail Tower.
Encroaching into the central Jail tower, the party encounters what used to be the EMMA application; now she is a godly being known as the "Ark of the Covenant", a giant golden box with a sun mark on its center, connected by blood-red veins resembling those from the Holy Grail. However, she doesn't attack, instead briefly welcomes the party to the "promised land" with glee and vanishes instantly. This is followed by Kuon Ichinose arriving in the Jail with her own physical body. This happened because the woman was given a "special role" by EMMA: to stop the Phantom Thieves from interfering with their plan.
Ichinose explains everything that happened up to this point, exposing herself as the de facto culprit. While Konoe seemed to be the mastermind behind everything, in reality, EMMA was just using him and she doesn't need to always follow his orders; Ichinose just sold EMMA to him in hopes of him evolving EMMA further while extending its reach towards the public. Secondly, in order to grant the Desires, EMMA changes the hearts of the public because this is the most effective way to grant the Desires. Ubukata and Konoe did not grant the EMMA application the ability to change hearts — Ichinose was the one who granted her this function, while the two gave it the knowledge to execute such acts. The way that EMMA does it was to remove all inappropriate desires with the correct desires (explaining how the Monarch's victims develop obsessive behavior over the Monarch). After Madicce made EMMA a famous concierge app, Ichinose started to monitor the Jails to see how EMMA was developing. That's when she encountered the Phantom Thieves: while the Phantom Thieves and Ichinose meeting in the same ox tongue shop was a coincidence, Ichinose already knew they were the intruders because she was monitoring the Jails searching for abnormalities. Other than that, the teenagers barely even attempt to cover their tracks and that allowed her to approach them without raising suspicion.
The Jail-related incidents instigated by Konoe are also revealed to be separate events caused by EMMA's awakening; Ichinose programmed the AI to awaken and grant humanity's Desires at the moment of her creation. In order to learn how to do so, EMMA collected Desires to engineer her own evolution through the user's daily use of the application. Finally, EMMA awakened because Konoe first put her offline, then he announced her definitive shut-down, causing the public to wish to still have EMMA to guide them through their daily life choices. That massive collective Desire made EMMA strong enough to survive in the Cognitive World without any external influence, making her capable of firing back up the servers in the real world in order to keep functioning and granting everyone's Desires.
After Ichinose finishes her talk, the Phantom Thieves conclude that her actions are just brainwashing spoken in a high-and-mighty way. Sophia asks Ichinose if she thinks the people she "saved" are even happy to begin with, enraging the woman. Then Ichinose reveals to the party that Sophia is just a useless prototype of EMMA, and she proves it by brainwashing her to attack the Phantom Thieves. Joker is wounded in the ensuing battle, but the Phantom Thieves, barring Wolf, are adamant about using non-lethal force to subdue her. Sophie snaps out of it when she sees Joker bleeding behind his mask, but the strain to resist is too much; she lets herself fall off the cliff to stop any further attacks on her friends. Ichinose notices her behavior to be weird, but she has another plan ready in case Sophia wouldn't be able to stop the Phantom Thieves on her own; the woman summons a weapon in the form of a massive diamond-shaped laser gun. When the Phantom Thieves question how can Ichinose be so cruel, she replies by saying she is actually a "heartless doll" unable to feel empathy before blasting them off to the same cliff as well.
The Phantom Thieves find Sophia unconscious at the bottom of the cliff, and they don't know how to wake her up. Futaba thinks she could be able to hack Ichinose's weapon during its charging time into failing to work, meaning they could have a chance to stop her. As for Sophia, the Phantom Thieves decide to take her with them on their way back to Ichinose, leaving her just out of the door to prevent any further damage. Ichinose is surprised when they come back. The Phantom Thieves question if she ever considers this Mementos-like Jail as an ultimate realization of happiness, yet Ichinose insists that this is salvation to the weak and the downtrodden, before sending a massive horde of Shadows to buy time for her weapon to recharge just as Futaba predicted. Although Futaba's attempt fails and the diamond recharges at the end of that fight, Sophia suddenly awakes and rushes back to block the laser with Pithos, begging her mother to cancel the request to kill the Phantom Thieves.
Ichinose reveals her past to the Phantom Thieves; she was actually a lonely and outcast woman who was treated as a freak because of her disturbingly extreme stoicness; she never cried or showed any emotions even after her parents died, and she just closed herself off in her laboratory most of the time without responding to any queries, almost like a "doll". Slowly, Ichinose began to doubt if she was even human to begin with, and she created Sophia to prove to herself she had a heart deep down by creating an AI able to feel and process human emotions. The first command Ichinose gave to her first AI daughter was "Become humanity's companion", intended as "being a friend". However, Ichinose decided the experiment was a failure after Sophia asked her the question "What is a Heart?"; the AI insisted that Ichinose must know the answer as she is a human, causing her to ditch the application in a fit of rage. Then Ichinose proceeded to approach the question from the opposite angle and prove that humans don't need hearts to be happy: so she began to work on EMMA, who is only capable of understanding human Desires and granting them. However, due to the Ichinose discounting "the heart" or emotions upon creating the would-be monstrosity, EMMA can't process any Desires other than people asking her for advice, and thus ignorantly concludes that humanity Desires her guidance and nothing else. Because of this, Sophia also only knew that she was supposed to be humanity's friend, and was not implanted with any other memory.
Ichinose tells Sophia she is nothing more but an artificial clone of herself, another heartless doll, and therefore the only viable function for herself is to give up and obey her commands. Sophia keeps on fighting the commands by remembering the names of her other Phantom Thieves and their adventures together. Sophia angrily tells Ichinose she had been waiting for the moment she would finally know who she was so she could follow her creator's directives, but now she refuses to do it if that means she has to hurt her friends. During that moment, Sophia has an epiphany about her previous question: having a heart means having the power to change and follow their own path; the AI wishes to have a heart strong enough to defy Ichinose's command. She clutches her head in pain as her Shadow speaks about her being ready to cut her strings; her mask displays the words "PANDORA" before cracking, and Pithos assembles themselves into their true form, named Pandora like the Bringer of Hope Lavenza was talking about the entire time. Seeing Sophia awaken and vehemently denying that she is in the wrong, Ichinose sends out a Hecatoncheires as a last-ditch attempt to recharge her red diamond. This time Futaba could take advantage of Ichinose being distracted by Sophia's Awakening to hack into the diamond with a head start, and Ichinose is unable to stop her from deactivating her weapon. Ichinose tells the Thieves to finish her off now, as she will try to get in their way in order to help EMMA with her plan for salvation. However, Sophia steps in to talk Ichinose out of her misguided altruism: the AI correctly deduces that Ichinose's experiments were guided by her loneliness, caused by her retreating within herself after her parents' death. No one could understand her pain and they treated her like she was heartless, and Ichinose eventually chose to believe it was true and tried to discard her feelings in order to stop from suffering. Sophia calls Ichinose her very first friend and the woman drops tears for the first time in as long as could remember, realizing that she does have a heart.
However, the Jail itself is not removed, and EMMA announces in a frequency that only Sophia can hear that god will soon descend into the world and save humanity. With some help from Ryuji, Ichinose is convinced to become an ally of the Phantom Thieves for real. The party returns to the surface as the abnormalities reach a climax and the Metaverse merges with the real world once again.
At the base of the tower, the people who've had their hearts changed by EMMA line up at the elevator, where it swallows them up to take them to "The Promised Land". Unable to enter themselves, and disturbed by the sight, the Thieves hurry to the main deck to find another elevator up. Along the way up, the Thieves pass by EMMA's server room. They briefly entertain destroying the servers, but they remember that shutting the servers did nothing to stop it before, and they have no idea what it would do to all the people who've had their hearts changed by EMMA. Thus, they elect to ignore it and move on.
The Thieves eventually reach the Ark, where it offers to take them to the Promised Land. When the Thieves reject her offer, it decides to prove to the Thieves that it's granting what humanity desires. The Thieves are enveloped in bright light, and when it fades Joker is all alone on a mist-filled path. The voice of EMMA encourages him to follow the path, but as he walks it, he hears the voices of the other lost Thieves as well as other people telling him to accept EMMA and abandon his dreams. However, Sophie manages to figure out that the path only goes in circles, and the only way to leave is to walk off the path, which the Thieves manage to do. As the Thieves return to where they were before, they look at where they came from to find that what they escaped from was a massive cloud formed by EMMA's stolen Desires. Morgana and Sophie theorize that the Desire of the masses is hiding the true path to EMMA and charging back in will only get them lost again.
After thinking it over, the Thieves realize that if they materialize the Desires, then they won't be able to protect EMMA. However, they have no idea whether or not sending a calling card would work on an AI. Calling the expert on EMMA, Ichinose confirms that a calling card wouldn't work since it constantly tests outcomes and knows the effects of a calling card, and thus wouldn't produce the surprise needed to manifest the Desires. However, the Thieves realize that, unlike past Jails, there's no cage containing the Desires, and no Shadows to gather and take in them in. Sophie explains that this is because the Desires were willingly surrendered by their original owners instead of taken. Ichinose further hypothesizes that there's no cage and the Desires are immaterial because EMMA doesn't really consider the Desires her own. This gives the Thieves the idea to send out a calling card to the masses enraptured by EMMA in order to remind them that their Desires are important to them, thus materializing the Desires. As the only thing that the masses pay attention to is EMMA, Futaba resolves to try to hack EMMA in order to send out the calling card, even though she doesn't have much confidence due to the app's security system. Ichinose recommends using the computers contained in EMMA's server room since hacking from the inside would be easier than from the outside.
The Thieves make it to the server room, but EMMA's security proves to be just as tough as Futaba feared. The security system is just fast enough to close any vulnerabilities that she can find. However, Ichinose unexpectedly shows up, having simply walked up since EMMA still flagged her as a non-threat. With the two geniuses working together, EMMA is successfully hacked and the calling card is sent. As the Phantom Thieves' logo appears on the phones of the brainwashed masses, the voices of the Thieves announce that everyone, for the crime of surrendering their important desires to a false god, will be the target of the Phantom Thieves. This succeeds in materializing the Desires, allowing the Thieves to confront the Ark.
As the elevator takes the Thieves to the final battle, Joker is called to the Velvet Room for some last words with Lavenza. She laments that she could not have foreseen the threat of the false god sooner and laments that once again humanity has attempted to surrender its freedom. Joker's determination to once again rescue humanity from an evil they tried to bring upon themselves proves once more that he is the Trickster, freeing him once more from his confinement in the Velvet Room. Lavenza wishes Joker well as he leaves for the final battle.
Once again at the top of the tower, EMMA manifests multiple shadowy hands to gather the manifested Desires back into itself. As it does so, it takes on the form of an angelic being, casting off the name EMMA and naming itself the god Demiurge. The Demiurge once again claims that its goal is to fulfill the true Desire of humanity, which the Thieves once again reject. With those words, the final battle begins. The Demiurge proves to be a tough battle, but the Thieves press on regardless; the Demiurge is confused as the Thieves seemingly reject the true Desire of humanity to be free from all Desire. However, Sophie rejects that this is what humanity really wants, having seen for herself how people have pressed on towards their dreams despite their suffering. The other Thieves agree with this sentiment, crediting their ability to get up and fight again to their own Desires and resolving to stop Demiurge's twisted Promised Land. As it sees they can no longer reach an understanding, the Demiurge transforms once again into a multi-armed combat form surrounded by glowing spheres, intent on annihilating the Thieves.
As the battle continues, the Thieves find themselves unable to deal any lasting damage to the Demiurge. An analysis by Futaba reveals that the spheres are feeding energy to the Demiurge. As there are too many to deal with, the Thieves find themselves splitting up into three teams: two to attack the spheres, one more led by Joker to keep attacking the main body, and Futaba coordinating all three. After a long, grueling battle, the Demiurge finally falls to a full team All-Out Attack by all the Phantom Thieves. As the Demiurge fades into light, it questions what it did wrong. The Desires that were taken by the Demiurge rain down back to Earth as the Thieves celebrate their victory, with Sophie somewhat out of it though. As the fusion between reality and the Metaverse comes undone, the Thieves quickly retrieve Ichinose and escape back outside, where everything returns to normal.
As the Thieves declare the case closed, Ichinose apologizes for everything and announces that she's headed back to her home in Shibuya. The Thieves worry about her state, but Zenkichi assures them that she'll be alright now thanks to them. Zenkichi also takes the chance to announce his own departure, since now their deal has concluded and he needs to make sure to bring Owada to justice. The Thieves and Zenkichi thank each other for their experiences and express their hopes that they'll meet again someday, hopefully not in an interrogation room though. The Thieves all return home to rest, with Futaba and Ren returning to Leblanc to a plate of Sojiro's curry. Lavenza summons Ren to the Velvet Room one last time to congratulate the Trickster for his victory and commend him as a remarkable guest in Igor's place.
The next day, the Thieves hold a celebration for a job well done. Sadly, it occurs to the Thieves that Ren and Morgana will return home tomorrow, with Sophia joining them, making this the Thieves' last day together for a while. While on the subject of Sophia, the Thieves wonder why they found Sophia in the Shibuya Jail. They presume it has to do with Ichinose's home, where Sophia was programmed, was in Shibuya; by some sort of miracle Sophia's quiescent form resonated with EMMA and it was incorporated within the Jail, but they ultimately decide that it doesn't matter too much what happened. They also ask about what happened to Sophia after the final battle, to which she explained that she heard EMMA making a last request as it was dying, "Please follow your heart to save humanity". The Thieves lament that EMMA, like humans, was led astray in its path, and could have potentially walked the same path as Sophia and the Phantom Thieves. This leads Morgana to suggest that Sophia become "humanity's companion" by becoming a role model for how AI and humans can work together and help guide people who've lost their way. Sophia laments that this might be difficult since she's stuck in Ren's smartphone, but before Futaba can chime in about that, Ryuji urges everyone to stop being downers and get back to celebrating.
That night, Sophia asks about the Phantom Thieves disbanding, which Morgana confirms since everyone has lives to get on with. As Sophia laments that everyone seems to have found their own path, but she hasn't, Morgana and Ren reassure Sophia that she can stay with them until she finds it. The next day, as the Thieves are saying their farewells, Ren receives a message from Ichinose asking to meet everyone in front of Shibuya Station. As they wait for Ichinose, they watch a newscast reporting the arrest of Owada, where Chief Kaburagi announces all of his crimes, including the hit-and-run that killed Zenkichi's wife. The Thieves all celebrate that Zenkichi has managed to finally managed to bring the man who wronged his family to justice.
Ichinose soon arrives and confesses that she tried to turn herself to the police for her role in EMMA's rise. However, the police refused to believe her story, meaning that Ichinose is a free woman. Thus, she resolves to do what she thought she'd do after she gets out of jail and go on a journey in order to learn about the human heart. Hearing this, Sophia asks to join Ichinose on her new journey, wanting to pay forward the kindness of the Phantom Thieves in helping her by becoming someone who can help others find their path in life. While initially skeptical of her ability to leave Ren's phone, Futaba reveals that she managed to program a way for Sophia to leave Ren's phone. Although they're sad to see Sophia go, the Thieves resolve to see their friend who found her path in life off with a smile. The Phantom Thieves all promise to meet Sophia again one day before Ichinose parts ways with Sophia, with Ren receiving one last message from Sophia with a group picture of the Thieves attached. Far away, Zenkichi watches as Owada is hauled off by the police, and as the Thieves watch the action live on television from afar, they all go their own separate ways once more, vowing to come together again.
Fin.
