For the sake of convenience, the Player Character will be referred to by his "official" name from the anime adaptation, Ren Amamiya.
This page contains unmarked spoilers. Read at your own risk.
While his accomplices split off as he runs interference, Joker fights his way past security guards, one of whom suddenly contorts and morphs into a bizarre monster. This creature proves to be no match for Joker, who has an otherworldly power at his disposal. After disposing of the beast, Joker makes his escape, diving through a window and landing outside the casino.
Unfortunately, waiting for him outside is a large swarm of police officers. Joker has nowhere to run and nowhere to hide: he is captured, the arresting officer taunting him with the fact that he had been sold out by one of his compatriots.
In truth, "Joker" is a 16-year-old high school junior named Ren Amamiya. When Ren comes to, he is in an interrogation room, his body covered in bruises and his mind hazy from drugs injected into him to coerce a confession out of him.
After the officers finish with him, he is approached by Sae Niijima, of the public prosecutor's office. She is warned beforehand by guards that she will not be allowed to talk to Ren for long, but she is determined to unearth the truth.
Appalled at the abuse Ren had endured, she sits down across from him and asks him about his crimes, the mysterious "other world" he discovered, and how he was able to "steal hearts", advising him that his very survival depends on the veracity of his testimony.
That means telling her everything from the very beginning...
Because it is his first offense, Ren is sentenced to one year's probation. Because of his criminal record, he is expelled from his hometown's high school. Because continued school attendance is a condition of his probation, he is transferred to Shujin Academy, a prep school in Tokyo and the only academic institution willing to induct him. For the duration of his probation, he is assigned to live with Sojiro Sakura, the proprietor of a cafe in Yongen-Jaya called "Leblanc", who is less than thrilled with harboring a delinquent and only agrees to do it because he is a distant acquaintance of Ren's parents.
On his way to Leblanc for the first time, Ren discovers a strange app on his phone with an ominous eyeball design. Time seems to stand still, and Ren glimpses a fiery figure before the people around him start to move again. Deciding to pay it no mind, Ren deletes the app and continues on, unaware of the significance of that vision...
The evening after he moves into the attic of Leblanc, Ren has a strange dream where he finds himself in a prison cell. Outside of the cell are two young wardens, Justine and Caroline; and across from the cell is Igor, a strange old man with a long nose who welcomes him to the "Velvet Room". Igor tells Ren that he is to undergo "rehabilitation" in the hopes of averting a coming "ruin". Igor and his wardens would become a constant presence in Ren's life from that evening onward...
On his way to the first day of class, Ren meets Ryuji Sakamoto, another alleged "problem student"; and Ann Takamaki, a classmate who is seen accepting a ride to school with P.E. teacher Suguru Kamoshida. As Ren and Ryuji make their way to school on foot, however, the mysterious app reappears on Ren's phone and activates...
Ren and Ryuji arrive at school...but something is horrendously wrong: they find a castle where Shujin Academy should be! They enter the castle, only to be confronted by strange creatures led by a man bearing Kamoshida's resemblence, albeit with glowing yellow eyes and dressed in nothing but a crown, a cape, and pink underwear. The two are captured, taunted by the fake Kamoshida, and sentenced to death.
As the creatures prepare to execute Ryuji, a voice rings out in Ren's head. It asks if he intends to sit by and watch as Ryuji dies, and if his previous decision to stand up to the drunk in his hometown was a mistake. Ren is determined that he made the right decision then. His resolve drives him to fight back, to rebel against these miscarriages of justice.
For several moments as this voice speaks to him, Ren writhes in pain, until finally, a white domino mask appears on his face. Ren reaches up to it and pulls it off, a process that is excruciatingly painful and leaves his face bloodied. Once the mask is off, Ren's body becomes wreathed in blue and black flames that takes the form of his "Persona", Arsène. When the flames leave Ren's body, his school uniform is replaced with a flowing black trenchcoat, matching shirt, pants, and shoes, and red gloves.
With Arsène's power, Ren is able to fight off the monsters at the fake Kamoshida's beck and call. He begins to make his escape with Ryuji, along the way encountering and freeing "Morgana", a strange cat-like being with a Persona of his own named Zorro. Accepting this cat burglar's help, they escape from the castle and return to the real world, where Morgana transforms into a real cat that only Ren and Ryuji can understand.
Over the course of the next few days, Ren and Ryuji, along with Morgana, make more excursions into the castle, which Morgana states exists in the "Metaverse", a parallel dimension formed from humanity's collective unconsciousness. Morgana states that the castle is a "Palace", a location in the Metaverse given form due to the twisted and corrupted desires of a human. They are able to travel there with the Metaverse Navigation App that appeared on Ren's phone, using coordinates consisting of the subject's name, the real-world location, and the Palace's form: in this case, Suguru Kamoshida, Shujin Academy, and a castle, formed from Kamoshida believing himself to practically be the king of Shujin, able to do whatever he wanted without consequence due to the influence he wielded as a former Olympic gold medalist. As for the fake Kamoshida and the creatures therein: they were "Shadows", manifestations of negative human desires.
Within the Palace, the guards catch Ren and Morgana as Kamoshida's Shadow taunts Ryuji. Fed up with the Shadow, Ryuji's own Persona awakens: Captain Kidd. Ryuji uses his Persona to save Ren and Morgana and fend off Kamoshida's guards.
Morgana explains that contained within a Palace was a "Treasure", the core of the distortions that created the Palace. He is on his own personal quest to collect Treasures in the hopes of regaining his human form, but collecting the Treasure would also have the effect of removing the distorted desires of the person who created the Palace, bringing about a change of heart and causing them to repent for their misdeeds. It is thus that Ren and Ryuji decide to steal the Treasure of Kamoshida's palace, in the hopes of changing him.
The need to take the Treasure becomes all the more urgent one day, as one of the students at Shujin, Shiho Suzui, attempts suicide. Ann, Shiho's best friend, discovers before Shiho loses consciousness that she was driven to end her life by Kamoshida. Ren, Ryuji, and another student named Yuuki Mishima, a frequent victim of Kamoshida's abuse, confront Kamoshida. Kamoshida taunts the three with the fact that he broke Ryuji's leg and disbanded the track time out of spite when his bringing up Ryuji's lack of a father resulted in a violent outburst, and that he had Mishima spread rumors about Ren's criminal record. Regardless of whether he did something to Shiho, Kamoshida is secure in the knowledge that it was his word against a group of problem students, and that the faculty and even parents willing turn a blind eye to his abuses. To demonstrate the power he wields, he tells the three that at the next faculty meeting, he will recommend their immediate expulsion!
With only a couple of weeks until their expulsion, which would violate Ren's probation and result in his immediately going to juvenile detention, Ren, Ryuji, and Morgana delve back into Kamoshida's Palace. In doing so, they accidentally draw in Ann. Ann is captured by Shadows, and Kamoshida's Shadow taunts Ann with the fact that, since she wouldn't accept his advances, he decided to force himself onto Shiho. Angered beyond words, Ann's Persona, Carmen, awakens.
With Ann now on their side, Ren, Ryuji, and Morgana delve deeper into the Palace, eventually discovering the location of its Treasure. However, the Treasure's form is amorphous, and it cannot be stolen as is. In order to take the Treasure, they would need to force it to materialize by confronting Kamoshida with the possibility that his desires would be taken from him. To that end, they would need a "Calling Card".
Ryuji makes several Calling Cards and places them on the school's bulletin board in secret. The card, signed by the "Phantom Thieves of Hearts", warns Kamoshida that his will be taken. When Kamoshida sees the calling cards, he becomes incensed—and sure enough, it also causes Shadow Kamoshida to raise his Palace's security level.
The cards serve their purpose: when Ren and company enter the Treasure Room of the castle afterwards, the Treasure takes on the form of a crown. As the four attempt to take the crown, they are confronted by Kamoshida's Shadow, who morphs into a gargantuan monster. Nonetheless, Ren and his friends manage to subdue the Shadow. Ann restrains herself from killing the Shadow outright, which would have terrifying consequences; she decides the best punishment for Kamoshida would be to repent for his crimes until the end of his life.
Ren and company escape from the castle as it begins to crumble. When they return to the real world, the Meta-Nav stops registering the castle: with the Treasure stolen, the Palace has collapsed.
Over the next several days, Kamoshida is nowhere to be seen, apparently ill at home. On the day he promised to have Ren and Ryuji expelled, however, he returns to school during a morning assembly. In front of the entire student body and the faculty, he admits to his abuses and attempted rape of Shiho. He declares that he will atone by taking his own life; but Ann demands he live on and not run from the responsibility of repenting for his crimes.
With that, Kamoshida resigns himself to police custody, leaving everyone present stunned—especially the three "problem students" who caused this.
Afterwards, Morgana takes the Phantom Thieves back into the Metaverse, into a very peculiar Palace known as "Mementos": rather than being any one individual's Palace, Mementos was a Palace for the entirety of the human subconscious, located within Tokyo's subway tunnels. Shadows in Mementos are not powerful enough to have their own Palaces (yet), but pursuing them and forcing them to have a change of heart can have beneficial effects in the real world. Morgana believes that if they delve deep within this Palace, he can find a way to get this memory and human form back...but this will take a great deal of time and effort on their part.
It is in the pursuit of one such Shadow that they learn of Ichiryusai Madarame, a famed artist that, according to the reformed Shadow, is actually a notorious plagiarist who uses the artwork of other people to bolster his own career and wealth. The Shadow's corresponding human used to be a pupil under Madarame until he was no longer of any use to him, and now worries for another pupil of Madarame's—a young man and a passionate artist—that he fears is yet another victim.
The Thieves attend an art exhibition held for Madarame to gather more information. There, they meet Madarame's pupil: Yusuke Kitagawa, an art student at a prestigious boarding school in Tokyo. Yusuke, who becomes enchanted by Ann, talks of how he was inspired to take up painting because of one of Madarame's works, a painting called "Sayuri". When pressed about Madarame's abuses, however, he adamantly defends his teacher, who took him in when he was orphaned and raised him while helping him hone his craft.
The Thieves find Madarame's Palace at his atelier shack, which his twisted heart views as a lavish museum. Therein, they find several paintings of former pupils, as well as one of Yusuke. When they reach a dead end, Morgana suggests changing Madarame's cognition in the real world by gaining access into the locked room in Madarame's atelier.
To that end, Ann accepts an offer Yusuke made to model for a nude painting. Morgana picks the lock, and Ann pulls Yusuke into the now-unlocked room. Madarame catches them as they discover the locked room was used to store several forged paintings of the "Sayuri", along with what appears to be the real original "Sayuri".
Yusuke, now finally accepting in his heart the fact that his mentor was a fraud, accompanies the Phantom Thieves into Madarame's Palace. When they go to take the treasure, Madarame's Shadow appears, revealing to Yusuke that his mother was one of Madarame's pupils and the original painter of "Sayuri", which featured a young woman holding a baby: Yusuke and his mother! Yusuke's mother was physically ill and one day, when she was suffered a seizure, Madarame left her to die so he could steal the "Sayuri", modify it, and claim credit for painting it himself.
Enraged, Yusuke awakens his Persona, Goemon, and aids the Phantom Thieves in subduing Madarame's Shadow and taking the Treasure for themselves. Before the Palace begins to collapse, however, Madarame reveals the existence of another Metaverse user: one with a "black mask".
The Phantom Thieves escape with the original version of "Sayuri", which Yusuke gives to Sojiro for safekeeping. Not long after, Madarame holds a press conference wherein he confesses to plagiarizing his pupils' works.
In the meantime, Shujin students go on a school trip to a television studio, where, in addition to learning about how a show is produced, the students would be able to sit in the audience of a talk show featuring a very popular guest star: the high school detective prodigy, Goro Akechi. To the surprise of Ren and his friends, Akechi condemns the Phantom Thieves, stating that they are criminals who use reprehensible means to force others to confess their crimes, and that he has a vested interest in their capture and arrest. Nonetheless, he and Ren start to become friends.
With Makoto on their tail, the Phantom Thieves try to keep their activities a secret. Unfortunately for them, they slip up: Makoto manages to record a conversation wherein they refer to themselves as the Thieves. Instead of taking this evidence to Kobayakawa, however, she uses it to broker a deal with the Thieves: she wants help in taking down a notorious criminal ring targeting Shujin students in Shibuya. If the Thieves can change this ringleader's heart, she will delete the evidence. Otherwise, she will report them.
Ren discovers that this crime ring's leader is a thug named Junya Kaneshiro. The Phantom Thieves discover that his distortion is the largest they've discovered yet, encompassing the whole of the Shibuya district. With how Kaneshiro sees people as little more than walking ATMs from whom to take money, once they enter the distortion, they discover that his Palace has taken the form of a massive flying bank. They cannot reach the bank, however; only Kaneshiro's "customers" have that dubious privilege.
Noticing that they are stuck and already under pressure herself, Makoto attempts to help the Thieves meet with Kaneshiro in person; fearing for her safety, the Phantom Thieves go after her. Unfortunately, Kaneshiro takes a photo of them all in his seedy bar and extorts them, threatening to leak the incriminating photos unless they can pay him three million yen. While that puts them under a time crunch to change his heart, the fact that Kaneshiro is demanding money from them has caused the change in cognition needed to let the Thieves into the Palace.
Inside, the Phantom Thieves are contacted by the bank's owner, Kaneshiro's Shadow, who states his intent to bleed them dry, then turn his attention to Makoto's sister: the prosecutor Sae Niijima.
Makoto, refusing to allow that to happen, awakens her Persona, Johanna. Now a Phantom Thief herself, she helps the others steal Kaneshiro's Treasure. Before the Palace collapses, Kaneshiro warns the Phantom Thieves about the black-masked enemy.
As a result of the change of heart, Kaneshiro surrenders himself into police custody, his testimony to them causing his entire crime ring to collapse. Furthermore, Makoto reports to Kobayakawa that she has been unable to find anything on the Phantom Thieves' identities.
Realizing that Futaba shared the same family name as his caretaker, Ren tries to press Sojiro for information about Futaba, but to little avail. Eventually, however, the Phantom Thieves begin to suspect that "Alibaba" and Futaba are the same person.
One day, after coming home, Ren finds Sojiro being confronted by Sae, who threatens to have Sojiro's parental rights terminated unless he cooperates with her invesigation. Worried, the Phantom Thieves intrude in Sojiro's home for clues during a stormy evening, when they come across a young woman who retreats into her room upon being sighted.
Drawn home by the ruckus, Sojiro finds Ren and his friends in his house. He finally decides to come clean about Futaba's situation.
Sojiro was an old acquaintance of Futaba's mother, Wakaba Isshiki, an eccentric but brilliant scientist researching "cognitive psience". One day, however, something strange happened to Wakaba, driving her to end her own life. A young Futaba watched as her mother jumped into the path of an oncoming car. After a series of events, Sojiro adopted Futaba and raised her as his own daughter. But the mental trauma from watching her mother kill herself left Futaba depressed. It's gotten worse in the past few months, to the point of Futaba suffering visual and auditory hallucinations, her mother presumably among them. Sojiro tried to get her help, but Futaba had immediately shut herself in her room, refusing to come out or talk to anyone, even to Sojiro. Sojiro's efforts to not exacerbate this was the main reason why Ren wasn't allowed in the Sakura residence in the beginning.
Now more determined to help, Ren and his friends contact Futaba over texts at Sojiro's house to determine the nature of her distortion. They get the clue they need when Futaba describes her room as her "tomb", her final resting place once the guilt over her mother's untimely demise drives her to suicide. With that, the Phantom Thieves are able to infiltrate her Palace: a pyramid tomb, isolated by a vast desert.
The Phantom Thieves make their way through the pyramid, learning more about Futaba's guilt and suicidal ideation. When they reach the Treasure room, they are attacked by a monstrous apparition of Wakaba, created from Futaba's twisted perception of her mother, whom she believes despised her. Morgana's analytical abilities are soon proven insufficient to survive this foe. Suddenly, Futaba appears beside them, however, having received the Meta-Nav app herself. Doing so was a risky move, since she was confronted with the full brunt of her guilt.
Futaba's Shadow appears before her, however. She tells Futaba that everything she knew about her mother was a lie: she didn't actually kill herself, she was murdered! And she never hated her daughter, but loved her to her dying breath.
With the lies that had been brought before her broken down, Futaba awakens her Persona, Necronomicon, and uses its powerful analytical abilities and localized distortion-manipulation powers to help the Phantom Thieves destroy the false cognition of her mother.
With the lies that had shaped her life now put to rest, Wakaba appears before Futaba one last time, reaffirming her love for her daughter before Futaba, who was her own Treasure, leaves the Palace. The Phantom Thieves also make their escape as the Pyramid crumbles.
Sojiro is surprised to find Futaba able to leave their house to come to his cafe, but is relieved to see his daughter beginning to recover.
Afterwards, Futaba, the newest member of the Phantom Thieves, confides in her new teammates that she believes her mother was murdered because of her research into cognitive psience: someone must've had an interest in the discoveries she made and silenced her to keep them a secret.
As for Medjed: Futaba is the original Medjed, having used the identity during her hacktivist days. When other hackers took the identity for themselves during other less-scrupulous hacking incidents, she abandoned the name and became "Alibaba". The "Medjed" hacker who threatened and taunted the Phantom Thieves was a Japanese hacker whose personal information Futaba leaked onto the Internet after the Phantom Thieves helped her, forcing the copycat to stop.
To commemorate Futaba's joining the Phantom Thieves (and gradual recovery), a trip to the beach is arranged for Futaba. Morgana, however, begins to wonder if he has a place in the Phantom Thieves anymore...
Before school resumes, Principal Kobayakawa suddenly dies in front of a police station. Because the staff would be busy dealing with the aftermath, seniors are brought along as chaperones. While Ren and his classmates travel to Hawaii, Futaba and Morgana remain in Tokyo to sift through the information taken from Sae's laptop. When the Phantom Thieves return, Futaba reports that Sae had been finding links between the mental shutdown cases while also investigating the Phantom Thieves. All the while, Morgana and Ryuji have a falling out, prompting Morgana, who started to believe he no longer had a place in the Phantom Thieves, to leave.
With Medjed's defeat, the Phantom Thieves' popularity skyrockets, while Akechi's own popularity takes a hit as a result of his criticisms of the Thieves. A special poll is set up to determine the Thieves' next target, with the winner of the poll being Kunikazu Okumura, the CEO of Okumura Foods. Okumura, who is hoping to launch a career in politics, is rumored to be abusive to his employees, forcing them to work unpaid overtime to the point of serious illness. Rumors also abound of him resorting to underhanded means to stamp out competition, which the Phantom Thieves suspect is related to the mental shutdowns.
The Phantom Thieves investigate Okumura's Palace, which resembles a space station used to launch a UFO representing his political career, albeit at the cost of the space station representing his company, and the workers, who appear as run-down robots. While investigating the Palace, the Thieves reunite with Morgana, who has enlisted the aid of another Persona-user whom he calls the "Beauty Thief". The Beauty Thief demonstrates an ability to bypass biometric locks in the Palace, hinting at a relationship between her and Okumura.
It is soon revealed that the "Beauty Thief" is actually Haru Okumura, a Shujin Academy senior and the daughter of Kunikazu Okumura. Haru learned about Palaces and Personas from Morgana, but her power was still weak. She wanted to change her father's heart: as a means to achieve a strong political foothold, he had arranged for Haru to marry the son of another politician.
After Haru helps to mend the rift between Morgana and his friends, the Phantom Thieves return to the Palace, where Haru's power finally awakens, giving birth to the Persona Milady. Together, they take the Treasure and leave before the Palace collapses.
Unbeknownst to them, an assassin was waiting to execute Okumura's Shadow...
After taking the Treasure, Haru arranges a victory party at a famous theme park to celebrate, as well as to watch the press conference where Okumura confessed his crimes, as well as revealed the identity of the one behind the mental shutdowns.
...or so they thought. Before Okumura can reveal this sordid secret, however, he suddenly clutches his chest and collapses, his eyes turned completely white and his face covered in blood.
Okumura's death also causes approval and popularity for the Phantom Thieves to plummet.
To make matters worse, Akechi has evidence of the Phantom Thieves' true identities, having them dead to rights. During the school festival at Shujin, he makes a deal with Ren and his compatriots. There is a heart that Akechi wants changed: Sae Niijima, Makoto's sister. He was concerned that her desire to apprehend the Phantom Thieves was perverting her sense of justice, as she was willing to go to any lengths, no matter how ethically dubious, to have them arrested and imprisoned. The existence of her Palace confirms his concerns. As such, he asks for the Phantom Thieves to help him change Sae's heart. In exchange, he would not report them to the police. Furthermore, he asks that this job be the Phantom Thieves' last, and that they disband afterwards.
The Phantom Thieves are left with no choice but to cooperate with Akechi. They enter Sae's Palace, which is located at the courthouse, which Sae envisions as a place where people's freedom is gambled and where she must win at all costs. As a result, the Palace takes the form of a casino, where Sae is the proprietor and the house always wins.
Akechi aids the Phantom Thieves, having already awakened his Persona, Robin Hood, during an encounter with the black-masked assassin responsible for Okumura's demise. Together, the Phantom Thieves and Akechi defeat Sae's Shadow and take her treasure.
Unfortunately, just as they acquire the Treasure, a large contingent of enemies begins to converge on their position. The Phantom Thieves split up to evade capture, with Joker providing a diversion to help them escape.
It is during this escape that Joker is cornered and captured by the police...
Sae decides to put her faith in Ren and show the cell phone to Akechi as she passes him after leaving the interrogation room.
Afterwards, Akechi enters the interrogation room with an armed escort, supposedly to interrogate Ren himself. Suddenly, Akechi takes the guard's sidearm and shoots him before turning his gun on Ren: he had come not to interrogate him, but to assassinate him.
And thus, with a single bullet to the head, Ren Amamiya dies. Akechi places the gun in his hand, then reports his success to his conspirator, a politician named Masayoshi Shido.
The following day, news of the capture and subsequent suicide of the leader of the Phantom Thieves is broadcast.
...All According to Plan.
Unknowingly for Shido and Akechi, they had only killed a cognitive duplicate of Ren, while the real Ren successfully escaped from the police station with Sae's help. Sae later brought Ren back to Leblanc and told Sojiro to keep him safe for now.
Later on in the same day, the Phantom Thieves, including Ren, Sae, and Sojiro, meet at Leblanc. The group explains to Sae and Sojiro, both still clueless at this point, that they had realized something was amiss with Akechi for a long time: during the school trip to the TV studio, Morgana mentioned pancakes. Akechi responded to the mention of pancakes, which neither Ren, Ryuji, or Ann spoke of at that very moment. That could only mean that Akechi was aware of the Metaverse for a long time and had previously encountered Morgana at some point. To confirm their suspicions, they had Futaba put a wiretap on Akechi's phone before their excursion into Sae's Palace. From the recorded conversations Akechi had with Shido, they were able to conclude that Akechi was plotting to betray them and kill Ren, and come up with a countermeasure.
As for their caper in Sae's Palace: they never actually took her Treasure, allowing her Shadow to maintain a cognitive copy of the police station outside of the main Palace body. It is here where Sae's cognitive duplicate of Ren, being interrogated, manifested in the Metaverse. That way, when Sae showed the cell phone to Akechi, Futaba, who had wiretapped the phone, could remotely trigger the Meta-Nav, unwittingly pulling Akechi into the Metaverse. He had actually carried out an assassination on a cognitive duplicate of Ren, while the real Ren sat alone, unharmed, in the interrogation room in the real world after Sae left.
Thus, as far as the country knew, Ren Amamiya, the leader of the Phantom Thieves, was dead. Sae managed to use her connections with the police to keep the fact that there was no corpse a secret while Shido and Akechi had his death reported on the news.
Their problems have not ended with Ren's fake death, however: Shido is on the fast track to becoming the next Prime Minister of Japan, and it's only a matter of time until the authorities figure out that Ren was still alive.
While looking for the keywords needed to enter Shido's Palace, Ren remembers that Shido was the drunk that had him arrested on a trumped-up assault charge.
When the Phantom Thieves enter the Palace, they are taken aback at its appearance: a massive cruise liner sailing through the ocean, passing past ruined buildings as though the nation had sunk. Shido truly thinks very little of the country, further spurring the Phantom Thieves to change his heart.
As they fight their way through the Palace, they learn that Shido had been manipulating events surrounding the Phantom Thieves' actions from the very beginning!
Principal Kobayakawa let Kamoshida's crimes slide while using Makoto to keep the controversy under wraps.
Madarame's plagiarized art and Kaneshiro's extortion racket provided funding for Shido.
The Medjed hacker that threatened the Phantom Thieves was on Shido's payroll.
Okumura was also in on Shido's conspiracy, but had become a liability due to his using Shido's resources for personal gain, hence, he manipulated the Phantom Thieves into taking his Treasure so as to frame them for his death.
They are eventually confronted by Akechi, who realized something was amiss when Shido began to grow anxious. Akechi reveals that he is Shido's illegitimate son, born from an affair his mother had with him. Having only himself to rely on, he struggled to excel in the world so that someone would acknowledge him. He eventually found himself in Shido's employ, working to institute mental shutdowns and breakdowns on those who stood in the way of his rise to power, thanks to his Persona's ability to induce madness in the hearts of others in addition to killing his victims' Shadows.
Akechi planned to help Shido up until he achieved his goals, at which point he would exact his own revenge against his father.
When Ren and his friends overpower Akechi and his Persona, Akechi reveals the full extent of his power: with a second Persona named Loki, he transforms into the black-masked assassin that the Shadows of Madarame and Kaneshiro mentioned. Even with this power, however, Ren prevails.
As Akechi laments that he was powerless to defeat Ren and his allies, a doppleganger of Akechi born from Shido's cognition appears. The cognitive Akechi holds his counterpart at gunpoint and prepares to kill him. Akechi, deciding to leave the task of defeating Shido in Ren's hands, seals off the bulkhead in the engine room, trapping himself with the cognitive Akechi and sacrificing himself to give the Phantom Thieves a chance to escape.
Once the Thieves find their way to the Treasure Room, they make preparations to send a Calling Card. They can't do it the same way as before, however, since there is a likely chance that any conventional attempt to send the Calling Card to Shido would be thwarted.
Thankfully, Futaba has a plan...
That night, mass media across the entire country is hacked by Futaba, who broadcasts a message to the entire nation declaring that not only were the Phantom Thieves still around, but their leader was still alive and well. In addition, they call Shido out on his corruption and underhanded tactics, and vow to take his Treasure and make him confess his sins.
Concerned that the Phantom Thieves may succeed, Shido puts contingency plans in place as the Phantom Thieves invade his Palace.
In the Assembly Hall of the Palace, Shido's Shadow confronts the Phantom Thieves, revealing his intent to kill his own son Akechi once he became prime minister. Joker confronts Shido's Shadow, revealing himself to be the young man he had arrested on a trumped-up assault charge.
Determined to see his vision of "a powerful Japan" bear fruit, Shido's Shadow fights the Phantom Thieves, but is ultimately defeated. Realizing he had been bested, Shido's Shadow apologizes to Ren for having him arrested on false charges.
In the real world, Shido begins to sense his heart changing. Determined to keep his ambitions aloft, he takes a drug that would induce a false death, in the hopes that it would kill the Phantom Thieves when his Palace collapses.
The Phantom Thieves take the Treasure, a golden ship wheel, and make their escape as the ship begins to explode and sink. Ryuji manages to secure a lifeboat for the other Thieves using his long-lost sprinting prowess, and the Phantom Thieves escape from the collapsing Palace with Shido's Treasure: a legislative pin.
When Shido comes to, he begins to weep and talk of repenting for his crimes, striking fear into his conspirators.
On the day that the ballot is counted, Shido confesses to his crimes on live television. As the public are shocked at this turn of events, Shido's conspirators, including a psychiatrist, the new SIU director, and a Shido-supporting politician, plan to use what resources they have to take control of the country for themselves by using the Metaverse...
As the Phantom Thieves ponder their next move, Morgana makes a surprising proposition: that the heart of humanity as a whole has become distorted, and in order to save themselves and the country, they would need to take the treasure from the Palace of the general public: Mementos. Doing so, however, would cause the source of all cognitive distortions to vanish, and as such, the Phantom Thieves would no longer be able to access the Metaverse. This would be their final job, but it is one they agree to undertake regardless.
That night, Ren dreams of Igor and the Velvet Room once more. Shockingly, however, Igor deems that Ren's rehabilitation has failed, and that ruin is inevitable...
The following day, the Phantom Thieves make their way into the innermost depths of Mementos, which resembles a massive prison containing the Shadows of humanity. To their horror, the Shadows, including those of Kamoshida, Madarame, Kaneshiro, and Shido, all desire to be kept in this prison; they claim that it is where their desires would be granted; the freedom to live life without having to choose for themselves, a result of the Phantom Thieves stealing their desires. In addition, along the way, Morgana begins to recall some of his lost memories: he was actually born within the depths of Mementos!
The Thieves eventually make their way into the very core of Mementos and find the Treasure: a massive construct described by the inmates of the prison as the "Holy Grail". The Thieves attempt to destroy it, but the will of the prisoners keeps it intact and gives it a lustrous shine as a booming voice from within the Grail taunts the Thieves, calling their efforts to destroy it all for naught and their power and efforts meaningless against the will of humanity.
In a blinding flash of light, the Phantom Thieves find themselves back in Shibuya. However, something is horribly wrong: bone-like structures jut out of the ground, and blood rains from the sky. Worse still, the people seem oblivious to the monstrous transformation their world is undergoing. The voice of the Holy Grail states that reality and Mementos have been fused into a singular entity. As a result, nothing can exist in this world if it is not part of the general public's perception.
Because no one believes in the Phantom Thieves' existence anymore, they are no longer a part of the people's cognition. Thus, they begin to vanish one by one, with Ren being the last to go.
Ren awakens in the Velvet Room, where Igor dictates that because he has lost the "game", his life is forfeit. He sentences him to immediate execution, which he tasks Caroline and Justine with carrying out.
However, the twins begin to hesitate. When Ren's indomitable, rebellious will grants him his abilities as a Phantom Thief once more, the twins try to subdue him, but ultimately, the memories they had lost come back to them: they were once a singular being before being split in twain by a malevolent entity. They task Ren with fusing them back together using the guillotines used to fuse Personas, and once more become a single person: a little girl named Lavenza.
As it turns out, the "Igor" whom Ren had met at first was an impostor, a disguise used by the will of the Holy Grail. The fiend praises Ren for keeping him entertained, and makes him an offer: he would restore the world to the way it was before the fusion, and bring the Phantom Thieves back into the public's cognition. "Igor" could continue observing him and the Phantom Thieves, and they would be permitted to live out their fantasies in the Mementos-fused world.
Ren, however, refuses: taking the offer would mean condemning humanity to the Holy Grail's malevolent will.
With that, the Holy Grail dismisses Ren.
After the impostor leaves, the real Igor, the real master of the Velvet Room and of Lavenza, appears. Igor tells Ren that his friends may yet still live; they are similarly trapped in prisons within the Velvet Room. Ren visits each of his friends, restoring their rebellious spirits after they had fallen into despair at the state of the world.
The Phantom Thieves reconvene in Igor's chamber, where Lavenza explains that the malevolent god that had split her and imprisoned Igor had created a "game" to determine humanity's fate. The players were Goro Akechi, who sowed distortion in humanity's heart and would lead to the world's destruction if he won; and Ren, who embodied the "Trickster" who would lead the world to salvation. However, the selfsame malevolent god was born from the distorted desires of humanity, and as such, rigged the game to have the outcome he desired. Before he was imprisoned, however, Igor created a being that would guide the chosen "Trickster"; Morgana! Morgana, who finally regained all of his memories, confirms as much. He remembered being created in the depths of Mementos because the malevolent god had absorbed the Velvet Room into Mementos.
With their indomitable wills, Lavenza tells the Phantom Thieves that they possess the power to oppose the malevolent god. When they return to the real world, they find that people have started to see them and recognize them; they existed once more within humanity's perception!
The Phantom Thieves fight their way back to the shrine where the Holy Grail lies, defeating its guardians along the way. As they do, the public begin to recall their memories of the Phantom Thieves; but at the same time, people began to vanish like Ren and his friends had.
Finally, the Thieves return to the Holy Grail. After severing its link to the will of the people, the Grail transforms into its true form: the god of control, Yaldabaoth. Harnessing the power of the seven deadly sins, Yaldabaoth attacks the Thieves relentlessly. Nonetheless, they stand up to Yaldabaoth's onslaught.
When all hope seems lost, Mishima begins cheering on the Phantom Thieves. Mishima's act inspires the people of Tokyo, including everyone whose lives Ren touched, to cheer on the Phantom Thieves. Their belief in the Phantom Thieves becomes power in the cognitive world, power that Ren harnesses.
Ren summons Arsène once more, and breaks the chains binding him. No longer tethered, Arsène transforms into his true form: the demonic god, Satanael. With a single shot from its massive gun, Satanael blasts a hole through Yaldabaoth's head, destroying him once and for all.
With Yalbabaoth's death, Mementos begins to un-fuse itself from reality and vanish. As the world is restored to its proper state, Morgana, too, begins to vanish, leaving his friends with some parting words:
- "The whole world is a product of cognition, not just the Metaverse. It can be freely remade. The same goes for you and everyone else. ... Soon, a new world will come: one where mankind isn't held captive. The world will shine brightly as long as you hold hope in your hearts. ... Remember...there's no such thing as the "real" world. What each person sees and feels...Those are what shape reality. This is what gives the world infinite potential. Even if you feel that only darkness lies ahead, as long as you hold hands together...see it through as one...the world will never end! The world exists within all of you!"
That evening, Sae meets Ren. She thanks him for saving the world, but asks him to turn himself into the police. Doing so was not only necessary for ensuring Shido's conviction, but also the only way he can keep his friends out of trouble with the police and the public prosecutors who would lose face to them. In addition, Ren's probation would be revoked, and he would be sent to juvenile detention. With no other choice, for the sake of his friends and the society he helped reform, Ren agrees to Sae's offer.
As the new year begins, the plan to save Ren is put into motion: everyone who Ren helped over the course of the previous year gathers to vouch for Ren at his trial.
Ren awakens in the Velvet Room once more, where Igor and Lavenza offer him one last gift: the Arcana of the World, signifying his ability to follow his convictions and a testament to the fact that he is not alone in the world. Igor and Lavenza say their farewells to Ren, and the Velvet Room vanishes into white light...
Finally, just before Valentine's Day, Sae delivers the good news: Shido will be tried in a court of law. Also thanks to Shido's testimony, as well as the woman who was forced to bear false witness against him, Ren's sentence was to be rescinded: he is free to leave! Sae thanks Ren and the Phantom Thieves for their aid and announces her intention to quit her job as a prosecutor and become a defense attorney.
Ren returns to Leblanc that day to his fellow former Phantom Thieves, and they hold their long awaited celebratory party. As they mourn Morgana's absence, to their surprise, Morgana appears! He speculates he was still able to exist because his friends never forgot about him, making him a permanent fixture of their cognition.
Sadly, Ren would have to return back to his hometown next month. The group decides to celebrate Morgana's return and make the most of Ren's time left in Tokyo. Morgana also decides he would stay by Ren's side when he returns home, in the hopes that sticking by his side would help him become human.
After saying his goodbyes to all of the friends he made over the course of the year, on March 20, Ren makes his way to the train station. Along the way, he runs into his old friends, who offer to drive him home. They notice that they are being surveiled, but they pay it no heed: they are free to do as they please.
With the surveillance detail sabotaged thanks to Morgana, Ren and his friends disembark on a road trip.