Makoto Niijima is a playable character in Persona 5. She's the student council president of Shujin Academy and younger sister of Sae Niijima who lives a double life as a Phantom Thief.
The Niijima sisters Makoto and Sae lived alongside their father since their mother died when they were young. As he was not home often, the sisters disliked him. Unfortunately, three years ago, he was murdered by being ran over by a truck in the line of duty, forcing the elder sister Sae to juggle between handling cases in court and raising Makoto alone. In order to retain the 99% conviction rate of her country's courts, Sae also more often than not, found herself having to rig cases with a guilty charge against her will. As a result, she saw both Makoto and their father as a burden and did not hold her in high regard. Makoto also regretted disliking her father and wished that he would still be around.
Makoto was deeply apologetic that her sister has to shoulder the burden of supporting her on her own, which she absolutely hates being in a position at, and as a result studied very hard so that she can enter a top-notch university, and relieve Sae's burden once she graduates. Unfortunately, nobody in school treated her seriously, and even Sae's associates, such as Goro Akechi, mocked her for her submissive attitude. When Akira moves in Tokyo, she has become a third-year honor student and the president of the student council in Shujin Academy, although she was dissatisfied with the situation because the students view her as incompetent and unfit for the job.
She can initially be found in the school library on 4/18 studying at a table after school lets out for the day, and will appear semi-regularly there from then on. During the period where Suguru Kamoshida was sexually harassing students, blackmailing them and abusing his fellow athletes in Shujin, Makoto wanted to do something against him, only to back off in fear of Kobayakawa giving her a bad resume as retaliation.
After Madarame's confession, she was asked by Principal Kobayakawa to investigate the possibility that the Phantom Thieves are students from their school after their volleyball coach, Suguru Kamoshida's confession and arrest. She accepts the request and is quick to deduce that Akira and the others are the Phantom Thieves and starts to approach them. Ann Takamaki, in particular, does not like her presence due to a rumor that claims Makoto was aware of Kamoshida's true nature but kept quiet about it like everyone else in order to maintain a paragon image before the faculties and receive a recommendation for her own benefit, a thought that Ann bitterly tells Makoto, which disturbs her. (Unfortunately, this turned out to be true as she confirmed personally later on after Kaneshiro extorts the party.)
She begins to tail Akira for a time, following him whenever he is in school or even as far as Shibuya. On June 11th, Makoto finally confirms her suspicions when she hears Ryuji and Ann declares out loud in the courtyard of Shujin Academy that they are the Phantom Thieves. However, she decides not to give this proof to Kobayakawa and instead demands the Phantom Thieves to prove their justice by reforming an unknown mafia boss who has been extorting many students around Shibuya, including those attending Shujin Academy. If they can complete the task, she will not expose their identities to anyone (even the police). Deep down, Makoto actually approves of the thieves and believes her father would think the same way, which she told Sae when the sisters were having dinner at home, triggering Sae's anger, causing her to call Makoto a "burden." This disheartens Makoto heavily, even if Sae quickly apologized for insulting her because of an impulsive fit of rage. Sae then tells Makoto that she will not have dinner with Makoto from that point on, implying that she still holds grudges against her.
Makoto checks on the group as they have trouble reaching the center of mafia boss Kaneshiro's Palace. Ann, Ryuji and Yusuke point out how useless she is for not doing anything that can help them, but rely on the hard work of somebody else, something that greatly upsets Makoto after being told the same thing before by her sister and Akechi. To prove her worth, Makoto purposely acts as bait into the mafia so that the gang can follow behind. Once there, Kaneshiro takes photos of the group being merely present in his adult-exclusive nightclub for blackmail material. He demands 3 million yen within 3 weeks in exchange for the photos, which will ruin their reputations if leaked. Additionally, if they cannot pay the 3 million yen, he would force Makoto into prostitution to pay back the debt, adding that he may even keep Sae as his personal slave.
Makoto apologizes for her rash actions and explains how this folly could ruin Sae's effort in raising her. She tries to think of a way to pay Kaneshiro, but Morgana suggests to make her an ally by bringing her along to Kaneshiro's Palace because she is now the "special customer" to Kaneshiro's extortion business. Entering the Metaverse, a passageway is opened to allow the thieves and Makoto to access Kaneshiro's "floating bank."
Makoto is confronted by Shadow Kaneshiro who taunts her by revealing his plan to extort her sister. Kaneshiro's mocking display of exploiting the obedience of others would be met with a violent rebellion from Makoto, who would no longer let other people decide how to discipline herself, awakening to her Persona power of Johanna and deciding to join the Phantom Thieves.
If the party cannot complete Kaneshiro's Palace in time, the police come to arrest Akira, claiming they have found a drugged and brutalized schoolgirl (heavily implied to be Makoto) in one of Kaneshiro's nightclubs deliriously muttering his name. This scenario is a false recollection made by Akira during Sae's interrogation due to his mind being addled by drugs he was forcefully administered by the police. Sae proceeds to leave the room to give Akira time to recover, at which point Akechi takes the opportunity to assassinate him.
After changing Kaneshiro's heart, she receives a call from Kaneshiro who tells her he has deleted the photos and is going to turn himself in, relieving Makoto and the others. She then reports to Kobayakawa that she concludes her investigation of the Phantom Thieves by simply telling him that the Phantom Thieves are justice, lying that she does not have any proof that the Thieves are in their school, much to Kobayakawa's dismay. She even declines his recommendation letter for university when Kobayakawa persuades her once more, asserting she's going to establish her success on her own.
Upon showing her support for the Phantom Thieves, Makoto and Ann mend their relations by exchanging apologies for shifting blame off of themselves. Makoto asks if she can address Ann directly by her given name and without honorific, to which Ann happily agrees. Makoto also begins to act as the strategist of the Phantom Thieves by proposing direction and trouble solution for the gang. She usually analyzes the puzzles around the Palaces aside from cases where Akechi is around the party, as Akechi's deduction skills are sharper than hers. She goes so far that she installs spyware written by Futaba Sakura in Sae's laptop so the gang can learn the investigation progress of the Prosecutors Office.
During the group's rise to fame, Makoto would act as their voice of reason, as a majority of the group wanted to reveal their identities to the public. In addition, Morgana, who also disagreed with their views, would have lost his ability to think rationally under his misguided belief that he's useless, and would run away from the group.
Upon investigating and identifying Morgana's new ally, Haru Okumura, Makoto questions her about her origins as a phantom thief: although both sides had the same goal in mind and Makoto related to Haru's desire to change her family relative's heart, she failed to recruit her, as a reluctant Haru calls them out for their aimlessness and not helping their own teammates when they need it the most.
After the Thieves come under suspicion, Makoto proposes reaching out to Akechi in order to gain information, only to find that Akechi has already realized all of their identities. Akechi says that he will release the photos of the Thieves exiting the Palace to the police unless they work with him to find the true culprits behind Okumura and Kobayakawa's death, both of them who he committed under the orders of the Conspiracy head. However, the first step involves stealing Sae's heart before the investigation finds (or plants) incriminating evidence on the Thieves. Makoto admits that she has known for a while that her sister has a Palace, but had hoped to change Sae's heart through other means.
While progressing through Sae's Palace, Makoto is shocked to realize the depths of her sister's bitterness and cynicism, particularly her Shadow's belief that trials are nothing more than games to be won by any means necessary. She nearly has a breakdown upon facing the true nature of her sister's Shadow but is able to calm down when Akechi comforts her.
During the infiltration of Shido's Palace, the group arrives at a banquet hall as they try to look for invitation letters to enter the assembly hall. Due to her more formal nature, she decides to take a seat alongside Ryuji before Ooe's Shadow confronts them. Ryuji unintentionally escalates the situation by talking back but Makoto manages to appease the shadow with compliments and inquires about the subway accident, which Ooe claims that he had ordered to take down a diplomat and a rival CEO who supported the current government.
Makoto can be seen following along behind Akira on the way to school on April 15th. A short while later, she will be seen near the doors to the courtyard in the practice building, expressing shock about a teacher directing her to conduct the students back to their classrooms and be silent about the situation online in order to avoid a scandal, wondering about ensuring the safety of the students and directing paramedics.
In addition, she can also be found observing Akira and Ryuji during their first trip to Kichijoji.
In Royal, in the third semester events when Tokyo is in Takuto Maruki's reality, her father is back as if he had never died, and the family relations between Makoto and Sae have been repaired, having an almost strong sisterly bond. According to the two, their father also received an award for being an outstanding officer.
This is a result of Makoto's desires, as she wished for her father to be alive, so Sae wouldn't need to take care of her and treat her like a burden. In this reality, the sisters' father never died to begin with. Once Makoto chooses to deny Maruki's reality, her father is never heard of again.
If Akira maxes her Confidant and talks to her after she rejoins, she will berate herself for her selfishness of wanting to have a fulfilling life with her father and her sister going against her promise to protect Akira at all costs, and states that she will now move forward on her own, evolving Anat and Johanna into Agnes.
If Akira chooses to accept Maruki's reality, it becomes the true reality, and Makoto will graduate from Shujin on March 15 alongside Haru. During the credits, a man (revealed to be the Niijima sisters' father in the Thieves Den) can be seen serving dinner for his family.
A few weeks after Akira's release from prison following Maruki and the restoration of their reality, the Phantom Thieves then gathered at Leblanc with Sojiro participating in their meeting. Having been inspired by her experiences in the other reality, Makoto, along with Haru, revealed they will be moving far away after graduation to find new places to stay for their college years. She agreed with the Phantom Thieves to remain connected while they move forward with their futures.
After the group helped Akira evade the authorities who attempted to follow him back to his hometown (with the assistance of the reformed Maruki who now works as a taxi driver), Makoto is seen with Sae as they browsed over her accommodation options outside a real estate shop. The two of them disagreed over her options and have started arguing with each other for the first time before shortly laughing after, a sign of how much Makoto has matured after joining the Phantom Thieves.
Makoto is now a college student who is getting used to her new life. At some point after Akira's departure, she eventually witnessed Haru's driving firsthand and became terrified.
Six months after Akira and Morgana's departure, the Phantom Thieves planned to reunite in Tokyo and go on a camping trip together during their summer vacation. While discussing their camping trip, they use a popular mobile app called EMMA to look for their camping equipment and everything else that is necessary for their trip. However, after regrouping, they learn of the existence of a new Metaverse-related incident involving a fashion designer and idol known as Alice Hiiragi using an alternate reality known as a Jail overlaid onto Shibuya to mesmerize the public to her. Knowing the threat, they all decide to investigate, re-establishing the Phantom Thieves of Hearts.
During their investigation on Alice, they are approached by a police officer named Zenkichi Hasegawa, who saved them from drunkards before inviting himself to Leblanc so he can speak with the Phantom Thieves. His presence is welcomed negatively by the group, with Haru making it clear that they hate police and distrusts him, much to his dismay. Zenkichi reveals that the Phantom Thieves are the prime suspects of the new change of heart incidents, even if that incident was instigated by Alice, and he offers them a deal to clear their names in exchange that they work together with him. They reluctantly reject his offer, and instead focus on changing Alice's heart. However, their plan backfires as her confession has made the police convinced that the Phantom Thieves are involved, leaving the group no choice but to accept Zenkichi's offer. Only by this notification, the Phantom Thieves knew that the incident was Japan-wide, and Alice was only the tip of the iceberg within it.
Makoto and her friends take Zenkichi's deal, with her reminding the officer about the basics of conspirators. After Zenkichi suggested getting their own ride, Sojiro managed to acquire an RV for the group. Makoto served as the group's primary driver, as she was not comfortable with letting Haru drive. During their venture into Okinawa's Jail, its initially eerie nature scared Makoto to the point that she ended up clinging to Akira's leg.
During the trip back to Kyoto, Makoto becomes exhausted, reluctantly allowing Haru control of the wheel despite knowing of her dangerous driving. Haru managed to drive the group back within a single morning despite nauseating and terrifying them. When the group is warned by Zenkichi of a trap at the inn they're staying at, Makoto decides to contact Sae to help get Zenkichi out of jail. Makoto updates her sister on the recent events, which ends up saving the group from Shadow Akane's trap.
In the Legacy of Chris Thorndyke,
She is reprised by Cherami Leigh in the English dub and Rina Sato in the Japanese dub.