Misaka Mikoto/Chronology (Toaru Kagaku no Railgun)

Misaka Mikoto is the protagonist of Toaru Kagaku no Railgun, which involves with her dealing with the darker elements of Academy City, sometimes with a little help from her friends.

In spite of her power as the third-ranked Level 5 of Academy City, she is continually challenged by both situations and enemies that test the limits of her character. She first gets involved in an incident with people using the Level Upper, and though she helped in stopping the incident, it foreshadowed the Dark Side of Academy City. The turning point is of course the Sisters Arc, where she is shown to be utterly powerless against not only the first-ranked Level 5, Accelerator, but of the greater conspiracy that surrounds Academy City, her, and her clones, the Sisters. She experiences growth, humbled by her experience, that despite her power as a Level 5 there are things she cannot solve on her own and that she needs help. Kamijou Touma, who has recently lost his memories including of her, represents this character growth in the form of a crush on him.

Even after the resolution of the Sisters, conspiracies from the Dark Side of Academy City are still brewing up to take her down.

Toaru Kagaku no Railgun
Mikoto, Uiharu Kazari, Saten Ruiko, and Shirai Kuroko were going to a game center, but along the way, the girls get sidetracked to a crepe stand so that Mikoto can collect the figure being given away. The situation suddenly turns bad when a nearby bank gets robbed. In response, Kuroko and Uiharu go to the scene as members of Judgment, and Kuroko asks Mikoto not to get involved. While Kuroko is fighting the robbers, one of them manages to get away from her and tries to kidnap a little boy. Saten manages to grab the boy, but one the robbers kicks her. Seeing this angers Mikoto, deciding to use her Railgun ability on the robbers' car, throwing it into the air and wrecking it. When Anti-Skill shows up to arrest the man, Saten gets thanked by the boy’s mother, and even Mikoto compliments her.

In a flashback, one night Mikoto is shown being hit on by delinquents, when a certain boy named Kamijou Touma tries to save her from them - even though she doesn't need any help. After unintentionally insulting Mikoto while trying to convince the delinquents to stop bothering her, she discharges a powerful electrical attack on them out of rage. Believing that she has defeated them all, she goes to leave, but to her surprise she sees Touma is unharmed. Because of this initial encounter, Mikoto constantly tries to make the reluctant Touma fight her whenever they meet. This is due to him being the first person to not only walk away from her attack unscathed, but to also negate it completely.

Level Upper Arc
Uiharu Kazari gets a cold and cannot go to school, so Saten, Mikoto and Kuroko pay her a visit. Kuroko becomes curious as to how Hatsuya, a Level 2 esper, had powers equivalent to a Level 4's. Mikoto brings up the Level Upper urban legend Saten had mentioned, and Kuroko points out this is not the first time a user's power and the user's level have been vastly different. After discovering where they can get information on the Level Upper, Mikoto goes to a restaurant and pretends to be an interested customer to a group of teenagers who may have information about Level Upper. Mikoto eventually gives up the act when they won't tell her what she wants and soon faces their leader, a girl with the ability to manipulate asphalt. Mikoto wins the fight, but damages a nearby generator causing a city-wide blackout. The next day, Kuroko and Mikoto discover that Hatsuya, along with several others who have shown abnormally strong powers, have all fallen into comas. Meanwhile, Saten discovers the Level Upper on the internet by chance.

Mikoto and Kuroko talked with Kiyama Harumi, the AIM specialist Mikoto had previously met, about the Level Upper. They are later joined by Uiharu and Saten, the latter of which has the Level Upper, but decides to keep it to herself when Kuroko mentions it’s related to criminal activities. Mikoto later catches up with Saten, noticing she's a bit down, and gives her some advice that levels aren't that important, though this secretly irritates Saten. The next day, Saten stumbles upon someone being conned by three thugs over Level Upper and can't bring herself to just run away, so she confronts them. Kuruko coincidentally arrives before Saten gets hurt and subdues two of the thugs, but has trouble using her teleportation powers against their boss, due to his ability to distort light affecting her teleportation. He chases Kuroko throughout an abandoned building, but is defeated when Kuroko teleports the windows to cut through the building's supports, bringing the place down. Having barely just survived, the thug surrenders his Level Upper to Kuroko. Saten feels even more conflicted about what to do with the Level Upper, but an encounter with some of her friends leads her to tell them that she has it.

Saten uses the Level Upper on herself and her friends and is happy to have an ability. Meanwhile, Kuroko takes care of more Level Upper offenders and gains more injuries in the process, keeping them a secret from Mikoto. Remembering when they ate shaved ice, Mikoto and Kuroko come to the conclusion that the Level Upper is using synesthesia to manipulate brainwaves. Uiharu soon hears from Saten that her friends have fallen unconscious due to the Level Upper, and later finds her unconscious too. After admitting Saten to the hospital, Mikoto feels responsible for hurting her feelings with her advice and wants to help. They later learn from the frog-faced doctor that the Level Upper victims seem to share a brainwave pattern with someone. With the help of Mii, they theorize that Level Upper actually connects ability users like a network and learns the culprit is, to their surprise, Harumi. Uiharu, who had visited Harumi earlier and discovered her notes on synesthesia, is taken hostage by her. Noticing Kuroko's injuries, Mikoto decides to rescue Uiharu and stop Harumi by herself.

Harumi explains to Uiharu that she used the Level Upper Network as an alternative supercomputer as she wasn't allowed to use the Tree Diagram supercomputer. She assures Uiharu that she will release everyone once she's done, giving her a cure program. When she is road blocked by the Anti-Skill, she uses the Level Upper's Administrator power; Multi-Skill, to utilize the abilities of the victims to defeat them. Mikoto arrives and battles Harumi who blocks her every attack until she lets her guard down, during which Mikoto gets close enough to shock her. In the process, Mikoto experiences flashes of Harumi’s memories. In the past, Harumi was assigned by her boss, Kihara Gensei, to be a teacher to a group of Child Errors to prepare them for an experiment, growing fond of them in the process. However, the experiments went horribly wrong and the children ended up in comas, with Gensei deciding to cover it up. Harumi explains she wanted to find a cure to save her students by using Tree Diagram, but was denied every time which led to her creating the Level Upper Network. Her anger soon causes her to lose control of the network and fall unconscious, and a strange fetus-like creature emerges from her head.

Mikoto and the Anti-Skill fight back against the creature but it only causes it to regenerate its wounds and grow bigger as it heads towards a nuclear power plant. With the network out of control, the comatose Level Upper users starts screaming in pain. Realizing what has happen, Harumi explains the creature, called AIM Burst, is the result of the 10,000 Level Upper user's AIM fields and their negative thoughts. With the help of Anti-Skill members Yomikawa Aiho and Tessou Tsuzuri, Uiharu manages to upload the cure Harumi gave her, a song file, which is played all over the city, calming the Level Upper users and weakening AIM Burst. Despite losing its regenerative ability, AIM Burst is still able to use the Level Upper user's powers and emits their negative thoughts to Mikoto and Harumi. Mikoto battles AIM Burst again and apologizes to the users for not understanding their feelings and tells them not to give up on their dreams before shooting a Railgun to destroy the creature's core. As sunset arrives, a mysterious woman and her team inspect the damages at the power plant while Harumi is arrested by the Anti-Skill, still hoping to find a way to cure her students. Uiharu later meets up with Saten who, having recovered from her coma and lost her powers, apologizes to her for forgetting what was truly important.

Big Spider Arc
Mikoto becomes involved with Judgment's investigations with the rise of Skill-Out attacks by Big Spider on espers, on Kurozuma Wataru's orders (actually Hebitani Tsuguo). She later meets Kurozuma Wataru the true leader of Big Spider, looking upon dreamily upon the moribund Strange. Much later, Mikoto and Kuroko discover Tsuguo's base and decide to take them all in, however, they are depowered by the use of Capacity Down. They are later saved by Wataru, who reveals that he has returned, prompting Tsuguo and his group to flee. Konori Mii, later appears before Wataru before he leaves, and calls him her senpai. Confused, Mikoto and company later visit her apartment to talk to her, and meet her roommate who reveals that Mii was a member of Big Spider. Mikoto remains confused on why Mii seems to hesitate in choosing the present over the past, and later confronts her in an old Big Spider, and ask her if she is going to tip-off Wataru regarding the Anti-Skill on the Strange. Wataru later appears before them, hither, Mikoto bears witness to Wataru urging Mii to move on.

Mii decides to choose the present, and Mikoto and Kuroko give her a red jacket to wear as remembrance to her past. Mikoto later joins Kuroko, Mii and Wataru on the final assault on the Big Spider. She later destroys Capacity Down, and with Kuroko, see Mii and Wataru finally disband Big Spider. Mikoto later witnesses Kurozuma's arrest by Mii.

Poltergeist Arc
Uiharu gets a new roommate, a transfer student named Haruue Erii. As Mikoto and Saten hang out with Erii, Uiharu, Kuroko and Mii attend a joint Anti-Skill and Judgment meeting held by Therestina of the Multi Active Rescue(MAR) Squad concerning earthquake-like "Poltergeist incidents" caused by multiple espers suffering from RSPK syndrome as a result of temporarily losing control of their abilities simultaneously. While Judgment are ordered to only debunk the rumors, Mii decides to do some investigating. Meanwhile the girls decide to celebrate Erii's arrival by attending the local Hanabi festival. As Erii starts to reminisce about her past with her new friends, she suddenly goes into a trance and wanders off on the hill they are on. Kuroko soon gets a call from Mii who reveals these Poltergeists are not natural but were created on purpose. At that moment, another Poltergeist event occurs over where the girls are. Uiharu tries to protect Erii from a falling lamppost but both are saved by Therestina in a powered armor. As the girls come to grip on what has happen, below the hill, a familiar woman is seen in the crowd.

Sisters Arc
The Railgun manga greatly expands upon Mikoto's actions during the Sister's arc. The first clone she meets is Misaka 9982, and she forms somewhat of a bond with the clone. After she witnesses Accelerator kill Misaka 9982, Mikoto attempts to avenge her death, but she fails. Mikoto attempts to stop the project by destroying the research facilities, and even has a confrontation with ITEM during her quest. Despite the destruction, the project continues. As in the Light Novels, Touma helps put an end to the project.

There is also an extended epilogue to this arc in the manga, where she recruits Saten's help to make cookies for Touma, but she is ultimately unable to.

Silent Party Arc
The arc serves a vehicle to force Mikoto into a situation where she is powerless just like in the Sisters Arc despite her power. However, it is used as a way to show her humbled attitude towards the dark side of Academy City, the limits of her powers despite being a level 5, and a way to involve her friends in helping her, similar to the Poltergeist Arc.

This is through Febrie, a Chemicaloid, an artificial human. When first introduced, she is suspicious of Mikoto, to which she is forced to try to gain her favor. This occurs after she saves her from the Security robots that were controlled by Diffusion Ghost by STUDY, the antagonistic organization in the arc. Febrie's circumstances are not unlike that of her clones, and her efforts to act sisterly towards her is commented upon by other characters like Mii, Saten, and Uiharu while they were in the public bath.

When Mikoto realizes that Febrie's circumstances goes deep into the dark side of Academy City, a world she is acquainted with. She initially tries to go out alone, with Kuroko supporting her once again knowing that she will once again do something on her own. It is not until she contemplates Kongou Mitsuko's words regarding friends, that she is forced to acquiesced to ask for help, where everyone jumps at the call despite Mikoto saying that she has no guarantee she can protect all of them. She later meets up with Therestina Kihara Lifeline again. Ever a difficult person to deal with, Therestina constantly mocks and belittles Mikoto, and even more so when she hears her asking for her help as she is familiar with the dark side. Therestina asks if she despises the city after discovering the truth within it, to which Mikoto says she doesn't because she has met good people in the city as well, which annoys Therestina. After much whining from Mikoto, Therestina finally acquiesces to Mikoto asking about artificial humans, telling her of Chemicaloids she used to hear of. She then says that those who have created the Chemicaloids are planning to show it to the city in an upcoming event, which Mikoto discovers is the Academy City Research Exhibition Assembly. Therestina, however, warns her that even though she can easily use the fact that she is a Level 5, a valuable guinea pig to the City, she knows not how deep the darkness of those who are not even considered guinea pigs.

After the girls discover one factory owned by STUDY, Mikoto goes there on her own, and has Kuroko on stand-by, to search for the neutralizer that would keep Febrie alive. While going there, she notices the bridge where she and Touma had often meet, and where she confronted and attacked him. Here she recalls on how Touma was being forceful in having his dream of achieving a happy ending where nobody is dead, though she keeps it mind. She later meets Shinobu there, who gives her the recipe for the neutralizer, as well as Aritomi Haruki, leader of STUDY. Here, he reveals that the data now in Mikoto's hands is a dummy, a part of his additional safety measures to keep vital information from leaking out. Now that Haruki has discovered that Shinobu is a traitor, he forces her to make a painful decision — to help detain Mikoto so that she can guarantee the safety of the recipe for the neutralizing agent she needs to keep Febrie alive. Although Shinobu is hesitant to do it, Mikoto tells her to push on for Febrie's sake. Shinobu stabs Mikoto with the injector as she requested, despite having the strength and numbers to overpower Haruki, and thus Mikoto instantly collapses due to the effects of the drug. However, much to the shock of the two girls, Haruki destroys the precious data in front of them.

With Mikoto no longer a threat to Haruki, he decides to talk to Shinobu and Mikoto about his actions. Haruki clarifies that Febrie's well-being is not important as she was just a spare for the greatest invention of STUDY Corporation, which they call "Janie". Haruki also relates to Mikoto his life story, recalling his achievements in the Academic Assembly and his frustrations as a scientist whose efforts are dwarfed by those of the espers of Academy City, both of which motivated him to initiate the Chemicaloid Project. Eventually, Mikoto succumbs to the drug injected into her by Shinobu and passes out. Haruki later has her and Shinobu transferred to an office space somewhere nearby. Here, Shinobu tells Mikoto on how she ended up with STUDY. Here, Mikoto thanks Shinobu for helping her Sisters and tells her as well of the despair that she had felt during the Sisters Arc that only was alleviated because of her friends, whom she has now come to rely on. As her friends arrive to bust Mikoto out, Shinobu opts to stay behind as so that she can keep a look out on Janie and finally asks Mikoto to save them.

Back in the office, Mikoto relates vital information regarding finding Janie, in which Febrie can track her own sister if she uses her powers, like when it takes control of the Powered Suits used by STUDY. They later discover that not only Anti-Skill unable to help, they are up against 20,000 and more Powered Suits by STUDY. Seemingly hopeless, Mikoto recalls Touma's speech to her, which gives motivates her. Mikoto is later with Febrie at the crack of dawn and the beginning of STUDY's Silent Party. Using Febrie, she narrows down STUDY's location. She defeats countless Powered Suits, and but STUDY tries to sic mobile weapons equipped with a gun that mimics Mugino Shizuri's Meltdowner to stop her. However, she is later aided unintentionally by Mugino herself and ITEM, wanting revenge on STUDY.

Haruki is soon confronted by Mikoto and Febrie as they reach his main console room. With his plans in the Academic Assembly falling apart, Haruki decides to resort to drastic measures, shutting down Janie's link with the many Powered Suits outside to turn Janie into an unstable entity and then ending his life. But, Mikoto was able to stop Haruki from committing suicide, although Haruki later admits that his "last resort" was irreversible. Haruki's colleague, Sakurai Jun, explains to her that they are in a grave situation, as Haruki's last resort involves releasing thousands of filaments from a missile fired 35,000 kilometers above the Earth, and the rampaging Diffusion Ghost will cause widespread AIM diffusion field interference that will affect each and every esper in Academy City. With the AIM bomb coming, Mikoto makes a conference with her friends to try and find a way to stop the bomb. She entrusts Febrie to Shinobu's care, now determined not to stand idly by and do nothing. The Sisters later contact her and offer their assistance. They are the ones who calculate on what to do in order for the Ekaterina II S mecha that was brought into the battlefield. As Kongou and Awatsuki Maaya prepare the mecha, Mikoto and Kuroko are in the cockpit. Here, Mikoto apologizes to Kuroko for involving her, to which she replies that she doesn't mind for she is finally fighting side by side with Mikoto. With that, they are launched into space by Kongou's Aero Hand. Kuroko becomes visibly sick upon arriving in the upper atmosphere, but manages to teleport away as Mikoto begins to do her part. Mikoto then uses her power to make the mecha as the ammunition for her Railgun, the force of which was enough to destroy the AIM bomb. Kuroko teleports an exhausted Mikoto back to earth after she destroyed the AIM bomb. As the Academic Assembly begins in earnest, Mikoto sleeps at the assembly grounds, alongside Kuroko, Uiharu, Saten, Kongou, Kinuho, and Maaya.

As Janie and Febrie are in a Kongou Airlines runway, preparing to leave to the outside for body readjustments, Mikoto talks to Shinobu once again, expressing her shame on how she had to leave so soon just as they've become friends. Here, Shinobu notes on how the digital records for what had transpired in the Silent Party was altered to give them a positive look, as well as the fact that some of the authorities have suspiciously seem to have their memories altered. Here, Mikoto flounders about, seemingly confirming that despite her distaste for Misaki and her powers, she lays down her pride (among other things) and ask Misaki for help.

Daihasei Festival Arc (Railgun)
Mikoto first appears as a competitor with Kongou Mitsuko for the three-legged race, which they win handily and even saving lives in danger during the course of the race. Mikoto, Uiharu, and Saten would later meet up with Misaka Misuzu. Mikoto notes that her clothes are dirty and that changing them would be difficult for the next event, to which Saten says that Mikoto should ask someone to go in her place. This however makes Mikoto accidentally divulge on her little bet with Kamijou Touma, which entices Misuzu and later has both Uiharu and Saten discuss the person who is "helping Mikoto a lot", much to her embarrassment.

Mikoto later decides to have a change of clothes, making her late for the next event: the Balloon Hunter Competition. After racing towards the venue where the match begins, she finds that Misaka 10032 has been mistaken for her and has taken up her position as part of the event. Mikoto could only hide and observe as Misaka 10032 competes in her place, though she is generally glad that she is doing well and hopes that she enjoys herself.

After the competition, Misaka 10032 later meets up with Mikoto, with the former apologizing for her performance and being unable to be her replacement. Mikoto however asks if Misaka 10032 had fun, to which she confirms. Mikoto then says after hearing her response that there is nothing to worry about, saying that there was nothing they could do about the situation and that she was at fault too for being late. Mikoto congratulates her sister for a job well done and gives her coupons for lunch. Unknown to Mikoto, Misaka 10032 would soon go missing afterwards.

During lunch, Mikoto and her mother later share a restaurant together with the Kamijou Family and Index. While Mikoto try to get some drinks, she meets up with Touma fresh out of the bathroom, showing his lack of delicacy to Mikoto. Touma later inquires what Mikoto is doing, mistaking her complaining about long lines as being unable to get to a lavatory, and says that she is out to buy drinks. Touma offers to buy her share of drinks, surprising Mikoto with his good nature.

While waiting for him, Mikoto meets with Misaki, and their usual antagonism between each other plays out once again. Misaki reveals on how she used her powers to cancel all her afternoon events, saying that she got tired just from the morning events. Touma later arrives and comes upon the two of them. Misaki is momentarily surprised when he meets Touma, but later perks up after Mikoto introduced her as her classmate to Touma after he asks. Misaki introduces herself as Mikoto's friend to Touma and says to him that they should get along, irritating Mikoto. Misaki acts scared and goes to Touma, grabbing his arm and referring to Mikoto as Piripri. This prompts Touma to refer to Mikoto as Biribiri as well, saying that Mikoto acts the same way towards him as well. As Misaki teases Mikoto through the use of her onomatopoeia nicknames, she becomes angered and uses her powers, forcing Touma to use his right hand to negate it and Misaki to run away, teasing her all the while.

Mikoto and Kuroko later arrive in Judgment 177 Branch Office. as the former have a bit of time before her next event as Uiharu jokes to Saten that she might be targeted by the organization who wants the Shadow Metal. Immediately after, Saten is attacked by men in hazmat suits. Concerned, Mikoto asks Uiharu what is going on, to which she explains that Saten is being attacked by someone on the other line. Hearing this, Kuroko and Mikoto mobilized after Uiharu says that Saten is in Kirigaoka Girls' Academy grounds in School District 18. Uiharu is left behind for a backup as they might need to contact Anti-Skill. Arriving there, Kuroko notices them, but Mikoto, seeing Saten being held down angers Mikoto and attacks them. Mikoto and Saten later prostrate themselves in apology to them after it is revealed that they are the one who clean the grounds after an event to prevent the DNA traces of espers from being stolen by outsiders. Seeing Saten as a trespasser in the grounds, it was only natural for them to apprehend her. They are later let go by them. Kuroko says that the rumors of Shadow Metal spread because of the fact that the grounds were heavily guarded to prevent DNA maps from being stolen, and berates Saten for being carried away by a baseless rumor, as well as Mikoto for the attack.

The others later arrive back to the office, and much to Kuroko and Mikoto's chagrin, Saten then immediately asks Uiharu if she had found any new information. Uiharu then says that she has done some searching herself but couldn't find anything. Little did they know that Misaki paid Uiharu a visit and have read her memories that she and the others are Mikoto's friends, modified her memories so she forgets about the website and have her erase the data of it from her computer, and have programmed her to lead her and her friends to her on the next day. Mikoto later celebrates the Night Parade with Kuroko, with Mikoto becoming too enthusiastic for the Gekota float for the parade along with little kids, much to Kuroko's chagrin.

The next day in the hotel Tokiwadai Middle School is staying in, Kinuho inquires when she can have her P.E. uniform back. This surprises Mikoto but manages to make up an excuse on how she got it dirty and that it was still in the cleaners. She tells Kinuho that she'll just have to get her a new one and deliver it to her room, but Kinuho politely refuses her offer. After she leaves, Mikoto becomes concerned on what happened to Misaka 10032. With some free time after her second event for the day, Mikoto begins investigating and hacks into nearby street cameras. She discovers that her Sister has been taken away by an ambulance, greatly concerning her of her condition as well as the fact that people may find out that she's a clone. Incognito, she finds the ambulance EMTs and inquires where they took the girl with brown and shoulder length hair yesterday, reasoning that she is her friend. The EMTs point towards the Heaven Canceller's Hospital, giving Mikoto a sigh of relief as the Heaven Canceller knows of her situation and the Sisters. She inquires about Misaka 10032 there, but is told no student was brought in there during that time. Mikoto says that the EMTs she talked to pointed to this hospital but the receptionist says that they may have taken her to some other hospital.

Returning to the EMTs, Mikoto inquires once more but the drivers still say the same story despite being no records in the hospital. Mikoto notes on how whether or not the EMTs are telling the truth, since her Sister is wearing a Tokiwadai uniform the school would've already been informed about it. Mikoto tries to press them further, asking the name of the hospital worker and the circumstances at the time. The EMT tries to answer but cannot recall anything, saying that not only does he not remember the person who took the girl from them, but the person who contacted them as well. Fed up, Mikoto goes to the ambulance to look at their navigation system. She uses her powers on it to bring up records at that time from yesterday and discover that the ambulance when into a large parking garage. Mikoto concludes that Misaka 10032 might have been transferred into another vehicle afterwards, and determines that she can hack into the cameras there to find out where she is. The EMTs later have had enough of Mikoto barging into their vehicle and pulls her out. Mikoto angrily tells them that their statement contradicts what the navigation system is showing, confusing them. However, her hat falls off to which the drivers discover that she looks exactly like the girl they've picked up yesterday. The other EMT recognizes her and says that she is one of the Level 5s and that she can control electricity. He then accuses her of tampering with the navigation system. Having enough of them, Mikoto pulls the collars of the hapless EMT and demands from him to stop lying and tell the truth. She cites on how they're forgetting things at the most convenient time, and then Mikoto realizes something—Shokuhou Misaki, an esper who can alter memories. Just as she realizes this, Mikoto is confronted by Anti-Skill and a bystander telling her to let the man go. Watanabe, already brainwashed by Misaki to take Mikoto to her clique, later picks up Mikoto, relieved that her little outburst hasn't become a major issue. Concerned, she asks what Mikoto's problem is. Though reluctant at first, she later tries to tell her that Misaki is abusing her powers, but could not fully divulge the reasons, because she would have talk about her clones. Watanabe disregards her concerns and lectures her on how she must not take any careless actions as she not only represents Tokiwadai but Academy City as a whole as well. She later leaves Mikoto with Misaki's faction, much to her horror. She is greeted enthusiastically by the benign though clingy members of Misaki's clique, one of which, Kobayashi Satori, is a telepath, preventing Mikoto from going out of a certain range from them.

Unknown to Mikoto, in order to constrict her movements even more, Misaki uses her powers on Kuroko, Uiharu, and Saten, erasing their memories of Mikoto. Back with Mikoto, as she tries to formulate a way to escape Misaki's clique, she notices Kuroko, Uiharu, and Saten walk along by. She is relieved and comes towards them, but much to her horror, discovers that they too have been brainwashed by Misaki. Mikoto is greatly angered by this affront, but is unable to do anything even if she tries to convince them that she is truly their friend. Moreover, Mikoto has another event to partake in.

Mikoto is part of the Balloon Sandwich with Kongou Mitsuko as her partner. They are to run in a race while holding a balloon between them without using their hands. As Mikoto wonders what she should to, Kongou mentions on how she saw her "twin sister" yesterday in the Balloon Hunter Competition, though she was unable to call to her as the competition has already started. This surprises Mikoto. As the race starts, Mikoto asks how she notice it wasn't her, to which Kongou says she has confidence in her perception and that her "twin sister" gave her a different impression compared to Mikoto. Hearing this, out of desperation, asks Kongou for a favor, explaining her situation regarding Misaki, her Sister, and the brainwashing of her friends. Kongou is sympathetic to Mikoto's situation, telling her that she will look into it while Mikoto has Misaki's clique focused on her. Mikoto apologizes for dragging Kongou in her personal matters, and says that Kongou shouldn't delve into deeply as she does not know what Misaki might do. Mikoto just asks Kongou to find a clue and that she will handle the rest. As they win the race, Kongou says that Mikoto shouldn't trust her with any information as she may have been already brainwashed by Misaki. Kongou also says that she shouldn't trust anyone else either. As such, Kongou tells Mikoto that she will instead bring back her "twin sister" instead of information, telling her that she may have told not to trust her but to believe in her. As such, Kongou leaves as Mikoto is greeted by Misaki's clique.

Meanwhile, Mikoto tries her hardest to escape Misaki's clique, though it doesn't take. She is completely unaware of the battles that is going for her. After wandering about with them, Mikoto comes upon Saten near a hospital, and later finds out much to her horror of what has befallen to Kongou due to her battle with Baba Yoshio. In the hospital Saten tries to tell Mikoto about what happened between her, Wannai Kinuho, and Awatsuki Maaya with Baba Yoshio and his robot dogs. All the while, Mikoto blames herself for involving Kongou, still believing that it is Misaki's doing. She finds Yoshio's Type: Mosquito on Kongou and tries to leave. The girls of Misaki's clique asks for Mikoto to wait for the other members of the clique to arrive, but Mikoto tells them that if they are prepared to kill her to stop her then they should go out of the way. Cowed by her sudden outbursts, the girls can't help but let Mikoto leave. She later uses the mosquito robot that was attached to Kongou to track its owner.

Yoshio, still reeling from his humiliation, believes that if he had known their powers from the beginning he wouldn't have been defeated. He activates a disguised truck to open to reveal Type: Mantis, intending to use it to humiliate Kinuho and Maaya for humiliating him. As the large robot moves, Mikoto appears before the large robot. Seeing this, Yoshio panics, but then assume that she is a Sister, and finally finding one, orders the machine to capture her. The Type: Mantis' easy destruction at her hands was enough for him to realize that it is the true Mikoto. Mikoto talks to Yoshio, telling him that she knows where he is from the communications signal. Yoshio tries to get away from his command center discovers that it may have been taken over by Mikoto already. Mikoto threatens to do to Yoshio what she did to the robot. However, believing him to be just being under the control of Shokuhou Misaki, she lets him go with a warning. She says that if she ever finds those robots around her friends again, she will find him and crush him. Yoshio later faints at the thought. He later reports his ordeal to Mitori, and asks her for a safe place to hide from Mikoto's wrath.

After Yoshio fled, Mikoto visits his truck for some information, still under the assumption that Misaki is behind everything. Here, she confirms her suspicions as she finds no real information she can find there, believing it was set up to prevent her from taking it over. As Mikoto leaves, she wonders if she can find the hideout of those who used the truck using the security cameras. She later quits on checking cameras at each important point as it takes too much time. She then receives Saten's call, surprising Mikoto. After Saten introduces herself, she tells Mikoto about the information they had gathered from Misaka 10032's cat. Mikoto says that she has no clue what that girl with the man from the cat's memories, who she says is likely Misaki, is talking about. Just then, Saten says that there is something that she is knowledgeable about that came about in the conversation that the cat has heard, and that she also wants to know whether she and Saten know each other. Saten requests that they should meet each other, to which Mikoto says her location and it is in School District 15, which Saten notes is quite close. Saten asks for Mikoto to stay there as she'll ask Kuroko to teleport her to where she is, much to Kuroko's frustration. After Mikoto discover that Kuroko is with Saten, Mitori's Liquid Shadow dummy approaches her, telling her that she wants her to tell her something. Mikoto, already suspicious, says that she is quite busy and has no time to talk to strangers, but she'll make an exception to those who are connected with the guy (Baba Yoshio) who hurt her friend. Mitori is unperturbed and shows that she has Uiharu hostage.

After getting Mikoto to end her phone call and throw her phone away, Mitori mentions that she had no need to introduce herself seeing as how Mikoto attacked their villas and stole their information. When Mikoto asks what she's talking about, Mitori tells her not to play dumb and that she should know what they were after—where the Sisters are being hidden. Mikoto asks why she was attacking her friends but Mitori asks her back if she could really say that, calling her an oddity for living a carefree life despite knowing what was going on in the city, mentioning about experiments on Child Errors, the trick used to obtain her DNA map and the inhuman Level 6 Shift experiments, all leading up to the highest levels of Academy City. Mitori says that Mikoto was different from the average ignorant student yet she turned a blind eye and lived an everyday life, asking her how she could remain calm despite all that has happened.

Mikoto starts to reply but changed her mind, saying that it has nothing to do with this and that none of this was an excuse to hurt her friends. Saying she has nothing to tell her, Mikoto warns Mitori to let Uiharu go, saying her electricity would reach her before she could move her knife. Mitori then mentions how she thought she was Mikoto's friend seeing how she knew her mother. She then points to Misuzu also being held hostage. Saying that not even Mikoto could save them both and that it was clear that she didn't need to weigh their lives against the location of the clones, Mitori once again asks where the clones are. Mikoto again says she has nothing to say to her. Mitori asks Mikoto if she thought she was bluffing or if she was willing to let one of them die. Mikoto then declares she would save Uiharu no matter what. Mitori laughs and asks if her mother was expendable. As she remarked how cruel that was, Mikoto attracts some pipes with magnetism to pull Uiharu away while attracting her phone to block the knife, before moving in and attacking with electricity.

Seeing that the negotiation had failed, Mitori attempts to carry through with her threat, saying she wouldn't like it to end with Mikoto underestimating her and telling Misuzu to resent Mikoto for abandoning her. At that moment, Shirai Kuroko teleports in and smashes her wheelchair down at her. Jumping out of the way, Mitori throws a knife at Kuroko, who evades it. She then escapes as Kuroko was teleporting Misuzu to safety. Kuroko wanted to apprehend her but knows that keeping civilians safe is the greater priority. She later takes Misuzu and hands her over to Mikoto, thinking that she can just apprehend and interrogate the one that held Uiharu hostage. After Mitori escapes, she has her Liquid Shadow puppet to attack Kuroko as she moves in closer, though she misses. Kuroko tries to attack with her darts though they simply right through the puppet. As the puppet comes closer, Mikoto tells Kuroko to take Uiharu and Misuzu to safety, though before she can do so, the puppet merely points towards her with a smirk before it dissolves as Mitori moves out of range.

After the conflict, Kuroko demands from Mikoto an explanation. Mikoto says that she didn't know who was that either, to which Kuroko explains that she wants to know why Mikoto acted like she knew she was there, saying that the line about Mikoto saving Uiharu was meant for her. Here, Mikoto explains that she noticed Saten calling Uiharu after she hung up through the electromagnetic waves, likely to see what had happened. As she has told them where she was, she expected Kuroko to come over as she can teleport and that she would be nearby. Mikoto thanks Kuroko for letting her save Uiharu, to which Kuroko says that Uiharu is part of Judgment and that it is only natural to prioritize visitors. Kuroko references that Mikoto left her mother's life in the hands of a stranger, to which Mikoto notes on how her mother would be mad if she chose her instead of her friend. Moreover, she tells Kuroko that she trusted her to protect her mother. Hearing this, Kuroko blushes and tries to shake it off, but it aggravates her injuries. Mikoto apologizes for letting her fight when she was injured and tries to help her walk, much to her embarrassment.

They later return to Judgment 177 Branch Office, and later lets Uiharu and Misuzu have some medicine and some sleep. With that they discuss about the situation at hand. Mikoto confirms to Saten that the girl that Misaka 10032's cat saw is definitely Shokuhou Misaki and has abducted her "sister". Saten then mentions Auribus oculi fideliores sunt, an urban legend website she knows of. Kuroko questions why Misaki would be interested in that, to which Saten says that the site not only gathers information about urban legends but has people go out and verify it. She relates on how yesterday after the midday break, the time after Mikoto's sister was abducted, she was out looking for Shadow Metal and had Uiharu look up the site. When she returned Uiharu says that she couldn't find it, prompting her to find it on her own only to find that the website got buried by a bunch of dummy sites. Saten explains that once something is on the Internet it can never fully be deleted. She says that somehow someone is trying to hide the website by making dummy pages that will have higher spots in the search results. Mikoto can only assume that there must be something in that website that someone doesn't want to see. Kuroko then mentions that Uiharu would have noticed something and had the skills to search for the cause of it. Mikoto conjectures that someone had detected her actions and attacked her. She imagines Misaki doing it, manipulating Uiharu to delete the data and then searching her memories to find that she is friends with Mikoto. Saten says that they have to force the clues together to reach the conclusion, but says that there still must be something remaining in the computer that could help them.

Using her powers, Mikoto recovers the deleted data. She finds a picture of Misaki from the website, confirming her suspicions. Mikoto asks Kuroko if she can identify where she is, to which Kuroko says that it might be School District 2 due to the building in the background. Before Mikoto can run off to confront Misaki herself. Saten asks Mikoto if their memories were truly altered, and that if they are truly their friends, to which Mikoto says that she will drag Misaki here and that they should wait.

Misaki, who has finally found where Kihara Gensei is hiding, detects Mikoto coming, and decides to meet her instead. Mikoto finally confronts Misaki. The Mental Out ensures that Misaka 10032 is currently safe in her custody, and directs the Railgun to a truck. Misaki reveals that she abducted Misaka 10032 herself after she had been incapacitated to try to keep her safe while searching for the aggressors. Misaki forced information about the Level 6 Shift out of a group of researchers, realizing that Kihara Gensei was behind the plot, and also that he is attempting to exploit the Misaka Network. Moreover, Misaki uses her ability to cut off the means of infecting the Misaka Network through an electrical virus input on an individual Sister, allowing for the Misaka Network not to be taken over once a Sister falls into enemy hands. Misaki tells Mikoto that they are en route to Gensei's hideout to end his schemes. Mikoto asks why Misaki erased her friends' memories of her, at first suggesting that it was Misaki's idea of being considerate by keeping them out of danger. Misaki denies this, stating that it stopped Mikoto from enlisting the aid of her friends and also from forcing her way out of Misaki's clique, and that it was necessary to prevent any variables and irregularities from interfering with her plan. A shocked Mikoto asks why she couldn't have just worked with her from the beginning, pointing out the extent of Kongou's injuries. Misaki says that although what happened to Kongou was unfortunate, it ultimately helped her since it resulted in the destruction of Baba Yoshio's robots, which Misaki had no way of dealing with. An enraged Mikoto demands once again why she did not simply ask for her help, but Misaki states that co-operation and trust are unreliable — it was Mikoto's trust in others, after all, that led to the Radio Noise Project and the Level 6 Shift. Misaki concludes that she has no intention of working with anybody whose mind she cannot read. They are only working together, Misaki says, because of her respect for Mikoto's devotion to her friends and the possibility of finishing the job before Gensei can react. Mikoto says that she doesn't think that she will ever be able to get along with Misaki. Before they are about to begin the assault on Gensei's hideout Mikoto asks why a person like Misaki would help the Sisters, to which the Mental Out says she has no obligation to tell her that much.

​​​​​​​The impromptu alliance between the Railgun and Mental Out begins with Mikoto hurrying forward, speeding past her ally. When Misaki doesn't catch up, Mikoto believes that she has been set up since the path they took was straight and there was no way that she could have gotten lost. An exhausted Misaki catches up moments later, chastising Mikoto for losing focus and getting worked up. Mikoto says that she thought she was jogging. Misaki hurriedly responds that Mikoto is simply lighter than her in certain areas and that she is more aerodynamic. Mikoto asks if she is simply out of shape and the two argue heatedly about the importance of athletic abilities and body shapes. They finally decide that they should not be moving together and split up, both Tokiwadai students telling the other not to get in each other's way. Misaki is later seen mind-controlling a group of Gensei's thugs, forcing several to fire on each other while sealing off the rest of the complex to prevent any escape. As the infiltration of Gensei's hideout progresses, Misaki's mental manipulation has completely broken apart the cohesion Gensei's troops as they cannot identify who is friend or foe. Misaki meets up with a disguised Mikoto, making a quip about her outfit as she is escorted by a pair of guards. She says that the building has been sealed off and is then told by a mind controlled guard that Gensei has been captured.

​​​​​​​Later, Mikoto and Misaki attempt to interrogate a restrained and blindfolded Gensei, but he only utters gibberish. Misaki says that she doesn't need him to talk, she only needs to ask his brain. When she uses her remote on him, she realizes that something is wrong. She grabs Gensei and yanks at his scalp, ripping it apart and revealing that they had only apprehended a disguised minion. Misaki hurries away from the body double and a confused Mikoto — her reading of the body double's mind shows that the real Gensei was a step ahead of Misaki and he quips that she is in the wrong place, and that she "can't protect Exterior like that." She rushes towards Exterior before Gensei can reach it. She tells Mikoto that Gensei might have used the urban legend website that was recently buried into the Internet in order to find it. As the car she is on races towards their destination, they are suddenly stopped by a huge traffic jam. The driver tells her that an Automated bus that exploded yesterday (due to the work of Stiyl Magnus), and since the City pulled out its main transportation for the Festival to find the cause, it caused a traffic jam. Running out of time, Misaki calls out to Exterior, allowing her to control many people for kilometers on end, forcing them to drive out of the way. This event amazes Mikoto, though questions how she was able to pull it off as Misaki begins to reminisce of her past with her ill-fated friend Dolly.

Level 6 Shift attempt of Misaka Mikoto
Arriving at the building where Exterior is kept, Misaki notes that her phone doesn't have a signal, to which Mikoto says that there is a powerful jamming signal being emitted in the area. They see the hole into its entrances, and here Mikoto says that she'll be going even if Misaki told her not to. Having no choice, Misaki allows Mikoto to go with her, stating that she might be of need of her powers. They find the building mysteriously bereft of both invaders and the employers needed to maintain Exterior. Mikoto then asks about Exterior after Misaki showed her power back in the jammed highway. Misaki says that officially Exterior allows her power to be amplified, but states that its true purpose is to allow registered users, regardless of being an esper or not, to use her powers. Misaki notes that before Exterior could be used by the researchers’ purposes on brainwashing great men, she took over the project, saying that Mental Out is for people with a pure personality such as hers. Mikoto is unbelieving of Misaki's story. She asks if that is the machine that is referred to by Urban Legend sites as one that produces esper powers, but Misaki just wonders where those rumors come from. Misaki then says that it isn't a machine, and much to her hesitation, allows Mikoto to see what Exterior is, a giant brain cut between the two sides inside a tube of liquid. Misaki notes that a part of her cerebral cortex has been taken out, cultivated, and enlarged to create Exterior, much to Mikoto's horror.

Misaki notes on the mysterious circumstances surrounding Gensei's invasion, saying that there is no signs of damage on Exterior as well as no signs in moving it. Mikoto conjectures that Gensei may be planning on using the brain for something, but notes that it will take several days to registration before anyone can use it. Misaki mulls over the facts again, as it would seem fruitless to take over the facility as he cannot use Exterior. Moreover, if he wants to take over the Misaka Network, he needs to get through the protection she has set-up, which requires Gensei to use Exterior. She puts her suspicions behind her and tries to direct where Misaka 10032 is treated. However, Keitz Nokleben is finally able to make contact with her. Misaki asks where he is, to which he says is on the rooftop along with Misaka 10032. Misaki is ecstatic, but Keitz interrupts her, saying that the attackers were a group of skilled special forces and that he may have been led up there in the first place. He tells her to be careful, but Misaki notes on how she has Mikoto there to aid her. Suddenly, something happens with Exterior, and Misaki falls to her knees. Gensei arrives on the roof and quickly stuns Keitz with the power of Mental Out, and later taunts Misaki on the phone regarding one he easily took over, asking her if she heard that rumors, the Level Upper. Gensei destroys the protection she implanted on Misaka 10032 with his Mental Out and quickly infects the Misaka Network. And thus every clone collapses all over the world.

Black electricity covers the sky as the power caused by the virus infecting the Misaka Network manifests itself through each Sister. Gensei is ecstatic of the results, but notes on how the energy is nothing more than show if it doesn't have any use. Mikoto finally arrives at the rooftop, and seeing a downed Misaka 10032, demands to know what Gensei had done to her. However, Gensei can only smile at her arrival, referring to Aleister's favorite hidden in the shadows of the main plan, whose power he intends to awaken using Mikoto as a vessel. Suddenly, the black lightning gathering outside gathers and jumps into Mikoto. Lightning flashes on the roof as Mikoto's form changes. Kihara Gensei smiles and says that the experiments will now begin, asking if Mikoto can become a Level 6.

With Mitori registered to Exterior she is able to use Mental Out as well. She then uses her access to communicate with Mikoto's psyche. She reminds Mikoto the atrocities in the city she has seen and the callous disregard it has for life, playing with Mikoto's innermost desires. Mitori points out to Mikoto the Windowless Building and that the bad things she has experienced will continue as long as it stood, suggesting she destroy it. Mitori watches in amazement as Mikoto unleashes a huge lightning strike on the Windowless Building. She then believes that the building has been destroyed, finally believing she has gained vengeance. To her dismay however, the smoke cleared to reveal that it was unharmed.

The strike was of course noticed by Misaki and Touma. The former later takes control of the chief of Anti-Skill, who also noticed the strike on the building, and through him, orders the evacuation of sightseers and nearby residents, as well as seal off both areas and prevent even Anti-Skill from entering. Misaki's actions would later prevent any harm to come upon any civilians during the incident. As Mikoto's transformation continues and dark clouds gather in the sky, Academy City suspends the Daihaseisai's outdoor activities and has some of them moved indoors.

With that done, Misaki seeks to find Gensei to end this, on her way up to the roof, she sees Touma on the streets and remarks how his timing is always so good, and if it didn't involve her, she'd be worried, but since it does involve her, he looks like a prince. As Mikoto appears before Touma in her current form, Misaki sends a telepathic message to Touma giving him a very succinct summary of what happened and what he needs to do to save Mikoto, confirming his suspicions that the creature in front of him is really the Number Three. Misaki asks Touma to use his power on Mikoto as it might be able to cut her from the Misaka Network that is currently being misused and slow down her transformation. With that, Touma is left alone to deal with Mikoto. Thus begins the battles for the sake of Mikoto.

As Mikoto's psyche becomes disappointed in being unable to destroy the Windowless Building, Touma closes in on her. She tries to use her powers on him but he manages to negate it with his right hand. Trying to move closer again, Mikoto then uses her electromagnetic powers on metals to sweep Touma away from her. Mikoto notices Touma, but only his right hand, becoming curious of it. Mitori however tells Mikoto that the one she is facing is a mere fly trying to get in her way and that she must shoo it away. With this, Mikoto uses her powers to attack Touma.

Although Touma can only negate her electric powers, he is able to dodge the metals that Mikoto rains upon him. Becoming confident of this, Touma however then sees Mikoto magnetize large chunks of metal into a single ball, something that he has no way of dodging. As Mikoto throws it towards Touma, Sogiita Gunha, the 7th-ranked Level 5, appears before him and destroys it with his power, surprising Touma. Gunha asks Touma if he is all right, to which he confirms and thanks him. Gunha is amazed by Mikoto and wonders if her growing horns is because of her guts. Gunha tells Touma to leave it to him, to which Touma opposes, saying that he knows Mikoto and that he can't just leave it to someone else. Gunha says that Mikoto is not a normal person and tells Touma to go hide. Touma explains that he doesn't want to defeat her, and he thinks someone is controlling her. As Gunha goes on about Mikoto just needing guts to come back to normal, Mikoto attacks with two powerful beams of electricity, to which Touma negates and Gunha punches down nonchalantly. Impressed by each other, they reintroduced themselves to the other, and then tell each other not to trip the other. And now begins Touma and Gunha's efforts against Mikoto.

With their teamwork, Gunha destroys the chunks of metal thrown at them, while Touma covers him by negating Mikoto's power. As Mikoto covers herself in iron sand and attacks it with them, Touma notes that he wants to get close and touch her with his right hand to see if she can turn back to normal. After negating the attack, Gunha uses his powers to blow the sphere that covered Mikoto, and then throws him at her. Despite being unprepared for it, Touma manages to maneuver himself midair and is able to touch Mikoto. Though the area where he touches her disappears, it was only a moment and returns back to normal. Gunha later catches Touma after doing so. Touma notes on how there is some kind of power constantly being sent in from the outside, so he can't fully negate it, as it turns back to normal after touching it. Gunha asks what they should do, to which Touma says that someone else is trying to turn her back to normal (Misaki), though he doesn't know who. He tells Gunha that they can only hold her back until that person cuts off the power source. Touma then says that Mikoto's transformation is restrained when he is nearby. Speaking of the devil however, Mikoto begins transforming before their very eyes, much to Touma's chagrin. As Touma and Gunha are observing, Mikoto attacks the latter, though he quickly recovers, though is not unscathed by it.

Touma and Gunha continues to do battle with her until Gunha is felled by Mikoto, knocking him unconscious. Left alone with Gunha unconscious, Touma witnesses another of Mikoto's transformation. Mitori then senses that the time is ripe for her to use Mikoto again. Mitori then guides Mikoto into creating a black sphere aimed at the Windowless Building. She mentions that though Mikoto could destroy the city she had to make sure that that person would definitely be eliminated. Mitori tells them to apologize to "her" in the afterlife, yelling for Mikoto to blow them away.

Both Gensei and Mitori are later defeated by Misaki and Kuroko respectively. Now with Exterior destroyed and nobody to control her psyche, and that Exterior is no longer able to connect her to the Misaka Network, Mikoto's subconsciousness wakes up, but she has no control over her transformed body, as the great black sphere of energy continues to grow, and energy exudes from the ground. After she wakes, her surroundings that have been black before slowly crumble, however, at the same time, tendril like objects coming from the darkness form a hand and try to grab her, likely coercing her to continue to destroy Academy City. This likely represents that part of her that wants to destroy Academy City. Moreover, Mikoto describes it as not her power.

As the sphere continue to grow, Touma notices the change, and later explains it to Gunha who has become conscious again this and that Mikoto cannot suppress her power. Gunha tries to convince Touma, saying that the thing that hit him before was compressed energy, but the sphere now is made of something not of their world and cannot be understood. Gunha says that he should be able to stop it with a self-destruction technique, sacrificing himself. However, Touma convinces him that he will deal with it himself and that Gunha should cover him. Impressed by his “guts”, Gunha uses his power to “part” the black mass of energy that covers the ground where Mikoto is floating on, allowing for Touma to move.

Meanwhile, Mikoto seeing that there is no way to stop the sphere, which she says that can now destroy more than the city, formulates a plan to compress it enough so that her body can cover the ensuing explosion. Then Mikoto notices Touma coming towards the sphere, Mikoto screams towards him, saying that what he sees before him is not an esper power, and since it was called in by her desire to destroy the parts of the city she doesn’t like she should be the one to stop it. It is implied that Touma heard all that Mikoto says to him. Touma then touches the sphere with his right hand, but the power is too great for his arm to bear and it is ripped from his body intact.

At that moment, a dragon appears from where the right arm was ripped off, and then bites the sphere. It bites the black sphere and allows the seven other dragons to emerge from Touma's severed arm. The dragons viciously rip apart the black sphere and make Mikoto’s transformation crumbles away. The halo cracks as well as the “starry sky” form of her head and chest as if it was dried paint chipping away. Touma then taps her head with his left fist. He says that, although he knows that there is a side of Academy City that is bad and is being controlled by important people that they can’t touch, even if she eliminated it by force he doubts that it would bring about the kind of world she wants. He says that he is sure that there are people other than him who are working to help her, and that they will help her change things bit by bit, including him. And Mikoto agrees with tears in her eyes. With that Touma gives her his jacket, as the dark skies part away to make for the blue sky.

Touma’s arm later regenerates, much to the surprise of both of them. Meanwhile, Gunha, Touma, and Mikoto all notice the metal that has appeared on the ground.

Thus ends the long day. After the events of the story arc, Mikoto goes to Heaven Canceller's Hospital on her own to see the condition of Misaka 10032. According to Heaven Canceller, after she was delivered to the hospital by someone, at the same time the data on the virus that she was injected with was sent to him, thus he wad able to make a vaccine for it. He stated that she needs a few days to rest before she gets recovered. Mikoto gets a sigh of relief and checks on her Sister. She then asks the doctor the room that Kongou resides in the hospital. She then later visits Kongou during the night. Here, Mikoto apologizes for what happened to Kongou, to which she says that she doesn't regret what she did in choosing to aid Mikoto even if something worse befalls to her. Kongou says that she put her life on the line for her because she personally wanted to clear away Mikoto's troubles. She asks Mikoto if she knows about the saying of the peach and the plums, and tells her that "Peaches and plums cannot speak, but they will form a path leading to them". Kongou says that she still doesn't understand what that truly means yet, but says that her fondness for Mikoto's character is what led her to think about others.

Mikoto says that she is not that great of a person, to which Kongou says that it what for people around her to decide. Kongou contrasts her situation with Mikoto, saying that she tried to show off how wonderful she is and yet no one recognized it leading to her being alone. Mikoto says that it isn't true at least to her or even Kinuho and Maaya. Hearing this makes Kongou happy, and asks Mikoto what she should do as she should feel terrible but says that she feels happy. As Mikoto leaves as the visiting hours have ended, Kongou says that she is glad to have transferred to Tokiwadai Middle School.

Mikoto later returns to her friends, with Misaki using her power to restore the memories of Kuroko and the others' memories of her, though modified the events somewhat for them, making them believe that they were out trying to catch terrorists targeting the festival to avoid contradictions. Apparently all to hide the existence of both Exterior and the Sisters from public knowledge, as well as passing along the information on the virus to Heaven Canceller to treat the sisters. Mikoto's not participating in the festival events on the second day was changed as well to that of her eating too much and having her stay in the bathroom all day, much to her chagrin.

Now with the waning days of Daihaseisai coming, one night, the girls come upon the bonfire where the folk dance is happening, where they note on how they cannot participate. Mikoto goes away to buy them all drinks. In the meanwhile, Kamijou Touma later meets up with Saten, and thanks her for the protective charm she lent. Touma offers to buy her some food to make it up to her, though she says that it is all right. Mikoto later comes around with the drinks, and finds Touma talking with Saten. Touma says that he borrowed a protective charm from her, confusing Mikoto though later figures out it was for the borrowing race. Mikoto's stutters and awkward way of presenting herself to Touma does not go unnoticed before the eyes of Saten and Uiharu.

Capitalizing this new found knowledge, Saten approaches Touma and asks him to dance with her around the bonfire as a way to thank her for lending him her protective charm. Touma is fine with the idea, though asks if she is sure with it, to which she confirms. Saten then tells Touma to go on ahead, leaving the girls alone. Mikoto is utterly shocked by what has transpired, but with a knowing look between Saten and Uiharu, they make their move. Saten fakes an ailment finally catching up to her, prompting Mikoto to ask her if she is okay. However, Kuroko suddenly figures out their ruse and tries to tell Mikoto, but Uiharu comes up behind her and covers her mouth. With this ruse finally set up, Saten says that she can't move but tells Mikoto that she can dance with Touma in her place. Mikoto becomes embarrassed by this, and makes up a bunch of excuses. Fed up with this, Saten forces Mikoto to say that she wants to dance, to which she does.

Touma later sees Mikoto coming up to him and drags him to the dance, much to his surprise. Saten, Uiharu, and Kuroko later observes Mikoto's dancing with Touma. Back with the couple, Mikoto tells Touma that he saved her once again, though, ever his personality, points out that other people helped out as well, with him helping a bit in the end. Mikoto says that she was saved by a lot of different friends, and says that she can't forgive the unpleasant parts of Academy City that view espers as guinea pigs, but it was coming to the city that allowed her to meet everyone, and that those meetings are a treasure to her. She then says to Touma that next time, she wants to protect everyone, because she thinks that's the only way to pay everyone back. Touma teases that she must also consider meeting him a treasure as well, as the way she said it included him as well. Before a flustered Mikoto can reply, Saten and Uiharu are unable to keep Kuroko restrained any longer where she teleports away to kick Touma in the head, ending their dance.

Mikoto later visits Misaka 10032 after the festival. Misaka 10032 laments that the festival ended while she was lying in bed. Mikoto says that she shouldn't sulk, and tells her that she should take her somewhere at some point, and asks where she would want to go. Misaka 10032 immediately answers the beach, to which Mikoto says that the beach season has ended. Misaka 10032 says that she doesn't know why, but says that she wants to make an exciting promise with someone important with her, describing it as a sentimental sense of déjà vu.

Dream Ranker Arc
Mikoto has a swimming lesson at school after which she meets Hokaze Junko and then Misaki, getting into an argument with the latter. Junko later apologises for Misaki's behaviour and hands her a strange card to make up for it. Saten recognises it as an Indian Poker card, which lets the user have someone else's dream. Curious, Mikoto tries out the card that night. In the resulting dream, Mikoto initially gets to meet Gekota and is overjoyed. However, she is then taken to a castle where Misaki is queen and then forced to serve as a maid. When dream Misaki says that she can serve her for life, Mikoto is so enraged that she wakes up and yells that that's the last thing she wants.

The next morning, Mikoto meets with her friends and has a brief discussion with Saten about Indian Poker. She encounters Junko again and is asked to join her for tea after school, which she decides to accept. Unfortunately, Misaki is also present and thus the tea becomes uncomfortable for both her and Mikoto. They overhear another group of customers talking about Indian Poker, among them a card designer named Blau. They hear that Blau creates and distributes cards with erotic dreams, including dreams featuring Mikoto and Misaki. This enrages the two Level 5s, who destroy the cards and erase the group's memories. Junko tries to improve the atmosphere afterwards and asks them if they ever dream about a gentleman that they like, but this causes them to both make up an excuse and leave.

Mikoto again meets Saten, who demonstrates the kendama skills she has learned from using Indian Poker. She hears about merchants who trade in Indian Poker cards and later finds one in the street. She also finds Kinuhata Saiai browsing the merchant's wares. The merchant claims to have the S rank card "Bust Upper", which rouses interest from both the girls. The two of them fight over the card, eventually causing all of the merchant's cards to get mixed up. To compensate for this, Mikoto and Saiai decide to buy all of the cards. In an internet lounge, they collaborate to check through the cards until they find the Bust Upper, under the agreement that they will share it. Mikoto has dreams from the perspectives of Kuruwa, Yoshikawa Kikyou, a roadside musician, and Himegami Aisa. The two are kicked out for making a disturbance and have to move to the outside lounge of a hotel. Mikoto experiences an abnormal dream that isn't from the perspective of another person, in which a a strange girl speaks cryptically about a threat that cannot be ignored. The Bust Upper is stolen by a passing crow, and the two girls are unable to find it and assume that it was fake.

Mikoto is approached by Hazamaya Kana, who asks her to accompany her to her bus stop. When Kana starts insulting her with words unfitting for a child (including talking about the search for the Bust Upper), Mikoto realises that Misaki is controlling Kana and angrily calls her out. After Misaki releases Kana, she laughs at Mikoto for seemingly being unaffected by the Bust Upper. Mikoto angrily fondles Misaki only to get depressed at the sensation.

The two head to a restaurant to talk. Misaki begins explaining what she knows about Indian Poker, but has to hit a still-depressed Mikoto to get her attention. She reveals that Kuriba Ryouko is the creator of Indian Poker and that Ryouko underwent a cyborg experiment involving her body being split in two. She then talks about what effect this experiment had on Ryouko's soul. Mikoto is sceptical of Misaki's theory that Ryouko's soul was left in machines. Misaki asks Mikoto to infiltrate Ryouko's lab to find out more, offering to help her with the Sisters in return.

Mikoto climbs up to the top of a high rise building to reach the lab, but it explodes before she reaches it. Someone who looks like Ryouko falls from above and Mikoto tries to save her by magnetically pulling banners into her path, but she falls through the banners. Mikoto returns to the ground and finds that the Doppelgänger has disappeared.

Mikoto and a Misaki-controlled pawn go to the real Ryouko's apartment and trick their way in. Ryouko recognises the Railgun and they head to a nearby park (where Misaki is hiding) to talk. They discuss the Doppelgänger and Ryouko calls her an extremely dangerous problem. She says that the Doppelgänger could survive the destruction of her body as a free soul and then possess other things. She also explains that she created Indian Poker to try and find a solution to the problem. After Ryouko leaves, Misaki comes out and talks briefly with Mikoto about her. She tells Mikoto the rest of Ryouko's past, which causes Mikoto to run off after her.

Mikoto comes to the rescue when Scavenger attacks Ryouko and the Doppelgänger, having been tasked to capture the latter. She fights and defeats Seike, then heads over to the rest of the group. Thinking quickly, Leader persuades Mikoto to work with them. Mikoto leads them to Seike, and Yakumaru and Naru take Seike away for treatment. She then asks Leader about their organisation, so Leader lies and claims that they're part of Judgment. Mikoto receives a call from Misaki and learns that the laboratory has backed up their data on a stealth airship. Leader gives her a Gekota-shaped communications device for them to keep in touch, and Mikoto praises Leader for her taste. They then track down the Doppelgänger.

Mikoto attempts to trap the Doppelgänger with concrete blocks, but the cyborg breaks free and then then drops a water tank on them. Mikoto has to pull Leader out of the way, giving the Doppelgänger the chance to escape. Mikoto and Leader pursue her using the latter's ability. To avoid civilian casualties, they redirect her to a less-populated area and Leader calls her allies to evacuate the Skill Out members there. At Leader's suggestion, Mikoto directs the Doppelgänger towards a warehouse where Scavenger is meeting with client (and Leader exploits this to convince the client to sign off on their job).

The Doppelgänger creates a massive puppet out of rubble, forcing Mikoto to go all out. The Level 5 creates a comparable puppet out of iron sand and overwhelms the Doppelgänger's. The Doppelgänger then creates numerous copies of herself and uses threads extending from the copies and herself to reach the airship. The real Ryouko arrives to talk to the Doppelgänger, and Mikoto is unable to stop them reaching the airship. Mikoto uses an iron sand pillar to ascend and, when Ryouko jumps off the airship, tries and fails to save her. However, Scavenger intervenes to save Ryouko.

Still climbing towards the airship, Mikoto contacts both Leader and Misaki and they work out that the Doppelgänger's power comes from self-replicating artificial muscles. She reaches the airship and confronts the Doppelgänger. The Doppelganger threatens to destroy the city. They fight, with Mikoto receiving support from Leader. Mikoto tries to persuade the Doppelgänger to continue living, but she refuses, forcing Mikoto to destroy the airship with powerful lightning. On the ground, Mikoto tells the damaged Doppelgänger that she's realised the truth, that the Doppelgänger was trying to destroy herself and any means of recreating her. Ryouko arrives, shortly followed by the lab's chief researcher. The researcher wants to retrieve the Doppelgänger and threatens Ryouko at gunpoint when they disagree. He eventually shoots Ryouko by accident and runs away in fear. The Doppelgänger tells Mikoto that Ryouko is fortunate, as the cyborg's organs can be transplanted into Ryouko.

Mikoto visits Ryouko in the hospital and learns that she sees the Doppelgänger in her dreams because of the transplanted organs. Ryouko apologises for getting Mikoto involved and says that the Doppelgänger seemed most content when fighting her. Mikoto asks her to tell the Doppelgänger that she was a similarly formidable opponent.

After Mikoto realises her feelings for Touma (during the Acqua of the Back Arc in Toaru Majutsu no Index), she walks unsteadily through the streets. She meets Uiharu and Saten and tells them about her troubles, claiming that it's about a friend. She becomes depressed as she thinks that Touma is interested in girls with large breasts. Uiharu suggests that "Mikoto's friend" would need to stay in a tragic situation in order for him to stay interested in her.

Jailbreaker Arc
Mikoto watches the TV and learns about a jailbreak trial being held at the Private juvenile hall: an event in which esters attempt to break into the hall and break out a pretend prisoner, in exchange for a reward of one billion yen. Mikoto initially doesn't plan on participating but is goaded by the juvenile hall's director insulting Tokiwadai. She and her friends line up to join the event, with Kuroko staring at Mikoto disapprovingly.

The event begins, and Mikoto sees other competitors try to breach the wall and fail. They get close to the wall with Kuroko's teleportation, but face greater difficulty from then on due to the juvenile hall's AIM Jammers. After others continue failing to breach the wall, Mikoto uses her Railgun with a giant ball of scrap metal. This succeeds in blasting a hole in the wall, but the self-repair system seals the hole. Mikoto then works with other competitors to make a lasting hole. She enters the facility with Kuroko and Saten, with Uiharu telling them to continue without her.

While in the outdoor part of the juvenile hall, Mikoto's group is able to proceed thanks to Yakumaru of Scavenger discreetly taking out the security robots for them. However, they end up at the boys' building by mistake, instead of the girls' building where the target is.

Mikoto's group goes to the correct building, finding that others have already entered it and witnessing Raifu run away from a robot only to be saved by Yamashiro Shoubu. They then find the ninja Oumi Shuri, who pretends to be a helpless little girl to convince them to escort her (and hence get information from them). They encounter another group of competitors about to use their power and try to intervene, but Oumi persuades them to stay away (so that she can see the effects of an AIM Jammer on an esper). The resulting out-of-control power sends rubber bullets flying everywhere, so Mikoto and Kuroko block the bullets with makeshift shields while Saten covers Oumi. Despite their efforts, Oumi is hit and decides to flee.

Mikoto and her group come to a room where they are surrounded by security robots. However, the War Armadillo robots attack the others, revealing that Mikoto had reprogrammed them in advance to fight on her side. With the robots, the group easily advances through the prison and eventually runs into Kongou Mitsuko and her group. Kongou offers to give them special suits that hide them from the sensors, but Mikoto declines because of how the suits emphasise one's figure. They finally reach the room where the target is supposed to be, but find it unlocked and empty. It turns out that Uiharu had used her hacking skills to break out the fake prisoner before any of the others.

After the trial is over, Mikoto reveals that she had suspected Uiharu's actions since the door to the girls' buildings had been opened without force (suggesting it had been hacked). They talk about what to do with the prize money and Uiharu says she'll donate it to charity. However, they are unaware that the person Uiharu broke out was an actual prisoner in disguise, and that said prisoner has plans for the skilled hacker.

Mikoto discusses the trial with Uiharu and Saten in a restaurant. She and Saten praise Uiharu's skills but Uiharu is dragged away by Kuroko to do her duties.

That night, Uiharu goes missing, so the other three gather at her apartment to investigate. They find that Uiharu was likely taken away in a recreational vehicle (RV) that is now heading east. Saten asks them to bring her along, so Mikoto carries her with magnetised pieces of metal.

They catch up to the RV. Kuroko first teleports onto the roof and is attacked by the ninja Tsurigane, confirming that the kidnappers are in the RV. Mikoto then uses barbed wire to bring the RV to a stop. She orders the kidnappers to release Uiharu immediately, only for Kimi to step out. Kimi claims that she only needs Uiharu to do a job for her and will return her afterwards, which Mikoto refuses to accept. Kimi then unleashes the dragon in her right arm, which Mikoto recognises as one of the dragons that emerged from Touma's right arm during the Daihaseisai. She creates a giant iron sand puppet and attacks Kimi, angrily asking why she has the dragon. However, the dragon transforms the iron sand into a mysterious white substance and then lunges at Mikoto, destroying a building. She is saved by Kuroko, though she loses consciousness for less than a minute. Kuroko tells her that two vehicles drove away and towards District 11. She adds that something about the situation bothers her, but Mikoto says that they need to continue the chase. Saten suggests an idea, which involves her being left behind to tell Anti-Skill that she caused the destruction.

Mikoto and Kuroko continue the chase and see the two vehicles split up. Kuroko decides to follow the one carrying Kimi and Uiharu while Mikoto follows the other. Mikoto follows the vehicle to a garage in District 11. She finds Raifu, another of the kidnappers, who pretends to be a civilian taken hostage by someone who is actually her subordinate. Mikoto recognises Raifu as a participant in the jailbreak trial but doesn't fall for the trick, noting that the subordinate seems scared of Raifu. She destroys the vehicle, calls Kuroko to tell her that Uiharu isn't here, then turns to leave. Raifu stops the act and now threatens to kill her subordinate if Mikoto leaves. This forces Mikoto to follow Raifu into the garage and fight her. She feels uneasy due to Raifu seemingly reflecting an attack, but notes that it can't be a lower-level version of Vector Control. Raifu attacks Mikoto in various ways, including causing a gasoline explosion.

Mikoto manages to escape the burning building. She doubts that Raifu expected to kill her with the fire and wonders why she started it. Her question is answered when she catches up to Raifu at the wall and notices Six Wings approaching, alerted by the fire. She deduces that Raifu did this deliberately as she knew the security system in advance. They fight, with Raifu redirecting missiles and then an entire Six Wings at Mikoto, which she intercepts.

When Raifu redirects a second Six Wings, Mikoto prepares to use her Railgun on it. She realises that Raifu is up to something, allowing her to dodge when Raifu redirects her Railgun at her. While lying on the ground, Mikoto realises that Raifu's power is actually control over gravity. She gets up and makes several failed attacks on Raifu, the last being a gas tank that Raifu redirects back at her. However, Mikoto creates a decoy out of dust to receive this attack, giving her the opportunity to shock Raifu. Raifu tries one last attack, but Mikoto destroys her weapons using iron sand and kicks her in the head. Mikoto says that she's no hero, and the hero she knows is a huge idiot who can't rest until he saves everyone in need, even people like Raifu. She incapacitates Raifu with more electricity. Finally, she says that she can't support the people closest to her but she is willing to hear Raifu out.