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|Personality and Relationships • Abilities • Index • Shinyaku • Souyaku • Railgun|
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 RailgunMikoto, 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 Judgement, 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
- Main article: 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
- Main article: 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.
- Main article: 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.
- Main article: 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
- Main article: 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)
- Main article: Daihasei Festival Arc (Railgun)
Level 6 Shift attempt of Misaka Mikoto
- Main article: Level 6 Shift attempt on Misaka Mikoto
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 deja vu.
Dream Ranker Arc
- Main article: 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.
- Main article: 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.