Shokuhou Misaki/Chronology (Toaru Kagaku no Railgun)

This article covers Shokuhou Misaki's chronological history in Toaru Kagaku no Railgun.

Toaru Kagaku no Railgun
Prior to her debut, she has heard of the collapse of the Level 6 Shift, and has become interested in the fate of the clones. She hires Keitz Nokleben, former security supervisor of the project, and sets up meeting with him, to which he woefully concludes that he has no idea what happened to the clones. He tells him that all liability was pushed towards Amai Ao, and that another agency has taken care of the Sisters. However, he says that there is another group searching for the clones. Hearing this, Misaki tells him to investigate and continue to search about the whereabouts of the clones.

At some unknown point in time, the urban legend website Auribus oculi fideliores sunt begins plaguing her as they discover the whereabouts of an institute where Misaki keeps Exterior.

She is finally formally introduced in Toaru Kagaku no Railgun, where Mikoto is already aware of her status as well as displaying her animosity towards her. Here, she warns Mikoto if she attempts to create a clique of her own and challenge her, controlling several Tokiwadai students at the same time to get the point straight. Finally, after letting go, Mikoto asks if she truly is a middle school student after seeing her bust size, to which Misaki states the ambiguity of her appearance may be due to her powers before leaving.

Silent Party Arc
Despite Mikoto's distaste for Misaki and her powers, getting her friends out of trouble from the authorities during the failed terroristic event known as Silent Party was apparently enough for her to cast aside her pride (among other things) and ask Misaki for help. It is unknown what Mikoto did to convince Misaki to help her or what her reaction was, but Shinobu mentions that not only were the digital records modified to make them look in a favorable light she suspects that some people's memories have been modified as well. Allowing for the girls to slip by the authorities conveniently without consequences of their actions.

Daihasei Festival Arc
She is later seen with members of her clique as they discuss the proposal by the Daihaseisai committee for a showing of Level 5s. Misaki says she doesn't feel it'd be right to take Mikoto's spotlight. One of her underlings expresses concern when Misaki has a second crepe when she just had one, and the girl with ringlet curls takes it away. Suddenly, Keitz Nokleben prompts up Misaki as he drinks a cup of coffee from an adjacent table. Her underlings are about to intervene but she uses her powers to rewrite their memories and shoo them away, adding on that they should eat twenty éclairs as fast as possible while they're at it. When they are gone, Keitz and Misaki speak on an arrangement about certain knowledge she wants. The man says he has what she wants but that Misaki shouldn't concern herself with that; the top priority this time is to get the client to trust them. He says Misaki's help is appreciated and the two beam contrasting smiles at each other that perhaps aren't that different.

During the opening of the Daihaseisai, she speaks along with Sogiita Gunha, but is quickly overshadowed by Gunha's fiery speech, drowning out her own. Since he didn't memorize the real speech and was going on guts alone, there was no coordination. She sulks afterwards, saying she was beaten.

She is later seen preparing for a competition and boasting she can just mind control the referees and player to easily win. However, Fukiyose Seiri (in the anime, her cameo was replaced by Konori Mii) barges in and takes the purse that contains her remote control, saying Misaki can't have gear on her that isn't for sports. Misaki stand idly with a blank look, realizing she's been had. She is absent during Tokiwadai's ill-fated ball hunting competition, but reappears at the end with the ex-security supervisor of the Level 6 Shift, looming over a tired and unconscious Misaka 10032. She reappears later during the lunch break, talking to Mikoto on how about she's too tired on doing anything else for the day, hither comes Touma, who just talked to Mikoto before Misaki showed up, and is allured by her appearance. She teases Mikoto regarding her temper, and alludes to her knowledge of his name (Touma did not introduce himself to her) and of their acquaintance from before Touma's memory loss, before leaving.

Right after lunch, Misaki intercepts an inquiry on Auribus oculi fideliores sunt, an urban legend website from Judgment 177 Branch Office. However, Misaki is well aware of Mikoto's connections with the office and visits the office herself. She finds Uiharu Kazari has read the website and erases her memories of its contents as well as the data in their computers, determined to erase all traces of Exterior. She also reads Uiharu's memories and finds out Mikoto's friends, knowing full well that Mikoto would get involved when it comes to her Sisters. She also implants Uiharu with instructions on going on a different patrol route in order for her to gather Kuroko and Saten in a single spot for her and Keitz to intercept. With that, she has Keitz have inquries regarding the urban legend websites redirect to dummy websites.

It is later revealed that she has altered the memories of the paramedics that took Misaka 10032, as well as her own teacher, Watanabe, whom she fully controlled, putting Mikoto in a tight spot. Having manipulated Uiharu yesterday, she follows Misaki's instructions into going a different patrol route. There, together with Keitz, she uses her powers to completely erase the memories of Misaka Mikoto from Uiharu Kazari, Shirai Kuroko, and Saten Ruiko. Knowing that her true enemy is Kihara Gensei, she attacks Kouzaku Mitori's "villas" to search for information and making Mikoto look like the culprit my messing with eyewitnesses' memories, it is likely here that Misaki discovers the presumed whereabouts of Gensei in District 9, not knowing it's a ruse by him.

Misaki is later shown once again standing over a collapsed Misaka 10032 in the building that houses Exterior, seemingly coordinating her actions with Baba Yoshio while members of her clique continue to stall Mikoto's attempts to uncover her plots. However, it is later revealed to be a misunderstanding. Yoshio has mistaken Misaka 10032 for Misaka Mikoto in attempt to leash her as she might attempt to interfere with the mission they were given after her intrusion in the Level 6 Shift. Keitz and Misaki comes upon the clone and tells her how she was injected with a nanodevice, as such the antivirus software for her would not be able to heal her. Misaki says that if it is a danger to her life, she might be forced to ask Misaka Mikoto for help, but Keitz says that the opportunity might allow them to do the first move against their enemy, Kihara Gensei. Misaki later asks about the urban legend website called Auribus oculi fideliores sunt, which was somehow able to monitor her whereabouts within a secret institution in District 2. Keitz tells her that he has prepared a program that creates dummy sites to bury the website in the web. With that done, Misaki later takes her in to protect her against, keeping her inside the secret institution in District 2.

After the conclusion of Kongou and Baba Yoshio's battle, the former is taken to a hospital, where Mikoto witnesses her serious condition. After that, Misaki's clique members are unable to further stall the furious Railgun. Next, after the appearance of Kouzaku Mitori, seemingly another constituent of, it's raised the possibility that Misaki may not be involved with the attack on her friends.

Later, when Keitz is monitoring his program, he discovers that someone was able to break through his setup and reach the website, annoying Misaki and berating him. However, he reveals that he can trace the intruder, to which it reveals that it was from Judgment 177 Branch Office. Seeing that it is Mikoto's interference, Misaki leaves Keitz to meet up with her.

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 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.

It is revealed in a flashback that Misaki was part of an experiment used to develop her powers further. This involved gathering data on a clone named Dolly—though the only means to do this was by the pretext of befriending her, as Dolly had been traumatized by the loss of a friend in the past due to the latter seeing her disfigured, machine-embedded body (a necessity to keep her alive). However, as Misaki, who Dolly refers to as Mii-chan, begins to spend more time with Dolly she slowly warms up to her. Misaki reveals to Dolly that her powers tend to alienate her at school, hence her ambivalence towards it. Their relationship culminates in Misaki's promise to take Dolly to the ocean when she is released from the institute.

Unfortunately, by the time they have become close friends Dolly's condition deteriorates immensely and she is taken away, asking Misaki for her real name just before she leaves her. When Misaki asks a researcher if Dolly's condition will improve and if she will return soon he coldly replies that this will be the last time she sees Dolly, and that the full details are murky at best; he explains to a shocked Misaki that Dolly's body had "long since passed its limit", even with Academy City's scientific capabilities. He then states that everything is going according to plan, and that even Dolly was aware of it. Misaki sinks into a stupor at this development and ceases to further any of her curriculum. A researcher passes by to chastise her lack of activity and also to inform her that Dolly has died—Misaki does not react to this at all. Later, the scientists discuss Misaki becoming a problem due to her inactivity and her negativity over Dolly's death. One scientist in particular notes that "even that girl has human emotions", while another suggests telling Misaki that Dolly was simply a clone to improve her attitude. One researcher explains the significance of the Exterior project and that the Clone Dolly Workshop is the crystallization of our greatest wishes," another adding that the substantial growth of Misaki's power will soon render their mental guard helmets useless, and finally that the truth of the project will be impossible to hide at that point. The other researcher replies that it is not a problem, and a certain figure asks why; he replies that once Exterior is complete, there will be no further use for Shokuhou Misaki and that she can be disposed of when the opportunity presents itself. It is then revealed that Misaki has been among the meeting all along, having brainwashed every single scientist in the project starting with the lower-level researcher they had experimented on earlier, using him to tamper with the other researchers' helmets while she asserted her influence everywhere else.

Misaki notes that she brainwashed everybody related to Exterior before she had entered Tokiwadai Middle, and that none of them would leak any information even if they were tortured—there should be no way Gensei should have known about Exterior otherwise.

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. He is entralled by Mikoto's arrival in the building, saying that it saved him the effort. With Misaki collapsing after Gensei took over her giant brain (Exterior), Misaka Mikoto tries to intercept Gensei up on the roof, leaving Misaki alone as Mikoto quickly becomes the next subject for Gensei's plans to create a Level 6.

Following Mikoto's transformation, 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's be worried, but since it does involve her, he looks like a Prince. After this, 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. Following this, she heads to the ceiling, where she meets Keitz, noting that Gensei has disappeared, and remarks that only someone with Mental Out can defeat someone with the same ability. At this time she is attacked by the liquid metal humanoid created by Kouzaku's Liquid Shadow, however she is saved by Kuroko's timely intervention.

After discovering that the puppet is at the maximum control range she has for maintaining control over both the puppes and Mikoto, she has Kuroko teleport both Misaka 10032 and Keitz away to safety, after teleporting them back inside the facility, gives her a briefing with her powers on the likely area where Kouzaku is hiding and sending her off to find her. She later sees Gensei making his way to release Exterior's controls and she surmises as to why Kouzaku was trying to capture her and not kill her. With that in mind, she decides to memorize the code for Exterior's limiters and leave no data behind, forcing Gensei to go after her as there is no other alternative. She later uses her powers on herself. She later watches as Gensei easily bypasses the facilities defenses by the powers he gained by using Level Upper unknown number of espers, Multi-Skill, Gensei then reveals that upon reaching level 6 Mikoto will overload and destroy Academy City in the processes as he pins her to a wall with his Ice Beam ability. He then states that by incapacitating her he can bypass the mental blocks she placed on herself to prevent Mental Out being used on her and proceeds to use Aero Shooter to try do this by asphyxiating her. While doing this he becomes distracted with his Clairvoyance power not only noticing by the arrival of Touma, but also the fact that Sogiita has shown up as well, Misaki takes this opportunity to free herself and escape. As she escapes she comments to herself that with Sogiita now interfering as well Academy City should survive, but still believes that Mikoto will perish.

The game of cat and mouse continues as Misaki makes a bluff against Gensei, who sees right through it. However, Misaki tricks him, though using his Multi-Skill ability, specifically the Aero Shooter, allows him to escape the pit that Misaki hidden through the Exterior building's Graviton Panels. After being hit by and downed by Gensei, it is seemingly for Misaki. However, she once again uses the Graviton Panels to appear inexplicably appear at the hole Gensei was going through, trapping his hand. However, her relief only lasts for only a moment as Gensei reveals to her that his hand is merely a prosthetic from one of the times he nearly died when to focused on something else. Gensei says that it is due to his experiments that led to this state. Moreover, Misaki cannot fool him, for he knew that she still had hope when she was running away and had relied too much on her power to read peoples motives. With that Gensei used his Aero Shooter again to choke Misaki, making her pass out. He is then able to retrieve the release code. After retrieving his hand, he later senses Mikoto's transforming, something he claims as her "Opening Stage" and then uses the release code to fully open Exterior.

However, unknown to Gensei, Misaki had previously considered how she was unlikely to be able to trap him with the Graviton Panels, whether she actually needed Exterior anymore, the need to heal the Sisters of the virus and that this was likely her last chance to capture Gensei. As such, she had taken a gamble by switching her own concepts of the limiter release code with the self-destruct code. Exterior begins to crumble and Gensei collapses from the backlash. Regaining consciousness, Misaki figures out what she must have done.

She later decides to read Gensei's memories, and later learns from it that Dolly has a little sister that was created at the same time as her. Sometime after both Touma and Gunha successfully got Mikoto back to normal and Kuroko defeating Kouzaku, Misaki goes down to where Kouzaku is being held by Kuroko's handcuffs. She tells her she will have her turn herself in but before that she tells her what she knew from reading Gensei's memories. She tells her that Dolly's little sister had Dolly's memories and experiences transferred into her. She tells her that though she isn't Dolly, she just can't let her be, and tells her to come with her. Kouzaku escapes her bonds and asks why she didn't just use her powers on her instead of explaining things to her. Misaki asks if she needed to use her power, to which Kouzaku says she didn't. Thus with a mutual understanding, Kouzaku stands once more to bring an end to the tragedy that has befallen on Dolly.

Misaki first restores 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.

Back with Misaki and Kouzaku, they enter the building where Dolly is kept, Misaki tells her that Dolly perceived her as Kouzaku, as at the time she still didn't have the ability to manipulate memories. Misaki says that at some point, Dolly noticed that she was a fake, to which Kouzaku notes that Dolly surprisingly good intuition. Kouzaku then says thanks as the elevator comes to their intended floor. She says to Misaki that with her at the end of Dolly's life, at least she wasn't alone, and says that was her biggest regret. The door opens to reveal the capsule where the clone of Dolly is kept, and runs up to it. The clone's consciousness wavers until finally it awakens and calls out to Kouzaku's name at the sight of her.

Misaki is in the shadows observing in the shadows during Dolly and Kouzaku's tearful reunion. She finally tries to leave. However, Dolly calls out to her, knowing who she is. Misaki tries to play it off, but Dolly says she knows she is Misaki because they are always together in their dreams, and says the time they've spent together is the only memories they both have. Misaki is at loss for words, and then finally, she apologizes to Dolly. With emotions overcoming her, Misaki says that she is sorry for deceiving her, manipulating her memories, and her getting lost in the comfortable lie of being her friend. She says that if she had looked into who "Mi-chan" was then she could've reunited her with Dolly, and if she had known the truth of the experiment she is sure that Dolly wouldn't have died. Misaki says that it is all her fault for selfishly putting herself between the two of them. And then states that she'll do anything to make it up to her.

Then, Dolly with Kouzaku, come from behind Misaki and embraces her, telling her that she wants her to take her to the beach, let her ride a roller coaster at an amusement park, let her see a hippopotamus at the zoo, ride an airplane, and see an aurora in Finland. She continues on with many more requests, to which Kouzaku says that it is way too much. But Dolly can only help but laugh. She says, as she leans on Kouzaku, that if they are all together, anywhere is fine, and asks if they can do that. Hearing this, Misaki says that Dolly still ignores what everyone says and force her opinion on them. She turns to them to reveal the tears upon her face and says that Dolly is selfish and that there's no arguing with her.

Dream Ranker Arc
Misaki meets Mikoto and Junko just after a swimming lesson. As usual, she and Mikoto get into an argument. However, Misaki retreats when she sees the dorm supervisor approaching.

Misaki later appears in a dream of Mikoto's (said dream was originally Junko's, and Mikoto is experiencing it using the technology of Indian Poker). The dream Misaki mistakes Mikoto for her new maid and makes her do all sorts of tasks for her. She eventually declares that Mikoto can serve her for life, which angers Mikoto so much that it causes her to wake up.

Later, Junko makes Misaki have tea with Mikoto in an attempt to deepen the "friendship" between the two Level 5s. Misaki rejects Junko's attempt and tells her to stop. However, they are interrupted by someone nearby shouting. They overhear a conversation between Aogami Pierce, a Dream Ranker (someone who makes Indian Poker cards), and his customers. They learn that Aogami sells cards containing erotic dreams, some of which feature Misaki and Mikoto, which naturally enrages the two. They head over to stop the practice, with Misaki altering the memories of witnesses while Mikoto destroys the cards. Afterwards, Junko attempts to improve the mood by asking if either of them dreams about a gentleman that they like. The two Level 5s excuse themselves and head in opposite directions (presumably because they do have such dreams).

Misaki investigates Indian Poker on her own, reading the memories of an Indian Poker Merchant and hiring Keitz again. From the latter, she learned that the creator of Indian Poker is a student named Kuriba Ryouko.

Eventually, Misaki controls the young Hazamaya Kana and has her insult Mikoto repeatedly (at one point bringing up Mikoto's attempt at increasing her bust size with Indian Poker). Mikoto realises the truth and calls Misaki out, so Misaki ends the mind control and Kana leaves. Misaki comments on how Mikoto wasn't able to grow her bust, causing Mikoto to grab Misaki's breasts out of anger. However, this only causes Mikoto to collapse in despair.

The two go to a restaurant to talk. Misaki begins explaining what she knows about Indian Poker but Mikoto is still preoccupied with her bust size, so Misaki hits her with her handbag. She continues, explaining that Ryouko was the subject of an experiment that involved splitting her in two, replacing the missing parts with machines to create two independent bodies, then reconnecting her after a year. Misaki then discusses the implications of this experiment for Ryouko's soul. She suggests that Ryouko's soul may reside in the machines left behind, which Mikoto is skeptical of. She asks Mikoto to infiltrate the laboratory where the experiment occurred, both to prevent the experiment from being repeated on unwilling test subjects (such as Child Errors or human clones) and in exchange for Misaki's help in letting the Sisters integrate into society. Mikoto accepts and leaves.

After Mikoto's departure, a miniature puppet of Kouzaku Mitori appears from under the table, having overheard the conversation. Through her puppet, Kouzaku makes fun of Misaki, pointing out that Mikoto would have acted even without the deal and that Misaki just wanted an excuse to help the Sisters. Misaki attempts to crush the puppet with her handbag. Kouzaku then passes on a message: Keitz has tracked down Kuriba Ryouko.

Mikoto's attempt to infiltrate the laboratory fails as a cybernetic doppelgänger of Kuriba Ryouko escapes. She and Misaki therefore head to the real Ryouko's apartment (Misaki via a mind-controlled proxy) and force their way in. Ryouko recognises Mikoto as the Railgun and agrees to go with her to a nearby park to talk. Misaki herself hides among the trees to listen in on the conversation. Ryouko explains the nature of the doppelgänger and the threat that it could pose. Supposedly, the doppelgänger's soul could survive the destruction of its body and possess other things. After explaining everything, Ryouko leaves. Misaki releases the person she was controlling and talks with Mikoto. She tells her the rest of Ryouko's history and Mikoto hurries off.

However, the dark side organisation Scavenger has also become involved, having been hired by the laboratory to retrieve the doppelgänger. Misaki calls Mikoto while the latter is talking to Scavenger's Leader. She suggests meeting up, which causes Leader (currently pretending to be part of Judgement) to convince Mikoto that this isn't necessary (as Misaki's power would let her see through Leader's deception). Misaki also reveals that the laboratory keeps a backup of its data on a stealth airship.

Misaki calls Mikoto again and tells her that the doppelgänger seems to be heading for a radar facility that would allow her to locate the airship.

While Mikoto fights the doppelgänger, Misaki reads Ryouko's scientific papers. In a conversation between her, Mikoto and Leader, they work out that the doppelgänger's power comes from self-replicating artificial muscles.

Misaki tracks down the head scientist of the cyborg experiment and takes control of him. She plans to make him recall his original intent: developing cyborgs to help medical refugees.

Jailbreaker Arc
Shokuhou was mentioned by Dolly at the start of the Second Reformatory's Jailbreak Trial. Dolly was sad that Misaki wasn't taking part in the event, to which Kouzaku responded that she would never take part in a physical event in which her power was being jammed. She had apparently given the excuse that only a simple-minded fool would fall for such a cheap provocation as the one the director made. She did, however, send two members of her clique, Kii and Mei, to watch over Dolly and Kouzaku, intending to wipe their memories afterwards.

First Year Arc
During the events of Shokuhou's first year at Tokiwadai, one year before the main story, Shokuhou encountered Misaka Mikoto for the first time at some point prior to the summer uniform switch. Recognizing her appearance and recalling Dolly, Shokuhou began to ask why she gave up her DNA map before stopping herself and expressing that she never wanted to see Mikoto's face again. Having gotten off on the wrong foot, the two would subsequently encounter one another again, being observed bickering by Kessai Kiyoshi a week later, after the summer uniform switch.

Shortly before the incident which triggered a conflict between the Mikagami Clique and Hasekura Clique, Shokuhou was by a window in a first floor corridor at the school and witnessed an altercation near the gates between Enjou Kasumi and Kazan'in Tsukasa, which nearly led to a fight before their respective friends stopped them.

A few days later, as the clique conflict was progressing, Shokuhou was walking through one of the gardens and experiencing leg cramps. She was then confronted by Lily of the Sha Clique, accompanied by Ouyang Qian and Lin Lihua, who suspected Shokuhou's involvement and intended to take her for questioning. When Shokuhou refused to go along with them, they attempted to quickly deprive her of her remotes, seizing her and her bag with vines. Attempting to activate her power while experiencing leg pain, Shokuhou caused the vines around her to wither. She then tried to grab her bag on the ground before a called hawk could snatch it, but misjudged the distance, accidentally kicking it away before tripping and falling forward. While the other girls were talking about what had just happened in surprise, an embarrassed Shokuhou called for Junko, who swiftly arrived and dispatched the attackers.

After the attack, Shokuhou read Lily's memories and determined that she had jumped to conclusions. She and Hokaze searched for the bag afterwards, but were unable to find it, given that the hawk had dropped it somewhere by the time they had found the bird. Shokuhou expressed her anger at the affair when having tea with Hokaze afterwards. Although Hokaze suggested that Shokuhou could resolve the situation with her powers, Shokuhou declined, given the unlikeliness that people would trust her word and the likelihood of making more enemies.