Sisters Arc

The Sisters Arc is a major story arc in the Toaru Majutsu no Index universe. Originally only lasting a single volume in the light novels, it is later expanded greatly in the Toaru Kagaku no Railgun manga.

The arc focuses on the ordeals of Misaka Mikoto after discovering the existence of the Sisters that are being used in the Level 6 Shift, an experiment where they are killed in order for the highest-ranking Level 5, Accelerator, to achieve Level 6. The arc not only focuses on Mikoto, but with various individuals and factions involved in the experiment; as well as the effects of her struggle on the people that are close to her as well. The arc later coincides with the Toaru Majutsu no Index main storyline, after Kamijou Touma meets Mikoto again for the first time since losing his memories.

Sisters Project

 * Main article: Sisters Project

At a young age, Mikoto willingly gave her DNA to the researchers at the Higuchi Pharmacology Laboratory 7, after being convinced by them that using her DNA to help children who were unable to control their muscles due to a certain illness. However, this was all a ruse to obtain her DNA to produce military clones, and Mikoto is left unaware of it.

Before the mass production of the clones could begin, Tree Diagram calculated that the clones were unsuitable for use as they could not reach the level of Mikoto. This forces the involved parties to stop the experiment to cut their losses.

Level 6 Shift

 * Main article: Level 6 Shift

The Sisters project is later reused by the Level 6 Shift experiment – an experiment to make Accelerator reach level 6, whose main proponent was Kihara Gensei. This due to the calculations of Tree Diagram that states that the killing of 20,000 clones by Accelerator in combat is a sufficient substitute for Accelerator to achieve level 6, as killing the Level 5 Misaka Mikoto 128 times is impossible.

Rumors begin
Before Mikoto knew of the existence of the sisters, rumors began to spread all around Academy City that clones of Misaka Mikoto are being used for military purposes. Though Mikoto did not believe in the rumors, and thought nothing of them, a little part of Mikoto remained suspicious of the rumors.

Bank Cards in the Alleyways
Mikoto wakes up from a dream regarding her giving the DNA sample to the researcher to help the children; though disturbed by it she continues her day as usual. Shirai Kuroko shows her a shortcut through the alleyways and finds out that there are more people than usual frequenting them. They later discover that someone is throwing away bank cards in the 7th School District, with at least 56 similar cases being reported. Uiharu Kazari of Judgment notes that is not illegal to throw away bank cards and that the amount of the bank cards varies, amounting about less than 1000 yen up to more than a thousand, which are then distributed around roads and alleys rarely visited by people.

The rumors spread about this occurrence, making students visit the places more often looking for the bank cards as a sort of treasure hunt. Mikoto leaves Kazari and Kuroko to do some more investigation regarding the case, as it would attract the attention of certain groups that have no esper powers.

Mikoto later sees Saten Ruiko, looking for bank cards herself and forcibly invites Mikoto to come search with her. Ruiko leaves Mikoto alone after the both of them has yielded a considerable amount of bank cards for themselves. After which Mikoto overhears the conversation of a group of Skill-Outs, who are saying that they have found the one responsible for distributing the bank cards. Mikoto follows them to an old apartment where a lone girl resides. She eavesdrop on what was happening between the delinquents and the girl, and discovers she truly is the one distributing the bank cards and is a student of Nagatenjouki Academy.

Wanting more money from the girl, the delinquents tried to use force on her, however, Mikoto witnesses how the girl dispatched them by simply using fear and trickery to cause them to mentally breakdown. Impressed by this, Mikoto comes out from hiding and compliments the girl for her feat.

Seeing her, the girl notes that Mikoto is the original, to which confuses her. The girls asks Mikoto if she has at least heard the rumors of her clones, realizing what she just said, Mikoto tries to coerce answers from the girl, only to get hit by her stating that she should respect her as she is her senior. The girl tells Mikoto that she distributed the bank cards to deliberately force people into the alleyways, as so to cover the blind spots that in the city’s security system and stop ‘the experiment’ that were to be held there. The girl then burns her documents and the apartment she is using, as she is afraid that her operations would be compromised. She later leaves Mikoto, much to her chagrin as she had to haul the fallen delinquents all by herself.

Unsatisfied by the girl’s responses, Mikoto hacks into the Nagatenjouki Academy database and discovers her name, Nunotaba Shinobu, a child prodigy gifted in the field of biopsychology and formerly worked in the Higuchi Pharmacology Laboratory 7 – the place where Mikoto gave her DNA.

The First Production Plan
Using the Bank Cards she acquired with Ruiko, Mikoto buys new clothes as a disguise, and successfully infiltrates the Higuchi Pharmacology Laboratory 7. Using her electric abilities she hacks her way through the facility's security system, disabling the cameras and alarms, she later uses it to discover a hidden room within the facility where the local area network is not connected, though electrical power is still being sent to it.

Here, Mikoto discovers cultivation tanks large enough for an average person to fit in. Getting more suspicious of this, Mikoto uses a computer in the facility and discovers much to horror that there was a plan in mass producing clones of the Railgun. Mikoto keeps on reading the report on the plan, on how she was tricked to hand over her DNA, on how the clones were produced and how knowledge and information would be inputted into their brain using the Testament machine, supervised by Shinobu. Reading further, Mikoto comes across a report on how the Tree Diagram calculated that it was impossible to produce a level 5 clone of Mikoto, as such the plan was stopped and data of it was to be destroyed. Much to Mikoto’s relief, the plan was scrapped before the mass production of plans could take place. She leaves the facility with a smile on her face, though unbeknownst to her a someone that looks like her, erases the data about the clones in the computer that Mikoto was using earlier.

The next day Mikoto is highly elated after last night's ordeal, which surprises Kuroko. They later talk about the rumor of Mikoto's clones, to which Kuroko says that it would be incredibly convenient for her to have a clone to get her out of sticky situations. Kuroko asks Mikoto what she would do if a clone were to appear before her, to which she replies that she would feel sick and would want her to disappear from her sight, words that would haunt Mikoto later on.

August 15
Mikoto spends the day with children as Kuroko is busy with Judgment, and later acquires a Gekota badge from gachapon machine (after many tries), though is unable to use it herself due to her shame of her liking kid stuff. Earlier that day, Mikoto meets a young boy with a really weak electric powers, and is asked if they could talk like a radio if he becomes stronger; Mikoto states that is impossible for them to communicate through electricity, though they could detect each other if there were no interferences, and notes that they could make a brain network if they had the same brainwave pattern like the Level Upper.

Misaka 9982
After escorting the children, Mikoto detects a power eerily similar to hers and rushes to find its source. She discovers the source a person who is similar to her, where Mikoto then demands to know who she is. The girl answers with a meow similar to a cat, much to Mikoto's confusion. The person point to a black cat stuck on a tree, and manipulates Mikoto into helping her by making her feel guilty for the cat's fate if it falls. Using a human ladder (with Mikoto under), the cat is saved after it falls by the person using her skirt, much to Mikoto's embarrassment as the person looks exactly like her.

However, Mikoto gets frustrated and scares the cat away. Here, she confirms to the person that she is a clone of hers, and demands answer from her, though each time she asks a question, Mikoto is denied of answers. Angered because of her unwillingness to divulge information, Mikoto tries to use force on her, though she stops and leaves the clone, saying that she'll just grab the clones' creators instead to tell her. After leaving, Mikoto suddenly realizes the prospect of there being more than one clone, and goes back to her. In a series of bizarre of occurrences, both Mikoto and the clone is given free treats by an ice-cream merchant, and later Mikoto is forced to treat her clone to a snack.

Nightfall arrives with Mikoto still unable to gain any answers. The clone states that she will be leaving for the 'experiment' and that Mikoto is free to follow her if she wants, though she says that Mikoto will not find her creators there. Mikoto minds starts to diverge and realizes that she can check how the Gekota badge would look on her thanks to the clone and puts the badge on her to get an idea; however the clone asumes this to be a gift and states that Mikoto's preferences are childish yet the clone accepts the first gift Mikoto has ever given her and recognize this as something valuable. The clone says farewell to Mikoto, leaving her in a state of disbelief and frustration on what has occurred between them, and deep down Mikoto has this feeling as if they were really sisters.

Still wanting answers, Mikoto acquires the assistance of Kazari in figuring out what experiment her clone is in, meanwhile the clone picks up a suspicious case from a locker and meets up in an alleyway with Academy City's strongest esper – Accelerator. The clone calls herself 9982 and states that the experiment will now begin.

Misaka 9982 vs. Accelerator
The experiment begins, with Misaka 9982 battling Accelerator. Predictably, nothing Misaka 9982 throws can touch him, with the bullets the clone shoots from her rifle being reflected towards her, and injuring her. She runs at the sight of her own blood, with Accelerator merely taunting her helplessness. They arrive at a rocky clearing, with Accelerator catching up to her. He uses his powers on her, which propels the rocks and dust to hit her.

Severely injured by Accelerator's attacks, Misaka 9982 deduces that there is some barrier surrounding Accelerator, and since he is walking Misaka 9982 states that maybe the feet is unaffected by his powers. Stating this, she reveals to Accelerator that she has lured him in her trap, a land mine, which Accelerator steps on, causing a large explosion.

Meanwhile, Mikoto has finally discovered the experiment the clones were involved in, and is unable to grasp the situation. She soon notices the coordinates of the 9982nd experiment, and opts to get there. When she arrived, she finds no one is there, except for a lone pair of broken goggles. Suddenly, Mikoto hears a terrifying explosion and decides to find its source.

Back with the clone, Accelerator comes out of the smoke unharmed. He is impressed by the clones ingenuity, though notes the flaw on her deduction of his powers. Accelerator then grabs her left leg and rips it from her body. Though in tremendous pain, Misaka 9982 attacks Accelerator, however the attack is reflected back towards her. With all that is happening, the badge that Mikoto gave her fell from her uniform and unto the ground. Misaka 9982 tries to crawl her way to the badge, with blood seeping from her wound. Accelerator tries to talk with her but he gets no answer; seeing her struggle, Accelerator decides to end the experiment.

Mikoto finally arrives at the experiment location, however, she is too late, as Misaka 9982 reaches for the gift Mikoto gave her, Accelerator crushes her body with a train, ending the experiment.

Misaka Mikoto vs. Accelerator
Enraged by what Accelerator has done, Mikoto charges towards him. She extracts the ferrous sand from the ground using her magnetic abilities, and creates a whirlwind with it, and flies it towards him. However, she is shocked to find that he is unharmed by her attacks. Accelerator is impressed by her power and states the weakness of her attack. Mikoto suddenly notices the leg that Accelerator ripped off of Misaka 9982, and fills with wrath. She uses her powers to unhinged the metal rails from the train tracks, and attacks Accelerator with it. Though surprised by her power, Accelerator simply stands as his power redirects the metal rails back to Mikoto, to which she is forced to dodge them.

Mikoto is utterly dumbfounded on how he is unaffected by her powers, and notes that other than Touma, there is only one other person who can possibly do such a feat. Meanwhile, Accelerator finally notices that Mikoto is not a clone; wanting to speed up the program he states that he should kill her. Mikoto however, pulls out a coin preparing to fire her Railgun, and demands to know why he is participating in the experiment where clones are killed. He answers by saying that merely being Level 5 is not enough, and as such he simply wants absolute power, a title that is beyond any human can ever dare to challenge. Angered by his response, Mikoto fires her Railgun towards him, which he predictably redirects, though missing Mikoto and hitting a few metal beams behind her.

Accelerator laughs at Mikoto's signature move, and states that it is his turn. However, other Mikoto clones come by and convince Accelerator to not harm Mikoto, as it would create discrepancies. He leaves but not before introducing himself to a shaken Mikoto. She later collapses into her knees, asking the clones that are present why they are participating in an experiment that gets them killed, to which the clones reply that they are simply artificial being created for the experiment, simple lab animals to a now broken Mikoto.

August 16 to 19
Mikoto does not return to the Tokiwadai Dormitory after the events with Accelerator and the clones, and stays up all night outside, dispirited. She meets Shinobu again, where she deduces that Mikoto has finally discovered the experiments. Here, Mikoto asks, why people are willingly killing people for their experiment, to which Shinobu states that to the researchers, the clones are simply lab animals that are required to be sacrificed for a greater use. Shinobu then says to Mikoto that she used to think that way, until she realized that the clones were more than that. Shinobu asks what Mikoto thinks of them to which she replies that she does not think of them as humans, but she cannot overlook the people who use her DNA for experiment. Mikoto leaves stating that this is her problem, but not before Shinobu tells her that Mikoto is being dishonest to herself and warns her that there are more than 20 facilities involved in the experiment.

Terrorist attacks on research facilities
Using her hacking abilities, she uses cyberterrorism to destroy several facilities involved with the experiment. However, Mikoto is forced to personally raid the facilities herself after the researchers cut-off her means of attack.

When Mikoto later returns to the dormitory, she hides the documents regarding the experiment in her stuffed bear, Kirugumar (きるぐまー). She runs into Kuroko who is aware that Mikoto is in some kind of trouble, though, Kuroko knows that Mikoto don't want to rely on her.

List of known facilities taken down by Mikoto
Facilities taken down by Mikoto during the course of her attacks from August 16 to 19, before the trap set up by Keitz Nokleben, the security supervisor of the Level 6 Shift.
 * Shinaame University DNA Map Analysis Laboratory
 * Geomagnetic Anomaly Research Laboratory
 * Foreign Medicine Resarch Center
 * Biomedical Genetic Research Facility
 * Movement and Cognitive Research Institute
 * Ryuden Sports Human Engineering Development Center
 * Duchenne Dystrophy Research Center
 * Mizuho Organization Pathology Analysis Laboratory
 * Kanasaki University Muscular Dystrophy Research Institution

Response to the terrorist attacks
The security supervisor over the experiments successfully deduced that Mikoto could be behind the attacks on the research facilities, although unsure of it, he did surmised that the attacker is a proficient Electromaster. Because of this, he hires team ITEM from the dark side of Academy City, to protect another research facility long enough so they can move important data and equipment, to other branch facilities, which was planned by the security supervisor to discourage the attacker and to cut losses while still maintaining the experiment. Moreover, due to the secrecy of their actions, the attacked facilities merely declare bankruptcy.

Predicting Mikoto's next target, Frenda of ITEM is sent as first line of defense by Mugino Shizuri – the leader, while Kinuhata Saiai is ordered to investigate a potential inside job that might occur in another part of the facility, as Shizuri assumed that Mikoto's attacks were merely a distraction.

Misaka Mikoto vs. Frenda
Mikoto goes to the facility, S-Processor Pathology Analysis Research Laboratory, and faces-off against Frenda while being in a complete disadvantage against her, due to her being stressed because of recent events and having little rest, and the fact that Frenda has set-up various traps all around the facility Mikoto is attacking. After exchanging attacks with Mikoto and allowing her to chase her, Frenda later lures Mikoto in an enclosed space, though at first Frenda is at a disadvantage due to Mikoto's sheer power as a level 5, she is later able to stand on somewhat equal footing, after blinds Mikoto using a flash-bang. She uses the opportunity to attack Mikoto with missiles, however, Mikoto was able to dodge them due to her sensing her environment using electromagnetism, and corners Frenda.

However, Frenda bluffs her way into a close-combat with Mikoto, after throwing an explosive bottle of chemicals, and then using the steam control in the room to enhance the effect of a highly volatile chemical floating in the air. Frenda overwhelms Mikoto in combat, however she slips up and allowed Mikoto to strangle her from behind, forcing Frenda to throw with enough force to dislodge the spark emitters that she keeps in her skirt to activate the explosive tape that she covered in the entire facility. Coincidentally, one of the emitters lands on the tape causing the tape to explode, however, because of this Mikoto figured out Frenda's bluff and has cornered her.

Misaka Mikoto vs. Mugino Shizuri, Frenda and Takitsubo Rikou
Now with Frenda beaten, Mikoto intimidates her to answer her questions, displaying her tremendous power to scare her. However, before Frenda is able to speak, a beam of energy emerges between Mikoto and Frenda from the seal that she used to trap Mikoto in the room, melting it and forcing Mikoto to dodge. Mugino Shizuri and Takitsubo Rikou have arrived as back-up. Mikoto tries to attack using a large piece of equipment, but is completely obliterated by Shizuri's abilities. Shizuri retaliates with another energy beam attack, to which Mikoto dodges by magnetically clinging to the walls of the facility. Mikoto attacks using smaller pieces of equipment, though they are destroyed by the shield Shizuri generates using her powers. Seeing the battle going nowhere with Mikoto being able to move around, Shizuri commands Rikou to use Body Crystal a drug that allows her to use her ability – AIM Stalker.

Due to this, Mikoto's movements are tracked by Rikou completely, allowing for either Shizuri or Frenda to attack depending on the location Rikou designates where Mikoto is. Shizuri notes Mikoto going into the defensive, trying to buy some time and with her movements dulled due to the battle, she needs only to stall long enough for Mikoto to tire her self-enough for her to slip-up, though she also takes Rikou's condition into account, who is also at her limits due to the drug. However, one attack by Shizuri forced Mikoto to use her powers on the beam of energy, both of which realizing that their powers are similar on a basic level.

After confirming the attacker's identity, Shizuri orders Frenda and Rikou to pull back and meet-up with Saiai, as they have both reached their limits. Also, Shizuri does not want anyone to win her victory in numbers against, the 3rd level 5 – Tokiwadai's Railgun.

Misaka Mikoto vs. Mugino Shizuri
Shizuri confronts Mikoto in their battle as fellow level 5s of Academy. Though Mikoto comes prepared, utilizing Frenda's bombs – which are inside dolls – as an advantage, and controlling them magnetically through their metallic parts. At first, Mikoto nearly overwhelms Shizuri due to the large amount of bombs, and due to Shizuri being only capable of producing four energy beams simultaneously. However, Shizuri covers this weakness by using silicon cards to disperse her beams. This leveled the playing field somewhat, with Shizuri destroying Mikoto's remaining bombs; however, this was a deception set-up by Mikoto. She uses the remaining bomb which Mikoto hid behind her back to attack Shizuri; seeing this Shizuri her powers to affect Mikoto's control over the bomb, however, Mikoto simply used the metal inside the doll to knock Shizuri out.

After Shizuri's defeat, Mikoto destroys the remaining equipment in the facility. However, Shizuri returns and attacks Mikoto, enraged and wanting revenge. Now with her goal completed and her body worn-out, Mikoto retreats from the facility, choosing a catwalk out of two other escape routes. Shizuri continues her pursuit until Mikoto stops running, however, it was a trap by Mikoto; by using the tapes that Frenda covered on the catwalk, Mikoto destroys the catwalk by using her electric powers. Both Mikoto and Shizuri fall shortly afterwards, though Mikoto used her magnetic abilities to hold on to the metal rails and tries to save Shizuri from falling with a cable, to which she promptly denies her gesture by destroying it and rather fall, though she survives by using her powers to break her fall. Mikoto later escapes the facility.

Shizuri later stops her pursuit on Mikoto, after extorting information from one of the researchers and discovering the experiment that Mikoto wants to stop, realizing that she'd rather have Mikoto struggle in her attempts to stop the experiment.

Downfall of Nunotaba Shinobu
Meanwhile, Shinobu infiltrates the S-Processor Pathology Analysis Research Laboratory, using her prestige as a former member of the Sisters project to gain the trust of the researchers. She later tries to install emotions into the clones, believing that the clones would be able to fear the despair of dying and allowing the researchers to realize that they are not merely lab rats, or at the very least move a certain someone’s (Accelerator) heart. During installation of her program, she receives an error regarding the program not connecting to the Misaka Network, due to unit 20001's interference.

Suddenly, Saiai apprehends Shinobu, confirming Shizuri's suspicions. Despite this, Shinobu tries to fight back, stealing a gun from one of Saiai's lackeys and shoots Saiai – despite Shinobu's warnings. Though, she is unharmed by the bullet due to her ability. Shinobu is captured shortly afterwards.

August 20
Under the assumption that the facility that she attacked yesterday, bankrupt the project and terminating it, she starts getting back to her normal life. She meets with Kamijou Touma near a certain vending machine that just ate his money, and attacks him after he does not recognize who she is. She offers to give him drinks from the machine by using her powers on it as he has already paid for them, however, this causes the machine to short circuit, spilling out various drinks and alarming Kuroko (who is with Kazari and Ruiko asking for advice regarding Mikoto's recent behavior) and the Security bots.

Later, after Mikoto gives Touma the drinks he earned, they meet Kuroko who teases Mikoto regarding meeting-up with Touma, and is glad that Mikoto has returned her normal behavior. She later leaves just before the arrival of another clone, which surprises Touma as they look similar (thinking that she is Mikoto's sister) and that she refers to herself as Misaka. Seeing her arrival, Mikoto forces Misaka 10031 to come with her, and ask regarding the experiment's fate.

Much to Mikoto's horror, the experiment is still on-going, and becomes sick and disturbed. Misaka 10031 tries to cheer her up by using a cat nearby, however, she lashes out at her, demanding the clone to not come before her with that form (after remembering Misaka 9982). Though shocked, Misaka 10031 obliges and leaves, which however, makes Mikoto guilty.

Kamijou Touma meets Misaka 10032
While carrying the drinks from the vending machine, Touma loses his balance and falls to the ground, scattering the beverages to the ground. Here, Touma meets Misaka 10032, who offers him help to carry the juices, though Touma protested at first, though he eventually relents and allows Misaka 10032 to help her carry the beverages back to Touma's dormitory.

They later meet up with Tsuchimikado Maika, and later, as well as Index and Himegami Aisa (much to their surprise as Touma has somehow acquired another female), who are trying to remove the fleas that has apparently infested Sphynx. After a momentary argument dealing with the ethical issues regarding the method both Index and Aisa would try to get rid of the fleas, Misaka 10032 assists them by using her powers to kill the fleas off Sphynx, and leave him relatively unharmed before leaving, much to their amazement.

The eve before the 21st of August
Mikoto discovers that the experiment is still on-going as the project has been distributed to at least 183 research facilities. Mikoto realizes that Academy City's Board of Directors must have consented with the experiments; she also realizes that since there are no reports on her attacks, Academy City is obviously keeping it a secret. Mikoto opts to destroy the Tree Diagram as a way to make the city acknowledge experiments' existence, regardless of the cost, and asks Kuroko what she would do if she were to cause harm on the city, to which Kuroko states that she will do her job even if it was Mikoto who she was against. Mikoto accepts this, thinking it would not be such a bad end to be apprehended by Kuroko and goes to sleep, dreaming on how her mother would fix her problems after she'd wake up.

August 21
Touma meets Mikoto one last time in the afternoon, where she talks about how she hates people following the orders of machines—Tree Diagram —before leaving for the 23rd School District. Touma later meets with Misaka 10032 again, and is guilted by her into carrying a stray black cat, as her electromagnetic field is affecting it. They later visit a used bookstore where Touma, in order to buy a book for Index regarding the care of cats. Here, he later throws the cat to Misaka 10032, encouraging her to be friends with the regardless of the barrier of her powers. However, she notices Accelerator and leaves for another experiment is to take place.

Misaka 10031 on schedule and proceeds with the experiment with Accelerator, who obviously and utterly dominates her and mocks her weakness for it. In the end, Accelerator utilizes a painful death on Misaka 10031, by reversing her blood flow.

Destruction of Tree Diagram

 * Main article: Destruction of Tree Diagram

Planning to hack the Tree Diagram to change the outcome of the experiments, and eventually bankrupt the project, Mikoto infiltrates the Tree Diagram Information Receival Center and notes the apparent lack of personnel. Here, she discovers that the Tree Diagram has been destroyed by an unknown energy source from earth's surface on the 28th of July. Seeing that her final chance in stopping the experiment has been destroyed, and seeing that the experiments go on even without the Tree Diagram, Mikoto falls into despair.

She later destroys another facility involved in the experiment nearby, and discovers a live experiment taking place in the alleyways, being monitored. Here she sees the brutal death of Misaka 10031 at the hands of Accelerator.

Kamijou Touma and the Sister Clones
After leaving the bookstore, Touma finds the clone missing and the cat he gave her has been left behind on the pavement. He goes into a nearby alleyway where he discovers her disfigured corpse. He contacts Anti-Skill to investigate the case, however, they discover that the corpse has gone missing. Confused at this, Touma runs deeper still in the alleyways, where to his relief he discovers the sister alive and well.

However, she soon reveals that she truly did die and that she is a clone of Misaka Mikoto. The clone calls herself Misaka 10032, and says that she was the one interacting with him all this time, and apologizes for worrying him; suddenly, several more clones appear to explain their situation. Touma demands to know what they are involved in, though, they do not divulge the information he is seeking as Touma does not have the access code when asked for one to prove his involvement in the experiments and leaves. Worried about Mikoto's involvement, Touma travels towards the Tokiwadai Dormitory, hoping to get some answers from her, although, there is a sense of dread feeling within Touma, as he presumed the worst of Mikoto's involvement.

Kamijou Touma discovers the Level 6 Shift
Meanwhile, back in the Tokiwadai Dormitory, Kuroko mopes around worrying about Mikoto's behavior. Here, she wishes that "Mr. That Idiot" (Mikoto's nickname for Touma) would come to her aid, as he was the one who brought Mikoto's usual behavior back. Coincidentally, Touma visits the dorm and asks for Mikoto, Kuroko remembering his voice let's Touma into the room.

Here, they talk about Mikoto's reputation on how she gets enemies because she has power, and on how Kuroko managed to get rid of Mikoto's previous roommate due to that reason. Furthermore, Kuroko explains that since Mikoto stands in the center, she cannot intermingle with anyone, and in turn, since she is at the top, she can defeat her enemies, yet at the same time cannot help make more. Here, Touma discovers a part of Mikoto's nature, and begins to doubt her. Their conversation ends with the arrival of the Tokiwadai Dorm Supervisor, forcing Kuroko to hide Touma under the bed since her teleportation powers won't work on him. Kuroko talks with the Dorm Supervisor and later leaves with her.

Under the bed, Touma discovers the documents inside the Kirugumar stuffed bear Mikoto had under her bed. Touma is horrified and angered at the use of the clones for experiments to ascend Accelerator to level 6. Worried about Mikoto, he tries to search for her on windless night. Here, he notices that the wind turbine's rotors are moving on their own without the wind. Touma deduces that since the wind turbines use wind to generate electricity, inversely if electricity is flowed into the turbine the rotors will move, since Mikoto generates electricity every second, he opts to follow them, hoping to find Mikoto.

Kamijou Touma and Misaka Mikoto
Mikoto is on a familiar steel bridge, alone in a despondent state until she discovers the arrival of Touma. Here, he confronts Mikoto on the Level 6 Shift and confirms to him that her DNA was used as a means for researchers to clone her, and allow Accelerator to achieve Level 6. Mikoto puts up a facade of arrogance towards Touma, wanting him to condemn her as so she can finally sacrifice herself as a way to stop the experiment, and save the remaining sisters.

However, Touma does not condemn her and is genuinely worried about her. Regardless of this, Mikoto says she will go fight Accelerator, but is told by Touma that she is no match for him. Mikoto is aware of this and states that she will allow Accelerator kill her on the first move, as the Tree Diagram has calculated that she will be killed on the 128th move of their battle; as such, her dying on the first move will disprove Tree Diagram's calculations and hopefully ending the experiment, as she has no more ideas on how to stop the Experiment.

Touma however is against this and stops her from her suicide mission, and is asked by Mikoto if he is willing for the sisters to be killed. Touma responds that he does not want the sisters to die, however, he does not want Mikoto to be killed either, and is aware that he has no idea how to to do so. Angered by this Mikoto attacks Touma, although it was only for show, though he does not fight back, block or dodge her attacks. She demands Touma to fight or else he would die due to her attacks. Touma responds that he will not fight her. Mikoto unleashes a powerful adn true attack on a defenseless Touma, making him lose consciousness.

End of the Level 6 Shift
Touma wakes up on a weeping Mikoto's lap, worrying about him. Here, Touma states that he has found a way to stop the experiment. Touma states that the experiment was designed with the assumption that Accelerator is the strongest esper in Academy City, naturally, the experiment will be stopped as the assumption of Accelerator being the strongest is false. Touma goes on to say that he will be the one to defeat Accelerator, as the conditions are perfect for him, as he is a level 0 and he has the power to stop any supernatural occurrences—Imagine Breaker. Mikoto protests to his decision, and says a battle with Accelerator would be a slaughter instead, and that Touma's body is still hurt from Mikoto's attacks. Touma however, does not listen and asks Mikoto to stay behind as her presence as a Level 5 esper in the battle might be taken into account by the researchers, and destroying Touma's plan.

After leaving Mikoto behind with the cat, however, Mikoto decides to follow as she cannot stand idly by doing nothing.

Misaka 10032 vs. Accelerator
Misaka 10032 arrives at the Switchyard of School District 17, wary of Touma's concerns for her despite her rationale that she is but a mere guinea pig in a test subject. Accelerator later arrives and swaggers her, and later starts a small conversation regarding his goals to her. Here, Accelerator states that even though he is at the top of Academy City, he is still considered in a level where he can be fought for the sake of being fought, however, his goal is to become so powerful that fighting him is considered a sin.

At exactly 8:30 PM Japanese Standard Time, experiment 10032 of the Level 6 Shift begins in the Switchyard of the 17th School District. Misaka 10032 battles Accelerator as part of the experiment, the latter obviously playing around with her even though he could've ended the fight already. Here, she plans on defeating Accelerator by discharging electricty to create enough ozone to suffocate him, and with a windless night, the conditions are perfect. However, Accelerator soon discovers Misaka 10032's plan, and states that her plan would fail if he catches up to her.

Accelerator catches up to her by manipulating the vectors beneath his feet, and begins beating on her. However, Touma soon arrives; shocked on his arrival, Misaka 10032 asks her why she is trying to save her, a clone who can be made with a push of a button. Touma says that he is here to save her, and that she is the only one of herself in the world. Accelerator is impressed by Touma's heroic speech; Touma attacks him but is blown away by Accelerator's power.

Kamijou Touma vs. Accelerator
Touma and Accelerator's battle continue, with Touma totally overwhelmed and severely injured by Accelerator's attacks and is barely able to dodge them. Although, Touma confirms that his powers actually work on Accelerator, after slapping his hand away, much to Accelerator's rage and attacks Touma again. Their battle moves near shipping containers, where Accelerator's attacks spill their contents, which were wheat flour while attacking Touma. After Touma successfully escapes the falling containers, Accelerator begins to taunts Touma about the dust that had covered the battlefield, and quizzes him about dust explosions, which forces Touma to runaway as Accelerator ignites a dust explosion.

Touma however, survives the dust explosion and the Accelerator mockingly acknowledges Touma for surviving this long. However, Accelerator decides that he wants to end their battle and charges towards him. Cornered and with nothing left to do, Touma punches Accelerator in the face and realizes that Accelerator is physically weak. Touma hurls several more punches into Accelerator's face before the esper, careful not to linger around him as so his range, and later forces Accelerator to retreat.

Accelerator is surprised and shaken by the fact that he is hurt, however, Touma comes by and says that since Accelerator always ends his opponents in one attack and always deflects attacks just by standing there, it's natural that he'll never know how to brawl. Touma punches Accelerator again despite Accelerator using his powers. Enraged at what is happening, Accelerator controls the air into one point, using the windless night as advantage, and attacks Touma with a powerful gust of pressurized wind, severely injuring him and knocking him down to unconsciousness. Seeing that he can control the winds of Academy City, Accelerator becomes intrigue by his discovery and begins controlling the winds into a single spot above his head, creating it in an effort to utterly obliterate Touma.

Kamijou Touma and the Sister clones vs. Accelerator
Mikoto arrives after seeing enough of the brutal fight between Touma and Accelerator. Here, she intends to finally end the experiment by killing herself in a single move. And although she discovers that Touma is still alive and provided remonstrations against her plans, she insist to end it as she wants Touma to live. Her bluff comes to none however as she behelds the awesome power of Accelerator, through his plasma, uncaring of her existence and focused on annihilating Touma. Seeing that her powers are utterly mnuscule and useless against it, Mikoto goes to the unconscious Misaka 10032 to help her protect Touma's dream, as they (Sister clones) alone can (referring to the fact that she cannot, in any way, interfere with Touma's plan as she may affect the researchers conclusion). Misaka 10032 awakens from her slumber, and hears her words, she acquiesced to Mikoto's request, and although she does not understand Mikoto's words, Misaka 10032 feels that her words resonate strongly within her.

With the use of the Misaka Network, the Sister clones use their powers on the wind turbines in Academy City. Accelerator notices that the wind has changed, stopping his creation of plasma, he notices that it was Mikoto and Misaka 10032's doing, and threatens to attack them. However, Touma regains consciousness and enrages Accelerator and triest to charge towards him. He attacks Touma one final time, however, this in vain as Touma dodges his attacks. With Accelerator leaving an opening, Touma attacks Accelerator with a punch and defeating him.

Picking up the pieces
The next day Misaka 10032 visits Touma in the hospital, where she reports that the experiment has been suspended, and tells Touma that she cannot return into the world yet because her body needs readjustment as the body clones were given hormones and drugs to accelerate growth, though she also says that they will meet again. Mikoto later visits Touma in the hospital as well, bringing cookies with her as a gift for Touma, though he dismisses it as he sees homemade cookies baked by someone incompetent to be better, which leads to an argument. Before leaving, Touma reports to her that the sisters are going to have their bodies readjusted, and also says that the sisters are grateful for Mikoto for giving them life to assure Mikoto the sisters don't hate her for giving up her DNA, leading to their creation and eventual deaths. Touma is later visited by an angry Index, who promptly bites him. Index later asks Touma what he was fighting for this time, as per his usual behavior, and later he states that he has fought for himself.

Mikoto meets up with Misaka 10032, who isn't as severely injured, and later goes into a playground, and after some much needed bonding time with a couple of children, Misaka 10032 and Misaka Mikoto starts talking. Hither, Misaka 10032 speaks of the strange feeling of being alive, even though she was supposed to have been killed last night, even though that was the reason for her existence—to be killed. However, because of Mikoto and Touma, she no longer has any reason to exist, Misaka 10032 then asks Mikoto to help her find the meaning of living, to which Mikoto agrees. Mikoto arrives at Tokiwadai Dormitory later in the evening of August 22, into the arms of a worried Kuroko.

Later, Saten Ruiko aids Mikoto in baking homemade cookies—after Touma stated his preference the other day. Much to her embarassement, Ruiko keeps on teasing her about it, though, she states that she as well as Kazari and Kuroko, are relieved that she has returned to her normal state. Mikoto later tries to deliver the cookies to Touma, but is unable to since she discovers that he has already left the hospital on account of bills and Index. Here, she is unable to give him the cookies she made as she was too embarassed to tell him, as well as Touma mistaking her intentions. Before he leaves, Mikoto asks Touma to remember her name as "Misaka Mikoto" and stop calling her Biribiri, to which he acquiesced. Kuroko later comes by after Touma has already left and discovers that Mikoto is showing a strange expression upon her face.

Effects and future implications
Meanwhile, Anti-Skill and Judgment (which included Kuroko), is later tasked to clean up the recent explosion in the carriage park where Touma and Accelerator fought. Under the orders of Aleister Crowley – General Superintendent of Academy City – the information regarding the inicident has been controlled, as such Kuroko was unable to know who defeated Accelerator. Here, she sees the coin which Mikoto uses for her Railgun, and with the events that included with Touma visiting the dormitory and Mikoto's strange behavior, made Kuroko suspicious of Mikoto's involvement, which does not become apparent until during the Tree Diagram Remnant Arc.

Although later Touma is sent outside of Academy City for the authorities to clean up and to stop the information leaks to delinquents coming after Touma for the title of "Academy City's Strongest", the "Dark Side" of Academy City as a whole knows about Touma's involvement in Accelerator's defeat. However, none took action as Aleister have given information out that Kamijou Touma is involved in his plans and Touma has the General Superintendent's protection.

Later, Mikoto says to Touma during their fake date on August 31 the Sister clones have been distributed all around the world to undergo treatment, and with 10 clones remaining in the city. It later becomes apparent that Aleister Crowley planned the end of the Level 6 Shift in the first place, as an excuse to distribute the Sisters clones all around the world as part of his plan to set up Artificial Heaven, though he did not plan for Touma to be the one ending this experiment. Meanwhile, Accelerator is severely shaken after his defeat and is unable to grasp the understanding that he has apparently changed on that day he was defeated, this would later translate as Accelerator's utter admiration for Touma, his ideal hero.

It is later revealed that Aleister Crowley intended for the clones to be spread out across the world, probably coming out with a plan that would make the Level 6 Shift fail without the need for Touma or Mikoto's interference, in order for the Imaginary Number District to cover the entire globe, which, if brought forth into their world, would cause magicians to self-destruct.

Concurrent scenes
During the night of August 21st, seeing as Touma is once again nowhere in sight, Index decides to go to Komoe's house for food. Here, alongside Komoe and Aisa, Komoe lectures them regarding the nature of Esper powers, to which she states that the ultimate goal of Academy City is to reach SYSTEM—those who are not gods who reach the will of the heavens. Her lecture is used as background information for Accelerator's goals. This scene is used in the anime, although, the later parts regarding SYSTEM is shown in the recurring bathhouse. The entire scene is redacted from the manga adaptation of Toaru Majutsu no Index, and is non-existent in the Toaru Kagaku no Railgun manga.

Trivia

 * With 21 chapters published, this arc is currently the longest one in the Toaru Kagaku no Railgun manga. Moreover, with 16 episodes in the Toaru Kagaku no Railgun S anime adaptation, it is the longest story arc in the animated series.
 * This is the first arc in the Toaru Kagaku no Railgun sidestory to intersect with the main story of Toaru Majutsu no Index.