Touma reunites with Misaka Mikoto for the first time after losing his memories, and ends up getting involved in her dark secret where unbeknownst to her, sister clones were created from Mikoto's DNA through the Radio Noise Projectnote .However, the clones ended up being considered too weak in comparison to the original, and were instead established for use in the Level 6 Shift Project to be continuously killed off by the #1 Level 5 esper of Academy City, Accelerator, in the hopes that he will achieve the next stage.Realizing Mikoto's struggle, Touma sets out to put an end to the project by fighting Accelerator himself.
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 her 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.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.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; and she once even mentioned this to Kamijou Touma.
The Level 6 Shift Project
Mikoto 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.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.
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.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.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 lets 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.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.
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 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.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.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.
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.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.
- A Day in the Limelight: For Mikoto and the Misaka Sisters
- Arc Villain: Accelerator
- Cloning Blues/Clones Are People Too: Starts off as the first one, with the Sisters placing zero weight on individual lives. But by the end, Touma convinces them that they're still each unique, and they start treating themselves as people more.
- Hive Mind: This is the arc where we meet the Sisters Network, a network of 9,969 (remaining) clones of Mikoto Misaka, using their level 2 Electromaster powers to remain in constant contact with each other.
- Not So Different: The conclusion Index and Himegami reach about the Science and Magic Sides.
- Power Levels: Accelerator is a level 5, like Mikoto, but he is far more powerful than her, and is easily the most powerful esper in Academy City. The clones, on the other hand, each have 1/20,000th of Mikoto's power, and are ranked at level 2. Despite Touma's ability, he is ranked a level 0.
- Reality Warper: This is the arc where Komoe explains more of how esper powers work. Specifically, they each have a "Personal Reality" they impress on the world, which allows them to make minor alterations. More powerful espers are ones with a stronger belief in their Personal Reality, and thus have a larger effect on the world.