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 Radio Noise sisters that are being used in the Level 6 Shift, an experiment where they are killed as so Accelerator can 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 as to herself conscious. 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.

Project Radio Noise

 * Main article: Radio Noise

Mikoto willingly gave her DNA to the researchers at the 7th Medical Institute Research Center, after being convinced by them that using her DNA to help children who were unable to control their muscles. 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 Radio Noise project is later reused by the Level 6 Shift experiment – an experiment to make Accelerator reach level 6. 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, where they 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 blindspots 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 7th Medical Research Center – 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 7th Medical Research Center. 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, to which surprise 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 Mikot 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 embarassment 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 gives the Gekota badge she acquired earlier to the clone as a gift, though the clone states that Mikoto's preferences are childish, the clone accepts the first gift Mikoto has ever given her. The clone says farewell to Mikoto, leaving her in a state of disbelief and frustration on what has occurred between them, 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. Predictbly, 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 from his body. Though in tremendous pain, Misaka 9982 attacks Accelerator though it 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 rerturns to the dormitory, she hides the documents regarding the experiment in her stuffed bear, Kirugumar. 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.

Response to the terrorist attacks
The 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 supervisor to discourage the attacker and to cut losses while still maintaining the experiment.

Predicting Mikoto's next target, Frendaof 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 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 exchaning 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 flashbang. 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 Clear 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 tier 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 another building of the same research facility Mikoto is attacking, using her prestige as a former member of the Radio Noise 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 2001'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.