Misaka Mikoto/Chronology (Shinyaku Toaru Majutsu no Index)

As an extension to her role from Toaru Majusu no Index, Misaka Mikoto continues her similarly in Shinyaku Toaru Majutsu no Index, with her constantly trying to aid Touma and the battles that he is in, making her an important supporting character. Touma eventually relents to her, and brings her along for the invasion of Hawaii. She proves her mettle, and Touma comes to trust her during battle. Much later Touma would allow her to join him if she chooses to, though doesn’t actively seek out for help. It is not until the GREMLIN invasion of Tokyo, that she and even Index finally achieve getting Touma to believe in them, with him asking them to help her save Freyja. Much later, similarly to the Will of the Whole Misaka Network, she becomes instrumental in helping Touma get rid of the emotional baggage he had felt towards the Perfect World, forcing him to look at the value of the world that they live in, the world he left behind another world for, and finally achieving bittersweet victory over him. Since most of her focus is on Touma, Mikoto doesn’t actively seek out information or knowledge regarding the magic side, simply taking Touma or the other’s word for the importance of the situation that they are in.

Freshmen Arc
It is hinted that Hamazura Shiage bumped into her in the School District 7, but was ignored, showing that she was still depressed and worried about Touma.

Homecoming Arc
Sometime later, she decides to hack into Academy City's database to find out more about Touma. However, she is surprised by a heavily intoxicated Touma who gives her a box of sushi. Touma then begins to leave, along with the many other girls that appeared with him, and she ends up following him to his dorm. Mikoto and the other girls are persuaded to leave but not before Mikoto forcefully obtains a promise to explain everything.

She later catches up with him on a bridge after the excitement dies down and returns his phone strap, telling him not to lose it since their match. He states that the reason he can't stand still is due to the impending chaos that is about to befall Academy City. She then tells him that she will not stop him because she knows he won't listen to her anyway, but just as he is about to leave, she grabs his hand and states that this time he is not alone.

Hawaii Invasion Arc
Mikoto subsequently travels with Touma to Hawaii, where they encounter a GREMLIN agent, Cendrillon, at the airport and launch an attack her. She and Touma later get separated and she ends up with Misaka Worst where they have a chat and she gets severely teased. Eventually, she and Touma encounter Roberto Katze, who offers his help. So, to stop the Trigger they head to Pearl Harbor. Eventually, it results with her and Accelerator fighting off Trident forces that try to invade.

Eve of the Festival
Thor impersonates Mikoto as a means to get close to Kamijou Touma. By utilizing the information gained from the security cameras during the Hawaii Invasion Arc, Thor successfully adopts her character and personality and uses it to trick Touma.

Apparently not busy herself, Mikoto's first actual appearance in the arc is as an unofficial visitor of Touma's school, looking for him there. She is nervous because she stands out too much. Her actions, however, are noticed by Tsukuyomi Komoe, and they meet for the first time. Here, despite knowing that Mikoto is a Level 5, Komoe doesn't know what she looks like. Komoe tells her that unofficial visitors to the school are not allowed by Anti-Skill. However, Mikoto completely ignores her, and assumes that, since she looks like a child, that she too is a visitor like herself. Komoe is flabbergasted as Mikoto assumes that she is an elementary student and refers to her as such. As Mikoto is impressed by Touma's school's preparations despite its modest accommodations, she and Komoe overhear Fukiyose Seiri shouting that Touma has been arrested by Anti-Skill (due to his little scuffle with Thor earlier). Mikoto later apparently searches for Touma and somehow ends up in the area near the Windowless Building. She spots and demands answers from him, such as why he is not helping his school for the Ichihanaransai, regarding on how he was arrested by Anti-Skill, and how he managed to get back from Hawaii. Touma, however, believing that the Mikoto before him is still Thor (who changed into Mikoto before), tells her to stop joking around, confusing Mikoto. Touma then demonstrates how terrible "Thor's" disguise is and touches Mikoto's chest, ceaselessly bewildering her. Touma notes on how they feel so real, to which Mikoto stutters to say that they are not pads. Tired of this nonsense, Touma leaves Mikoto and tells "him" to stop joking around and get to the rendezvous point.

During the Festival
8 AM during the start of the festival, Mikoto decides to come back to Touma's school. When she approaches the main entrance of the school for the trial enrollment, she bumps into Shokukou Misaki, who was using her ability to make the crowd chase after Mikoto. She then curses at Misaki for always teasing her but soon stopped as she started to wonder what she was doing there in the first place. However, she quickly casts away the thought as the crowd catches up with her again.

Thor later spots Mikoto from a water tower, and deeming her to be useful to aid Touma, calls out to her. Calling her by Miko-chan, he immediately gets her attention. Thor then shows Mikoto a footage of Touma being tended by Cendrillon, to which Mikoto demands Thor to tell him where he is. Mikoto herself tries to confront Touma. She approaches Touma, who is still being taken care of by Cendrillon. She attacks him, and is surprised that he did not block it. She later discovers that he has gunshot injuries and feels sorry. Nonchalantly, Cendrillon comments on Mikoto's attacks but says that it is only natural for her to get angry as Touma is the only clue leading to GREMLIN. Touma seeing this opportunity, asks Mikoto to translate for him. Here, the both of them discover Cendrillon's circumstances, on how she snuck into Academy City, her new abilities, as well as the reason she got so small. The last one piques Touma's attention, as there is still leftovers from her reconstructing her body, which can be made into whatever they want. Touma asks Mikoto to tell Cendrillon that he needs her help in constructing a brain that would prevent Fräulein Kreutune from eating a certain person's brain. Only now does Mikoto realize Cendrillon is the same one from Hawaii, but Touma's urgency takes precedence and he tells Mikoto to do what she is told. Cendrillon tells Touma that she doubts she can help him as her vengeance with Maria Slingeneyer takes precedence, and that the leftovers, if lost, will no longer able to remake herself back to normal. Hearing Marian's name however, Touma casually comments on how he defeated Marian back in Baggage City. As Mikoto translates it to Cendrillon, she is caught by surprise by Touma's actions, and unreasonably concludes that Marian must be dead, but he makes no attempt to amend her misinterpretation. Cendrillon clicks her tongue, noting that not only did Touma save her life in Baggage City, but freed herself from her revenge, lamenting on the fact that he was supposed to be her enemy, but has grown more indebted to him. However, Mikoto refused to translate what she just said. Touma pleads for Mikoto to continue translating, and she acquiesces. Cendrillon tells Touma that she will pay back her debts, and asks Touma what she needs to do.



Leivinia Birdway soon finds Fräulein in the multi-level overpass, and is forced to engage against Touma for her fate. Silvia and Brunhild Eiktobel that were supposed to support her are confronted by Thor of GREMLIN and Mikoto of Academy City, respectively. Mikoto meaninglessly complains to Thor about how she has been forced to help him. Thor explains how people have gathered together to beat the already injured Touma, and then abduct a woman named Fräulein, use her for their own purpose, and then kill her. He then asks Mikoto what she is going to do about this, to which she sighs and mentions that it is the same pattern as always. Mikoto mentions on how Touma has not changed after disappearing in Hawaii and arriving in Baggage City. Thor tells Mikoto that despite what happened in the city there, Touma still managed to save lives. Thor says that he is just as much to blame for the events happening, and tells Mikoto that Touma is trying to finish things with Fräulein, the primary cause of all the events that are currently happening. He asks if she will support him or get in his way. Mikoto clicks her tongue and tells Thor that he owes her, but Thor tells her that complaint should be directed to Touma. But Mikoto says that doing so is embarrassing, as such she's saying it where he can't hear her. With the banter over, Mikoto faces her enemy, while Thor faces his own.

And so, magic and science clashed, Brunhild of the magic side, one of the 20 Saints in the world, against Mikoto of the science side, the third ranked Level 5 esper of Academy City. Despite the fierce titles bestowed upon the two, the battle seemed one-sided, for the great speed Brunhild held, and her steps if she wished were faster than sound. Brunhild charges towards Mikoto, and swings her sword down her like a steel fan. But Mikoto reacts before the blow even begins, and with her powers, tilts a part of the overpass they are fighting on, putting Brunhild's aim off, but as its power was still immense, many surrounding windows were shattered the instant her sword fell. Brunhild questions Mikoto's ability to know her location despite her superhuman speed, not knowing that Mikoto's powers allow control of iron sand on the road's surface, allowing her to see Brunhild's footprints. And with the same iron sand Mikoto consumes Brunhild inside a storm-like shower of needles. But no harm befalls Brunhild, for by swinging her claymore in a circle, the iron sand is blown away with a roar. The force of her swing threatened to knock Mikoto down, but Mikoto escapes by magnetizing a wall between her and the shockwave before it struck. Mikoto tries to gather the iron sand once more, but Brunhild falls upon her, aiming her sword to behead Mikoto's. Mikoto used her powers to forced the blade to halt, but Brunhild's strength is too great. However, Mikoto's use of powers buys enough time for her, and she throws a lightning spear, striking Brunhild's sword and therefore shocking Brunhild. Without holding back on her attacks, Mikoto hurls many reinforced concrete objects towards Brunhild. However, Brunhild manages to recover from the electrical shock, and with her strength stops the mass of objects that Mikoto had flung towards her.

As if acknowledging Mikoto as a worthy foe, Brunhild speaks to her, asking why she is participating in this conflict for Fräulein if she had little to do with magic. For a great risk did Mikoto bring upon herself when she wraps herself in the core of GREMLIN. Mikoto tells Brunhild that she doesn't want to listen to someone who is trying to kill her, and straight to the point, does not know nor care about the big picture surrounding their conflict. Moreover, she says that she has no good reason to be fighting. However, Mikoto says that there is not a need for a good reason to save a friend, as her friend once said, and now, she will support him in spite of the dangers that will befall him. With that, Brunhild cut down the obstacles in her way, making an opening for her with her sword, and at the same time, Mikoto swung her iron sand sword. Colliding, Mikoto saw that her vibrating iron sand sword could not slice the claymore, and released it. She then took a coin, and fired her Railgun towards Brunhild, shouting that she has her own reason to save Touma.

Despite the apparent danger of letting her guard down against Brunhild, Mikoto takes the time out of her battle to use her electromagnetic powers to control Leivinia's gun before she could fire it at Touma. This and Thor's later use of his fusion arc blades to cut up the road between them, allows Touma to recover enough in order to fight Leivinia anew.

However, with the defeat of Leivinia at the hands of Touma, Brunhild stops her attacks, her sword covered with various objects that Mikoto stuck into them to slow her down. And yet Mikoto does not dare take advantage of the opening. Mikoto asks what the matter is, to which Brunhild says that the issue has been resolved, and she is unsure if she should continue fighting, head over as reinforcements, or view the situation as unfavorable and make preparations to reorganize. As what happens later, Silvia takes the last option, and the many conflicts in the multi-level overpass ends.

Agitate Halation Arc
Mikoto first appears when returning to School Garden after a long day in a research facility. She jumps from rooftop to rooftop, but stops to discover that Touma is in School Garden, a place where boys are not allowed. Seeing him on a rooftop, she attempts to pull him towards her by magnetizing his belt, but he negates that with his right hand and falls into the gap between the buildings. She is worried at first but then realizes that he is fine and proceeds to continue her pursuit. She goes into the building but finds Touma not there. She soon discovers Misaki's clique acting suspicious and tails them. However, it is revealed that Misaki has tricked her by hiding Touma inside a bunch of flowers.

After the Agitate Halation Project has taken effect on the "heroes" in Academy City and they have begun gathering in Learning Core where Fremea Seivelun is located, Mikoto tags along with Shokuhou Misaki who, like Mikoto, is searching for Touma. Misaki takes control over some of the heroes and diverts them to Mikoto, who then proceeds to take them down, much to her annoyance. Misaki tells her that Mikoto has no reason to be there unlike her because she was abandoned before she could see the incident with Touma through its end. Mikoto points out that it is her reason for being here as well. Hearing this, Misaki challenges Mikoto that whoever gets to him first gets to do whatever they want, leading to Mikoto being confused about what she means by "whatever they want".

Later, Mikoto experiences firsthand the resourcefulness of heroes. She tells Misaki to help as she can use her power to stop them without making a scratch at them, but Misaki ignores her. Misaki is later nearly overwhelmed by an attack by both a leopard and the heroes. She asks Mikoto to help her despite Misaki ignoring Mikoto's complaints just a few moments ago. Mikoto tells her that she will but only after the leopard has eaten her "extra fat" in the chest area.

Due to the peculiar gathering of all the Level 5s in the location, it can be assumed that Mikoto may have been influenced by Agitate Halation. Neither Mikoto nor Misaki are able to meet with Touma after the incident.

Magic God Othinus Arc
On the way to school, Mikoto stood silently with one of her cheeks twitching. She saw Touma sitting on a bench with girls clinging to him then instead of going biribiri due to the unpleasant sight, she just muttered to herself that she is sick of this position. Suddenly an adult woman in showy suit spoke to her and she recognized that this woman was under Misaki's control. Misaki then teased her regarding Touma and asked if she wants to know what's going on to which she replied that she isn't at all interested. Misaki then provoked Mikoto by saying she will approach him, ask him and seduce him by controlling more girls stating that he will at least like one of them. Mikoto then panicked and told Misaki that if she continues doing this, there would be chaos. She then controlled magnetism to lift up the bench where Touma and the others are sitting and sent it to the other side of the river. Mikoto then landed on the bench and demanded an explanation from Touma.

Mikoto tagged along with Touma and the others and they were at School District 23. Lessar and Leivinia Birdway then proceeded to shop for swimsuits so as to prepare to go and hide to a resort after defeating GREMLIN since they would likely be the target by the churches after everything is finished. Mikoto then grab Touma's collar and shook him while asking him an explanation for all of this. Leivinia and Lessar insisted on going to "50% Less Skin Covered" swimsuit store to which Touma refused and instead suggested to have voting to which store to go. Touma then provoked Mikoto and thus got her vote. Touma won and they proceeded to the other swimsuit store (Tropical Bright Girl). On their way, Mikoto then asks Index if these crazy things always happen to him to which Index responded that this is just the third link of the chain. Touma was looking at the gadgets that are displayed with disappointment since they were old models. Mikoto then told him that it is natural in duty-free shops so as not to allow Academy City's technology to leak out and then argued with Touma that he was just disappointed because he won't be able to see those girls in sexy swimsuits to which Touma denied fully. As they enter the store, Index said that she would be fine with any store as long as it has food and Touma reacted that whether she has finally reached the point wherein she will also eat swimsuits or cellphones as well. Index then exclaimed that she can smell cafe's and bread shops around. Touma was amazed at her skill when it comes to food and Index told him that food doesn't change and as long as there is food, she will eat it. Mikoto then said to Index that she must not underestimate the advances made by science and said that even a trash meat in Academy City is much better than the average in the outside world. Index then screamed at Touma to which Touma responded that he can't afford such a high class meat. They then entered the swimsuit shop and Mikoto proceeded to buy a swimsuit so that she would be ready and won't be in a hassle in case she go to the newly opened indoor pool in the leisure facilities of School District 6. Touma then suggested that she just buy in a sports shop but Mikoto insisted that she would buy now to avoid hassle. Mikoto then proceeds on choosing a swimsuit and warned Touma not to peek on her to which Touma responded that he won't. Mikoto then shoot a lightning spear toward Touma which he negated and told him to pay attention on what she is saying. She then decided on a swimsuit and told Touma to not look at it. Touma then pointed out that it looks normal and she doesn't need to hide it but Mikoto insisted that its design is different then suddenly the cloth from the chest down to the abdomen peeled off much to both Mikoto and Touma's shock. Touma then urged Mikoto to put it back where she got it. Index, Leivinia and Mikoto then caught Lessar who was overcome by shock due to Touma defeating her sex appeal and Touma holding a swimsuit and misunderstood the situation.

They met Kumokawa Maria at the airport and asked Touma what does he do to know so many girls. After receiving word that Sargasso has already been located, there was a low rumbling in the earth. Touma ran off with Index and Mikoto following him. Mikoto then told him that her mother lives in Tokyo and this has something to do with her to which Touma let her go with him. Mikoto and the others proceeded to ride an electronic cart to the plane. As the plane left Academy City, it was sliced in half by a giant dragon (Níðhöggr). Mikoto and the others were mercilessly thrown out into empty air.

GREMLIN invasion of Tokyo
As Index and Mikoto are falling from the sky, Mikoto stopped using her parachute and caught Index who is chaotically rotating as she fell. Mikoto then controlled magnetism and landed vertically on the wall of a giant train station building while holding Index. Mikoto was dumbfounded that the place was so packed with people to the point that she can't see the sidewalk. Index then told her that it was GREMLIN's doing. Suddenly, a dragon flew over their heads but did not attacked them. Mikoto then tried to use her cellphone but it was of no avail since the lines were apparently overloaded. Mikoto then started to move from building to building using her magnetism while still holding Index. They are heading for Sargasso since Mikoto thought that Touma will probably head there. While moving, Index then warned Mikoto to watch out and they landed perpendicularly on the side of a high rise building. As soon as she did, countless sparks appeared floating down and each spark struck the glass wall and produced pillars of flame that took form. Index then explained that it is the Muspell from the Norse Mythology to which Mikoto doesn't understand.

While still holding Index, Mikoto used her magnetism to jump from wall to wall. They were being pursued by the Muspell but they tried to escape them. Mikoto then asked Index if she knew where they are right now to which Index responded that she doesn't know. They then wondered what happened to Touma then suddenly they saw an Academy City bomber and realized that Academy City has already made their move. They also saw an eagle-like creature that flew to which Index said that it was Hræsvelgr and explained it to Mikoto. Suddenly, the creature fell toward a wide open space.

Mikoto while holding Index just saved Touma just in time before he is about to fall. Index was then released by Mikoto and she proceeded to scold him to which Index said that it won't change Touma. Index then told Touma that she would be going this time and he won't be backing down no matter what he says. Touma's cellphone then fell down while some button was pressed and he heard his mother's voice saying that she is fine and they don't have to worry. After hearing that, Touma then told Index and Mikoto that the opponent he's facing now is Freyja and he asks them to lend him their power so that he would be able to save both Freyja and the mother to which the two responded that he leave it to them.

Just as Freyja commanded Níðhöggr Vol. 02 to attack them, Mikoto attacked it using her ability and repeatedly fired railguns at it at point blank range. The dragon was stopped and Freyja was dumbfounded. She got separated from Touma and Index after the fight with Freyja. Mikoto fell from the sky and used magnetism to land on the metal railing alongside the river mouth and scolded Touma for leaving her behind after that bold announcement, as well as the fact that he is going after a pregnant woman to which Touma dealt again due to misunderstanding. A great number of sparks appeared along the path of the rubber boat and Mikoto’s descent. Leivinia held up her wand and Mikoto flicked a coin up with her thumb then destroyed the Muspell before they could attack. They rode the boat and left for Sargasso. On their way, they were attacked by Níðhöggr and while they are preparing to counter it, Kihara Kagun defeated it. Maria then recognized that it was Kagun and decided to go with him, along with the pregnant woman. Mikoto and the others then continued on to Sargasso wherein they were met by Mokkerkalfe, but it was killed by Thor (Ollerus in disguise).

They later bear witness to Othinus becoming a perfect Magic God, due in part to the efforts of Ollerus and Fiamma not knowing that she need only to fail or succeed 100% to unify her infinite possibilities to become a magic god. Moreover, they later see the result of their failure, Othinus summoning Gungnir from her eye socket. They are left behind by Touma as he desperately tries to charge towards her, but all is in vain and the world is later destroyed.

Shifting and Fluctuating World
Prior to Touma accepting that the cruel worlds he is visiting is actually reality, he frequently calls out to his comrades that followed him to Sargasso, Index, Mikoto, Leivinia, and Lessar.

In the second recreation of the world by Othinus, known as the Version_Beta world in-text, where another "Kamijou Touma" exists living Touma's life. She meets "Touma" and Index as they are at the underground department stores since she was there to deal with the owner of a store that has been the sender of junk mail ads to Tokiwadai's dormitory.

In the final recreation of the world by Othinus created specifically to break Touma's spirit, known as the Version_Omega world in-text, where several characters from the original world have been "saved" or have not experienced great tragedy, it is Accelerator instead who saves all 20,000 Sisters, along with Last Order and Misaka Worst after stopping the Level 6 Shift Project. Here, Mikoto and Accelerator have solved both their issues and are first seen accompanying Last Order and a few clones chasing after a paper airplane in the park where Othinus puts Touma in after creating the world. Seeing this, Touma admits that he couldn't save over 10,000 clones, and wishes he realized the events surrounding them sooner that there might have been a different option. He begins blaming himself for accepting that the incident with the Sisters have been resolved. His self-deprecation allows Othinus to continue to break Touma, with him eventually realizing that his very existence and choices may have caused great tragedy to befall people.

After Othinus concedes the world to Touma, she recreates his original world using the Imagine Breaker. The group that went to Sargasso with Touma are back as well, unaware of what had transpired, and are about to face Othinus immediately after her confrontation with Touma in the Black World. With Othinus having lost Gungnir to Touma, she faces her fate in Touma's world. Index calls out to her, telling her that they won't let her get away with what she had done. Mikoto then speaks up, saying she won't hold back after Othinus got her mother involved. Lessar speaks as well, complaining about her and GREMLIN causing chaos. Finally, Leivinia says that she should be crushed right away otherwise she would go hide somewhere and cause problems later. The group later attacks Othinus with Touma still dumbfounded with Othinus' decision to bring him and his world back, causing her to be knocked backwards. Finally, after Touma asks Othinus if she knew of her fate when she saved him, the girls with him are surprised by his outburst. Touma later runs toward Othinus, all the while they try to call towards him. The group later witness Touma defending Othinus from the attack of the Anti-GREMLIN Alliance using magic missiles.

VS The World
Immediately after stopping the international coalition's magic attack on Othinus and declaring his intention on saving her even at the cost of making the world his enemy, Touma and Othinus spirits away from the group and vanish.

Index, Mikoto, Leivinia, and Lessar are flabbergasted by what happened as they are completely ignorant of what had transpired in the many worlds of suffering that Othinus created to break Touma's heart. With Touma and Othinus gone, they start forming conjectures on why Touma made a complete 180 the moment he arrived in Sargasso. Leivinia assumes that Othinus may have messed with him as she is a magic god, though they actually don't know what she can or can't do. In the meanwhile, Index keeps quiet as she contemplates the likelihood on what had happened, for she has 103,000 grimoires and from her position could predict what a magic god was and a magic god could do.

Leivinia says that in any case they must get Touma away from Othinus for though he is somewhat special, he will be in danger when the coalition army attacked and get caught in the crossfire. Lessar however takes this chance in teasing Leivinia, saying that she may be upset that someone took her "big brother" from her. While they are all preoccupied with themselves, Academy City sends out a message to all Level 5s, Mikoto included, to kill Magic God Othinus and Kamijou Touma.

Mikoto and Lessar later leave to deal with the situation regarding Touma on their own. After having a change of clothes, Mikoto somehow is able to travel to Denmark on her own and somehow manage to locate Touma and Othinus.

Mikoto arrives just in time before the FIVE_Over Modelcase_'RAILGUN" units could attack the powerless Touma and Othinus. Using her power, she manages to hack into all of them, destroying some, though many were used to confront Touma. Mikoto rides on top of one of them and shows herself to Touma, surprising him. Mikoto makes it clear to him that she isn't going to join his side for no reason as she isn't that convenient a girl. Mikoto threatens Touma and tells him to defeat her. Seeing this, Touma lays down Othinus on the ground and faces off against Mikoto. Touma asks if Mikoto is mad, to which she confirms and asks him why he became a spy for GREMLIN.

Touma gambles on his chances, knowing that with Mikoto's combined firepower, he goes to the nearest Modelcase_'RAILGUN" and negates the power that Mikoto uses to control it. Mikoto frantically tries to stop the mecha gone out of her control. In the meantime, Touma uses Imagine Breaker to free more of them, much to Mikoto's annoyance as the mechas begin attacking each other. Complicating matters more, Mikoto has no way to distinguish friend from foe, forcing her to destroy the mechas she had reason to suspect, in order for her to prevent unexpected attacks from a blind spot and to secure her safety. Still determined, Mikoto plans to use the remaining mechas to corner Touma from multiple angles, knowing that he can't overcome her with that using only his right hand. However, she loses track of Touma on the field, and later finds him already next to her on the same mecha. Touma casually tells Mikoto with a smile that he'd rather not use his right fist on her, and asks if she is going to make him. Knowing that she can't use the FIVE_Overs against Touma with this close a proximity to her, she angrily uses her power to gather iron sand. In spite of this, Touma is unworried and even teases her about her using tentacles. Angered, Mikoto says that though she doesn't know what had happened to him, she is going to beat him up regardless. Mikoto then uses the iron sand against Touma.

Mikoto attacks using all eight of the tentacles, but Touma merely touches one of them and her entire attack collapses. Touma explains to Mikoto how whenever she used her iron sand on him it would vanish from tip to base when he touched it with his right hand, and that principle still applies in their current battle, where all of the tentacles can be negated just by touching a single one. Touma teases Mikoto through his nonchalance, comparing their fight as a nice change of pace to the other battles which were legitimate threats. This annoys Mikoto, and starts rotating the FIVE_Over below them, making Touma fall to the ground. Mikoto closes in on Touma and tries to engage him in melee as she demands to know why he sided with Othinus. Touma says that there is no need for defeating Othinus anymore, leading to Mikoto to ask him why. Touma tries to explain to Mikoto that the world was destroyed, though she doesn't understand, asking what it had to do with him and Othinus being together. Touma tells her that it isn't just about Othinus anymore. As Mikoto is above him, Touma uses his feet to push her away, and once again he is able to stand up face Mikoto. Touma explains that there was a really long time between the time they arrived on Sargasso and when the attack on Othinus began, but everyone else didn't notice. Touma's voice starts shaking, and reveals that he still feels guilty about leaving behind the Perfect World for his own. He begins to ramble and tells Mikoto that though she wouldn't be able to believe it but there was truly a world where all the 20,000 Sisters were alive, she didn't have to suffer, and all of them were smiling together as friends. Mikoto is unbelieving of what he is saying, seeing it that is so unreal to her. Touma continues, and shows that he is blaming himself for taking away everyone's happiness just so he could come back. Even as Touma explains this, Mikoto still doesn't understand what Touma is saying. Touma tells her that he needs Othinus to understand what exactly the people of this world like Mikoto have gained and lost as a result of his choice to abandon the Perfect World. He tells her that if she saw the Perfect World then she might even stop hating Othinus and then her turn her hatred on to him. He tells her that though she may not understand, but she mustn't make up her mind and forgive him until she knows the truth of the Perfect World.

Mikoto is loss for words, but Touma continues to speak. He says that he doesn't want to destroy himself with this guilt of his anymore, and needs to settle everything and pay for all his sins in rejecting the Perfect World. And the way to do that is for Othinus to live, her testimony as the only other witness to the Perfect World. Naturally, Mikoto is unable to understand the true feelings behind Touma's cries. However, even so, Mikoto could grasp a fragment of what lied inside Touma's heart. With that, Mikoto calls Touma on him clinging to a convenient and terribly naïve "perfect" world. Angered by Touma's thinking, Mikoto asks him if he truly thinks is the same thing as saving people. She tries to strike Touma with her electricity, telling him not to unify everything under a single set of values, a single definition of happiness as what Othinus has done in the Perfect World, as it would only create misfortune and discrimination. As she continues attacking Touma, she says that she doesn't know and can't even imagine what had happened to him but says that doesn't mean he is always right, and that no one has to accept what he says, no one has to accept the Perfect World. She tells him as they continue to do battle, that even if the world and she was remade it would not have taken her away her sin of letting 10,000 Sisters die, and that she doesn't want it to be taken away as she doesn't want to run away from her sins.

Mikoto's words strike Touma's thoughts, and for a moment, stopped his thoughts. But then Mikoto continues to attack him, telling him that there is no such thing as a Perfect World. As he continues hearing her words, Touma's heart and by proxy his actions waver. She tells him that he would have found that there was something twisted in the perfect look, and compares what had happened in the Level 6 Shift Project, with him not accepting that her suicide to save the Sisters would make her happy. She asks him that if he understood back then why change his mind now. Mikoto then head-butts Touma and then shocks him with her powers. She tells him that the Perfect World is one where a single set of values were forced on everyone where they are only allowed to smile, and those who don't are treated like they don't belong. Mikoto says that Touma shouldn't be feeling jealous, and that no matter how painful and hard it is and even if he is alone he should be the one to clench his fist and say it is wrong. Mikoto, now having climbed on top of Touma continues her argument. She tells him that even if he sacrificed the Perfect World and everyone else living there to do so, he should be glad to have returned to this world even if it is imperfect and should be proud of it. Touma is finally able to reply, telling her that he changed his mind because he admited that he was wrong for abandoning the Perfect World because he still recalls and remembers where people like Mikoto were truly happy and smiling. Mikoto punches Touma in the face, though Touma still stubbornly continues to crucify himself, justifying that he is a mere high school student and that it is only natural for him to go back on his thoughts and even change his ideals. Hearing this, Mikoto says that Touma doesn't understand. She tells him that there's no reason be bound by meaningless principles and ideologies, and that if he is reaching for the happiness he alone believes in, it is fine to choose the best arguments for the situation. She tells him that in the end it doesn't matter if he spits on his own words so long as it all works out. Looking directly into Touma's eyes, she tells him to bear the weight of her future and the fate of the six billion people, the world he has chosen, to the point of his own destruction. And thus, with a smile, Mikoto gives Touma an embrace as she laid on top of him, and later shocks him with her power, making him lose consciousness. Now at last, Mikoto is able to beat Touma, though even she thinks her victory is empty.

When Touma comes to, he finds Mikoto sitting next to him in the snow. She asks him if he has awakened, to which he confirms. Now it has been completed. In the Perfect World, the Will of the Whole Misaka Network, saved him by saying he could pursue his own selfishness over the ideal of saving the world—the Perfect World. And now, Mikoto has taught him that humans are not so simple that saving the world and recreating it into a convenient form was enough to make everyone unconditionally happy. With this, Touma wonders what he had been doing all this time. Touma then stands up and apologizes to Mikoto and says that he'll be going. Mikoto asks if it because he has to, to which says because he wants to. Mikoto shrugs and gives off a smile, telling him to get going. Touma asks why she isn't stopping him, to which she says she cannot, as she believes that though she defeated him a while ago, she doubts she can beat him now. With that Mikoto watches as Touma leaves, waving his hand in parting. Mikoto then stays behind as she faces off the remaining FIVE_Overs in support of Touma's actions.

St. Germain Arc
Mikoto appears briefly in the arc, wanting to sneak out of her dorm during Christmas, which is somehow, much to her frustration, revolves around Touma. She later meets with a girl that is under the control of Shokuhou Misaki and once again exchange banters with each other. Misaki tells Mikoto to combine forces as the two Level 5s of Tokiwadai Middle School in order for them to be able to sneak out of their dorms for Christmas. The two however are suspicious of the other's intentions in wanting to go out during Christmas, and both concludes to betray the other at the very end.

Touma then arrives where he relates to Mikoto that he is afraid of going to School District 15, the district where the rich and famous gather, and that he would be forced to do so by two girls. This surprises both Mikoto and Misaki, and after Touma leaves both of them finally agree to team up in order to get out for Christmas Eve.

Magic God Invasion Arc
Wanting to talk to Touma about what had exactly transpired back in Denmark, Mikoto visits Touma's school again on December 3rd. However, she never really gets a chance to have that talk at all throughout the arc. When she finds Touma, she finds him in his Anti-Crime Orientation costume that makes him look like a pervert as he climbs up between the floors of his school building, and attacks him. She later comes to find him again in the locker room and is shocked to find Touma receiving a letter requesting Touma to go on a roof, which Touma thinks is a love letter from a girl. Both she and Kumokawa Seria are angry that Touma is excited at being confessed to, though they make no effort on stopping him, only cursing him behind his back.

Mikoto is later caught up in Touma's troubles as he is chased by the Magic God High Priest, the true author of the letter. Wanting Touma to be the scorer of the Magic Gods in the world, he chases after Touma. He on the other hand, nearly powerless against the might of a magic god, even a depowered one, is forced to flee, grabbing Mikoto on the way. Throughout the arc, Mikoto aids Touma in helping civilians caught in the rampage of the High Priest, as well as helping Touma try to defeat him through more unconventional means, though none of them work even after getting help from Fiamma of the Right, who was soundly defeated.

After Touma figures out that the High Priest uses dirt in his magic, he and Mikoto hitch a ride on a boat, where they meet up with the other magic gods who have descended the world alongside the High Priest: Nephthys and Niang-Niang. The two female magic gods make lewd passes on Touma, annoying Mikoto, but she is instantly silenced when Niang-Niang shows off her power before her, making it known to Mikoto how powerless she is before a magic god. The two gods later try to make a deal with Touma that they would help him defeat the High Priest, though Mikoto rejects the offer for Touma, intriguing them. Though they rejected their offer, he and Mikoto reluctantly accept their offer of advice and the two Magic Gods give Touma an explanation regarding the nature of the High Priest before leaving.

Armed with knowledge, Touma and Mikoto School District 23 to trap the High Priest in the district's mass driver to shoot him into space with Parasatellite 01 which was planned to be shot into the Arrowhead Comet. Touma's plan however relies heavily on Mikoto's connections with Judgment, which would allow them to focus on defeating High Priest instead of worrying about the city as the dirt from under it is used by the High Priest. Predictably, the High Priest does so, but through Mikoto's connections as well as the secret machinations of Kihara Noukan, they are able to keep the city out of harm's way. Throughout their final confrontation, the High Priest blames Mikoto for preventing Touma from acting who he is, referring to his various complicated actions and plans to defeat him instead of the usual method where he simply faces his opponent with his right fist as the Imagine Breaker. Mikoto however isn't all too pleased with Touma's reply. Touma disregards High Priest's accusations and says he is grateful for Mikoto being there instead of Othinus or Index as it is through her that allowed him to get through and ignore his despair at facing an unbeatable opponent like a magic god. The High Priest is later burned up by the power of the mass driver, and is catapulted into space.

Little did they know that the High Priest has hijacked control of the comet and planned to crash it down into the city. Just before Noukan intercepts the comet and kills the High Priest, Mikoto sees Touma hold out his right hand and nearly bears witness to Touma unleashing a hidden power from it. Noukan, however, destroys both the comet and High Priest before Touma could do so.

After going back to her dorm, Mikoto contemplates on the events that have unfolded. Despite not actually seeing the power, the mere fact that Touma was ready to face a comet that even a Level 5 like her couldn't face, making her utterly powerless despite Touma's reassuring words against the High Priest embittered her, and notes on how far away Touma is from her.

Salome Arc
On the night of December 4th, Mikoto was wandering through School District 7, hoping to find some sort of stimulus which would show her the path forward, thinking over the events of the previous day and the stage Touma was apparently at, even briefly considering the possibility that she might have developed in the wrong direction. She was then approached by Salome, who was targeting members of the Kamijou Faction and recognizing her position, picked a fight with her. Mikoto fought back, however her attacks were neutralized by Salome's External Offering, soon stockpiling enough power to neutralize Mikoto's railgun. Despite the dangerous situation, Mikoto was excited at having found the stimuli she was looking for. Her behavior prompted Salome to remark that although she herself was known as an insane mass murderer, Mikoto would likely take it further than her if she continued. Before the two could continue the battle, they were interrupted by Claire, who chastised her before dragging Salome off into a battle of her own. After the two leapt off the bridge, Mikoto came back to her senses, curled up and started sobbing. However she soon stood up and despite considering Salome's warning, decided to continue onward.

The next morning, while considering altering her selections for the third term to improve her skills, Mikoto met Touma on his way to school. She tried acting as though nothing was wrong, but Touma immediately sensed that something was off. On being asked if something had happened, Mikoto confirmed it but left without elaborating it before Touma could inquire further.

The following night, Mikoto was again walking around outside, looking for some excitement. She soon regretted it after finding Touma and Salome under attack from Kihara Yuiitsu, who had stolen Kamisato Kakeru's World Rejecter and was using it together with Sample Shoggoth, which she used to create fake versions of the Magic Gods as part of a bluff. After she escaped with Touma and Salome, Mikoto apologized for seeking excitement. Yuiitsu soon caught up with them and continued her attack, with Mikoto briefly freezing in fear at the apparent sight of Niang-Niang who had previously skewered her.

After being separated briefly, Mikoto tried to protect Touma from Yuiitsu, but was knocked away by a giant fist produced by Sample Shoggoth. By coincidence, she landed in a refrigeration facility, that is actually one of the hidden hangars which were used by Kihara Noukan to house the Anti-Art Attachment. Encountering the powered suit, which reared up as though appraising her as a potential user, Mikoto considered using it to fight against Yuiitsu. On attempting to read it though, she backed off, sensing danger from the 'black box' which she couldn't read and the risks if she used it. However on seeing Touma in Yuiitsu's grasp and about to be lost to either the St. Germain virus or Sample Shoggoth, Mikoto immediately decided that she had to stop her and end it in a decisive strike, even if it meant breaking a taboo, regardless of the danger. Calling the Anti-Art Attachment to her, Mikoto launched a massive attack on Yuiitsu, which would have spread destruction through the district if not cushioned by the Windowless Building.

Leaving the scene, the Anti-Art Attachment detached itself from Mikoto, who was caught in euphoria at apparently having found what she was looking for and looking up at the night sky, expressed a feeling that there were no limits for her. She was then called by a nearby Anti-Skill officer, who pointed out that her nose was bleeding, which puzzled her. Unknown to her, her contact with the Anti-Art Attachment was deemed by Aleister Crowley as a potential threat to his plan, leading him to consider eliminating her.

Element Arc
Following her initial encounter with the Anti-Art Attachment, Mikoto had her own version constructed and started her own club in order to get a hangar and manpower to maintain it. She made extensive use of the A.A.A. during the subsequent struggle against the Elements swarming Academy City in the midst of a 55 degree heat wave.

Kamisato Rescue Arc
After driving off Kihara Yuiitsu and defeating the Elements which attacked School Garden, Mikoto and the other defenders were left exhausted and unable to prevent Tokiwadai Middle School from being looted by people, who took advantage of the broken barricade while ignoring the wounded girls. Furious at the looters but unable to remember their faces, Mikoto set out to hunt them down. On December 9th, Touma encountered her during the riot by the residents of the Show Business shelter and the suppression operation by Useful Spider, where she was launching attacks with killing intent. He grabbed her to stop her before she went too far and after hearing what had happened, calmed her down and promised to resolve the situation. After Fran took over Show Business's Sphere and she received a brief explanation, Mikoto took the group to the shelter where the Tokiwadai students had been moved to, located at Heaven Canceller's Hospital, so they could gain the use of the Sphere located there.

Later that night, Mikoto guided Touma's group to School District 11, where she had stored the original Anti-Art Attachment, which the group hoped to use in their attempt to rescue Kamisato Kakeru from the 'new world'. However when she tried to access the core, she was struck down by a curse directed at her by Aleister Crowley. Despite the damage being done to her body, on hearing that the attack could be used to understand the A.A.A. and give them the solution needed to end the situation, Mikoto urged Touma to hold off using Imagine Breaker until Luca had finished her analysis. She was left heavily damaged and unconscious by the time Touma was allowed to negate the curse. Impeded by the actions of Useful Spider, the group eventually managed to return to the hospital at around 5 in the morning, where they left her in the care of Heaven Canceller. She was up and about in the early morning on December 11th, and encountered Touma again shortly after Useful Spider announced the end of the 48 Hours to Restore Order.

Aleister Crowley Arc
On December 11th, after leaving the hospital again, Mikoto made her way to Tokiwadai, where reconstruction was underway, while lost in thought. On arriving there, she encountered Shokuhou Misaki. After talking briefly about how the other students had become afraid of their own power after having to use it to survive, Mikoto asked Misaki if she could discuss a certain matter with her, with the latter agreeing after hearing it was linked to Touma. Following a discussion at one of Misaki's favored eating spots, the two went to School District 11 to reanalyze the original Anti-Art Attachment. During the analysis, they found that the A.A.A. was receiving a signal and the individual it was connected to was focused on Kamijou Touma.

When Mikoto determined that the signal was coming from the Windowless Building, the two soon realized that the linked individual was Academy City's Board Chairman. Despite knowing the potential consequences of going against him, they decided to act out of concern for Touma, with Misaki using her ability in order to ease the burden of the A.A.A. on Mikoto. With their combined abilities and the A.A.A., they were able to penetrate the Windowless Building's outer wall with the Liquid Proof Railgun.

As Aleister gathered the powers of the city's espers to summon Aiwass, Mikoto felt the drain but continued the attack on the Windowless Building with Shokuhou's help. Their efforts broke the building's closed-off environment, enabling Touma's allies inside to disrupt the ceremony and cause Aiwass to disappear, helping Touma to defeat Aleister. When Touma's group was blown out of the building in the aftermath, Mikoto managed to catch all of them except Touma, who was caught by one of Aleister's manifested possible selves riding a broomstick.

Coronzon Arc
Following the evacuation of Academy City on December 11th, Mikoto went with the rest of the Tokiwadai students to the Indonesian island of Bali, intending to stay until the situation was resolved. During the boat trip, she easily dispatched a group of Crowley's Hazards, who were at a considerable disadvantage against her, being on the ocean. While speaking with Shokuhou Misaki on the beaches of Bali, Mikoto received a phone call from her father, warning her to get to the nearest embassy due to what was likely to come and to stay away from London. The call was abruptly cut off, but her father's comment about a nearby boy and girl led her to realize that Touma was in the same place. After checking the call information, Mikoto found that it came from London and promptly warned Misaki not to follow her.

Despite this, the two ended up flying to the United Kingdom using the A.A.A., which they had secretly brought with them, disguised as a piece of modern art. On reaching London, Mikoto located her father near Piccadilly Circus and on seeing that he was being targeted by the reproduced William Wynn Westcott and Annie Horniman, launched an attack run on the two. As they circled round for another pass, the A.A.A. accidentally collided with the Qliphah Puzzle 545 and stalled, forcing them to make a crash landing. Due to the shallow angle they used to reduce damage, they ended up in Outer London.

While they were checking the damage to the A.A.A., having not changed out of their swimsuits, Misaki was left freezing cold and tearfully pleading with Mikoto (who could warm herself with microwaves). On seeing Kamijou Touma going past with the Female Knight on horseback and overhearing snippets of their conversation, the two immediately changed their focus and with the A.A.A. reconfigured into a motorcycle, they set off after him. However as Touma moved onto the motorway, they ended up missing the onramp and entered the road below, subsequently getting lost.

They eventually caught up in time to save Touma after he fell from the royal carriage during his clash with Samuel Liddell MacGregor Mathers. After a brief minor clash due to Touma falling between the two of them, front towards a rather pleased Misaki, and getting the rough situation from Touma, Mikoto fired a Liquid Proof Railgun shot at Mathers before helping Touma back onto the carriage. The girls then moved to fend off the other members of the reproduced Golden Dawn with the A.A.A. When Mathers intercepted Aleister Crowley's Babalon-based attack from the sky with Belzébuth, Aleister transferred his magic to the A.A.A. and fired a second shot out of it which sent Mathers flying.

Once the battle with the reproduced Golden Dawn ended, Mikoto and Misaki ended up accompanying Touma to Edinburgh Castle and his subsequent meeting in the graveyard with Aleister Crowley, whom they were surprised to see in the form of a young girl. They then witnessed the attempt to use the real Mathers' corpse against Coronzon and Aleister's stabbing following the demon's deception. Touma told them to take care of the wounded Aleister while he prepared to face Coronzon.