The Tree Diagram Remnant Arc is a story arc in Toaru Majutsu no Index. Focusing mostly on the point-of-view of Judgment member Shirai Kuroko, it deals with an important piece of the recently destroyed Tree Diagram, the Remnant, being stolen by Musujime Awaki a fellow teleporter, as well as Misaka Mikoto and her clones' struggle to stop the experiment from happening once again.
- Main article: Tree Diagram
After Index unknowingly destroyed Tree Diagram back in the 28th of July, the knowledge of it's destruction was seemingly kept secret by Academy City. However, it became quite apparent with that Academy City could not keep it's demise a secret any longer; such as the inaccurate weather predictions, as well as at some point 8 countries with space programs, as well as some 19 unnamed organizations, desiring to seek out the remains of the destroyed super computer with under the cover of "showing-off" their space programs to the world, and to prove their reliability to sponsors.
Despite the other countries' efforts, Academy City's space program based in the 23rd School District was successful in recovering the Remnant of Tree Diagram, and hired people from the outside of Academy City to deliver the Remnant (though unaware of the contents of the luggage bag), that was encased in a radiation-proof, air-tight luggage bag made out of silicorundum to the Tokiwadai Middle School Subsidiary Calculus Facility, a code to hide the true recipient of the Remnant. Meanwhile, Musujime Awaki – the guide to the Windowless Building – is assigned by the Science Association to retrieve the Remnant, with this her mission she also receives voluntary aid from her comrades as well.
Meanwhile, both Mikoto and her clones discover that the Remnant has been recovered, and have become worried that the experiment would restart if ever the Tree Diagram would be reassembled as the result of Remnant's recovery. Due to this they started individual efforts in hoping to stop it from occurring again, with Last Order – the administrator of the Misaka Network – giving full support to the clones' attempts to stop it.
PreludeKuroko notices Mikoto's unusual behavior, during their shopping of lingerie after seeing the news report regarding the recent influx of countries with space programs launching missions into space, with Academy City launching their rocket last week, though it was later completely disregarded and they returned to do their shopping. Kuroko is later called by fellow Judgment member Uiharu Kazari regarding a recent and unusual robbery, much to Kuroko's dismay since she rather spend time with Mikoto. Before leaving, Mikoto advises Kuroko regarding the weather, saying that it might rain later on, which Kuroko finds both unusual and suspicious.
Kuroko later arrives at the Judgment 177 Branch Office where she is briefed by Uiharu Kazari about the robbery. Looking, at a video recording, the robbers have stolen a luggage bag and later realize that both the victims and culprits of the robbery have suspicious backgrounds. Kuroko later decides to hunt down the culprits instead, as it was more convenient for her as a recent electrical outage which caused a traffic jam, has forced them to divert their escape to underground as well as the victim of the robbery being unable to be contacted. It was also more convenient for her, as a single unit to confront the culprits rather than an entire team of Anti-Skill members, as they are unable to reach the scene on time due to the traffic jam, as well as the difficulity dealing with procedures in order for them to take quick actions. Kuroko quickly leaves to pursue the culprits, with Uiharu backing her up by helping her locate the targets.
Battle in the streets
With Uiharu's help, Kuroko was able to find the culprits and the luggage bag easily. With the culprits general lack of knowledge regarding the espers of Academy City, Kuroko was easily able to defeat several of the armed men and acquire the luggae back easily, forcing the others who witnessed dominance to flee. In the light novel, Kuroko was able to defeat all the men.
Kuroko would later get a call from Mikoto, originally wanting to ask her if she could cover for her when the Tokiwadai Dorm Supervisor would begin her inspection of the students in their rooms, as she has other matters to attend to, though seeing as Kuroko is still working, she would ask one of her kouhais instead, ending her call immediately afterwards.
Teleporter vs. Teleporter
Kuroko's later falls to her back after the luggage bag that she took from the robbers, which she was sitting on, was teleported away from her, and is immediately followed by a corkscrew being teleported into her shoulder. Despite being in terrible pain, Kuroko is able to see the face of her attacker who is now sitting on the luggage bag. She tells Kuroko (which she apparently knows) that she is a teleporter as well, although she can teleport even without contacting the object being teleported. Kuroko tries to attack the girl with her needles, however, the girls quickly teleports the unconscious bodies of the outsiders Kuroko just defeated to block her view. 
However, Kuroko still teleports her needles to hit the girl (since teleportation is point-to-point movement and not linear), however, Kuroko missed entirely as the girl moved a few paces backwards utilizing the weakness of teleportation being point-to-point (points cannot be changed by the teleporter after teleportation). The girl takes one of Kuroko's needles and throws it towards her as a projectile, with no where else to go, Kuroko teleports forward trying to land a blow on the girl, however, the girl predicted this and is able to teleport a needle into Kuroko's body, disabling her momentarily.
The girl then mocks Mikoto for being desperate enough to involve Kuroko, her underclassman (kouhai) into her business. Hearing the girl mention Mikoto's name, Kuroko demands to know answers from the girl. Seeing Kuroko's ignorance, the girl reminds Kuroko on how a traffic jam just so happens to occur when her men were stealing the luggage bag, implying to Kuroko that Mikoto was somehow involved due to the nature of her power. This confuses Kuroko, though the girl gladly fills in the blanks, stating words such as "Remnant" or "Silicorundum". The girl says that what she is sitting on now is the Remnant of the Tree Diagram, the supercomputer installed on the Orihime-1 satellite that was destroyed. Kuroko is unable to believe this, stating that Tree Diagram should still be in orbit above the Earth's atmosphere. However, the girl pulls out photographic evidence, showing the scattered remains of the satellite in the vacuum of space; the girl reasons why people would want the "remnants" of the supercomputer, and mocks Mikoto's helplessness in the situation, seeing that her nightmare regarding the experiment is finally over since someone destroyed the Tree Diagram, but now people want to rebuild it again, which would mean the experiments would restart.
Seeing Kuroko is still confused, the girl mentions August 21st (the day Touma defeated Accelerator) and teases Kuroko if she could find the truth regarding what happened in August 21 the she would become friends with Kuroko. Seeing an opening, Kuroko quickly tries to draw up her skirt to touch one of her needles, this however, did not work, as the girl was too quick for Kuroko and pierced her again with one of her own needles, she later leaves with the luggage bag.
Preparation for the next battle
After Kuroko's loss to the girl, she drags her injured body back to the Tokiwadai Dormitory, and shut herself inside the bathroom of her dorm room. Here, she carefully removes the objects that were embedded into her body and then applies a special ointment created by the Heaven Canceler to treat her injuries, whilst pondering about the suspicious events that occurred during August 21 . At the same as this, Kuroko calls Uiharu to report on her situation and tells her to not report it to anyone, as well as asking her to gather relevant information. Uiharu tells Kuroko that the person she fought is named Musujime Awaki and that she is a teleporter like Kuroko, although somewhat different as she doesn't need to touch objects for her to teleport them as well as the fact that Awaki cannot teleport herself properly due to a an accident that occurred two years ago. Uiharu also states that the victims of the robbery were smugglers hired by District 23, and that they were in the process of delivering the luggage bag to another research facility until Awaki's group showed-up and stole it from them. Finally, Uiharu reports to Kuroko that Awaki is the guide to the Windowless Building, the base of Academy City's General Director, much to Kuroko's disbelief since she believes that the building and their guides are simply rumors.
Her conversation with Uiharu ends when Mikoto enters their dorm room, wondering why all the lights are out, locking herself inside the bathroom, Kuroko is forced to lie to Mikoto regarding this, else she would find out. Kuroko tries to ask where Mikoto has been, to which she responds that she was trying to buy an accessory, though came back to the dorm because she forgot something; even then, Kuroko realizes that they poorly constructed excuses. Mikoto later leaves shortly after Kuroko mentions to herself that she hopes that it will not rain, since the weather forecasts has been fairly incorrect recently, to which there was a moment of silence before Mikoto replies and agrees with Kuroko's statement, thanking Kuroko for her concern.
In the anime adaptation, it is shown that Mikoto took a bunch of arcade coins from her collection; this is also where Kuroko has a flashback to what occurred the day after August 21 and discovering one of the arcade coins Mikoto uses. Wanting to help Mikoto, Kuroko goes on her own to try and find Awaki, with the help of Uiharu tracking Awaki and her group. She later hears an explosion, and deduces that Misaka Mikoto might be involved with it.
Misaka Mikoto's Counterattack
Kuroko discovers that Mikoto has found Awaki and her allies, and has engaged them in battle, destroying a bus in the process. Here, Mikoto easily overwhelms Awaki's (who is viewing the spectacle nearby) allies with the use of her powers without killing anyone in the process, even when they are armed with handguns, and with the help of other espers. After defeating them, Mikoto confronts Awaki where she mocks Mikoto for her role in the experiment, which absolutely infuriates Mikoto. After hearing one of Awaki's insults, which states that Mikoto is simply fighting for her own benefit, Mikoto relents and accepts that she truly is angry and wants to destroy everything that is involved, however, Mikoto states that she is more angry at her self, for getting her kouhai (Kuroko) involved, and at that person who hurt her. Awaki responds that she is too kind, and says to Mikoto that she didn't need to enter the battlefield if she counted herself as a victim, just like her sisters.
Awaki reminds Mikoto that she can't get caught and states that she'll use any method just so she can escape. Mikoto comments on how it is impossible for Awaki to move fast enough to escape Mikoto (since she knows the weakness of her teleportation). However, Awaki proves her wrong by teleporting several of her companions in front of her, bluffing that some of them might be civilians, which forces Mikoto to hold back her attack, and allowing Awaki to teleport and escape in her confusion.
Seeing the affair from nearby, Kuroko quickly teleports away to confront Awaki.
Meanwhile, back in the Heaven Canceler's hospital, Misaka 10032 awakens to seek the aid of Kamijou Touma in ending the crisis of the experiments being restarted. Despite her body being in poor condition, as well as the concern for her by the other remaining clones in the city, her asking of Touma was still approved by the clones, as well with Last Order. Even though she and her clones want to settle the problem with the Remnant on their own, and not want Touma to hurt himself by trying to help them, Misaka 10032 simply opts to explain the situation to Touma instead as he will definitely come to their aid even without them asking. She runs through the dark streets of nighttime Academy City, and eventually reaches the Kamijou Residence, where she ask Touma to save her and her sisters, to which of course Touma accepts.
Teleporter vs. Teleporter II
Awaki arrives in a restaurant after escaping from Mikoto. Since she teleported herself, Awaki feels a little nauseous because of the trauma she has after teleporting accident two years before. However, her pain is multiplied by the arrival of Shirai Kuroko who teleports the corkscrew and the needles Awaki teleported into Kuroko before into Awaki mirroring Kuroko's injuries, as so she can be in equal footing with Awaki and would be able to predict her movements. As a gesture of insult and superiority, Kuroko offers Awaki the tube of ointment created by the Heaven Canceler, Awaki however, rejects her offer. Kuroko believes that she can at least keep Awaki busy enough for Mikoto to notice the ruckus they are creating, as Mikoto would be the winning condition to Awaki's defeat. Awaki knows this as well, as is the reason why she must beat Kuroko before the arrival of Mikoto. However, Awaki notices that if Kuroko wanted to win already, then she should've brought Mikoto with her; seeing that Kuroko seems to no want Mikoto to arrive. Because of this Awaki insults Mikoto's naive and childish wish for a fantasy world where they don't need to fight, and asks Kuroko if it is worth protecting. Kuroko acknowledges that it is a selfish wish of Mikoto, however, Kuroko states that it is something worth protecting, and says that she cannot trample on Mikoto's emotions on wanting an ending where neither of them need to fight and die. Kuroko declares to Awaki that in order for Mikoto's wish to be fulfilled she will drag Awaki back to the normal world. Hearing Kuroko's exclamation, Awaki smugly states that her winning would be her trampling on those feelings.
The battle starts with Kuroko trying to teleport a sharp fragment, however, Awaki moves faster and tries to teleport a tray into Kuroko, which Kuroko avoids. Seeing this, Awaki teleports several tables between them to block Kuroko's vision just like before, however, with Kuroko's previous experience, she decides to teleport in front of Awaki instead beyond the tables. Awaki however, anticipates this and tries to smack Kuroko with the luggage bag, however, Kuroko was able to avoid it by cutting the handle of the luggage bag, which surprises Awaki. Using this chance, Kuroko tries to hit Awaki with her fist, however it is countered by Awaki teleporting the luggage bag in front of Kuroko which smacks her in the face. Nearly knocked down by this, Kuroko teleports again and appears behind Awaki and elbowing her, sending her down to the floor. Kuroko tries to teleport again, however, due to the extreme pain from her wounds, is unable to, and is later pinned down by several tables teleported unto her by Awaki, and with this Kuroko is trapped in the hands of Awaki.
With the momentary cease in battle, Awaki teleports away all the items embedded into her by Kuroko and treats her wounds in front of Kuroko. While doing so, she tells Kuroko of the story about the Sisters Project, though not divulging any important information, such as Mikoto's involvement. Here, Awaki asks Kuroko why the clones of the original did not obtain the same amount of power that the original has, even though they went through the same power development training as with the original. She continues on by saying that there are most likely other factors in gaining powers other than the human brain, and that maybe beings other than humans could gain esper powers. Awaki basically states that the necessary condition to achieving esper powers is to have a high mental capacity. Hearing this, Kuroko asks Awaki if she is using the Remnant to give power to machines, which to Kuroko is ridiculous. Awaki agrees with her sentiment however, as a machine is merely a machine; Awaki however states that as long as they have a simulator such as Tree Diagram in their grasp, then maybe they could figure out if there are non-humans who could gain esper powers.
Bewildered by Awaki's statement, Kuroko asks if that is the reason why Awaki joined an outside organization, to which Awaki confirms since she can't repair Tree Diagram herself, and needs an organization to do it for her. Awaki then tells Kuroko on how she was scared when she got her powers and states that she was scared on how easily it could bring harm to other people. However, Awaki tells herself that she shouldn't be the only one who has such power, the power to kill with ease, and that humans shouldn't be the only ones to have power, and that if only humans could have power then why must humans have it. She tells Kuroko that's why the other people in the building allowed themselves to be used as shields for her, as they also hold these sentiments as well. Awaki then asks Kuroko if she felt the same as hers when she used her powers to hurt someone, and says that she knows because she and Kuroko are the same. She then offers Kuroko to find out the truth with her, however, she refuses and insults the reason for going through all this. Kuroko gets up from the stacked tables that pinned her, and says that powers are simply powers and that whether it is good or bad is dependent on its user. With a terrified Awaki, Kuroko grabs a lamp, even though she is bleeding from her wounds; she charges towards Awaki and swings the lamp. However, with Awaki unable to properly calculate and as such unable to use her Move Point, opts to use a gun and shoots Kuroko in the abdomen, ending her charge.
With Awaki's entire illusion regarding her powers destroyed, she collapses unto the ground and breaks down, along with this, her powers going out of her control, creating a vortex of objects being teleported in and out of space with her at the center. After regaining control, Awaki is determined in killing Kuroko for destroying all that she was; Awaki states that she can destroy Kuroko and destroy the building by teleporting 4,520 kg of weight unto her. She teleports away and leaves Kuroko to her fate after kicking her in the abdomen for asking why Awaki still needs Remnant.
End of the Tree Diagram Remnant Arc
Rescuing Shirai Kuroko
Shirai Kuroko lies motionless as a great distortion in spacetime displaces her surroundings, with her being powerless to runaway, despite this she doesn't want anyone to help her (especially Mikoto) as the attack would be impossible to stop. However, Mikoto and Touma arrives just in time before the huge weight could properly manifest itself from the 11th dimension and into the 3rd dimension. Using her signature move, The Railgun, Mikoto blows a hole from the first floor all the way up to the 4th floor where Kuroko was, using the hole that Mikoto made, Touma goes through it and saves Kuroko from the weight by using his Imagine Breaker, negating the teleportation.
In the anime adaptation, this is depicted differently as Kuroko falls from the hole that Mikoto created, which forced Touma to jump from debris to debris (instead of climbing electromagnetically held stair made out of debris) to rescue her and later use the Imagine Breaker to negate it. The anime adaptation also removes Touma and Kuroko's conversation regarding the reason why Touma is saving Kuroko despite having such power, as well as Touma's promise to Etzali in protecting Mikoto and the world around her, which would cue to Touma trying to fulfill it by trying to find Awaki. 
Accelerator vs. Musujime Awaki
After getting away from the scene, Awaki tries to contact the Science Association that she has successfully acquired the Remnant, however, she discovers that someone (Yomikawa Aiho) is raiding them. Awaki now being tired, injured, broken-hearted, as well as not knowing what to do with the Remnant, she tries moves on, however, while moving she meets someone unexpectedly, Accelerator. The strongest esper in Academy City appears before Awaki, seemingly irritated in going out of the way to help Last Order and the clones only to end up seeing that his opponent is only Awaki. Seeing Accelerator himself, Awaki is struck with absolute fear in facing him, however, Awaki remembers that Accelerator lost his power in August 31 and because of that he is not the strongest esper anymore, and believes that she might be able to match him in strength. However, Accelerator simply sighs at hearing this, refuting Awaki's declaration by saying that it is true that he lost his powers on that day, and now has to have others perform the calculations for him, but even then just because he became weaker doesn't mean she has become stronger.
At that moment, Accelerator attacks, shattering the glass of a nearby building, this forces Awaki to teleport up, which strains her body even further. However, Accelerator easily manages to catch up to her and attacks, which obliterates the luggage bag and Remnant in the process, when Awaki used it as a shield. With that, Accelerator uses his fist to hit Awaki right in the face, sending her flying and landing on a metal net, though she survives.
Kuroko is later sent to a certain hospital where the Heaven Canceler works for treatment, and is later forced to use a wheelchair due to her injuries. Touma reports to Index that he followed the most likely route Awaki would take given to him by Kuroko and discovers someone has already taken her out, and destroyed the Remnant, much to Touma's chagrin. Meanwhile inside the same hospital, Last Order reports to Accelerator that Yomikawa went outside of the city to destroy the Science Association, much to Accelerator's disinterest which irritates Last Order. In the light novel, Last Order cuts off Accelerator's connection to the Misaka network, disabling his speech and calculation ability. Accelerator tries to strangle Last Order because of this. Back to Kuroko and Mikoto, Kuroko promises that she would catch up to Mikoto in order for her to stand side-by-side with her in the battlefield.
With this, any possibilities of recreating Tree Diagram has been destroyed, and with Aleister Crowley's apparent apathy or simply aversion to its reconstruction, as its recreation would only hinder his plans on using the Sister clones.
- This marks the first story arc where nearly the entire narration is not in Touma's perspective, the first arc that featured this was with Accelerator in the 5th Light Novel Volume story arc where he shares the narration with Touma. Accelerator would not get an entire story arc centered around his perspective nearly entirely until the 15th Light Novel's story arc.
- ↑ Toaru Majutsu no Index Light Novel Volume 08 Prologue
- ↑ 2.0 2.1 Toaru Majutsu no Index Light Novel Volume 08 Between the Lines 3
- ↑ 3.0 3.1 3.2 Toaru Majutsu no Index Light Novel Volume 08 Chapter 1
- ↑ 4.0 4.1 4.2 4.3 4.4 4.5 4.6 Toaru Majutsu no Index II Episode 06
- ↑ 5.0 5.1 5.2 Toaru Majutsu no Index II Episode 07
- ↑ Toaru Majutsu no Index Light Novel Volume 08 Between the Lines 2
- ↑ 7.0 7.1 7.2 7.3 7.4 7.5 7.6 Toaru Majutsu no Index Light Novel Volume 08 Chapter 2
- ↑ 8.0 8.1 8.2 8.3 Toaru Majutsu no Index Light Novel Volume 08 Chapter 3
- ↑ 9.0 9.1 9.2 9.3 Toaru Majutsu no Index Light Novel Volume 08 Chapter 4
- ↑ Toaru Majutsu no Index Light Novel Volume 05
- ↑ 11.0 11.1 11.2 Toaru Majutsu no Index Light Novel Volume 08 Between the Lines 4
- ↑ Toaru Majutsu no Index Light Novel Volume 08 Epilogue