Academy City Invasion Arc

The Academy Invasion Arc is a major story arc in Toaru Majutsu no Index. It features a series interrelated events occurring in Academy City during Vento of the Front's attempt to search and kill Kamijou Touma, who has now become an enemy of God and the Roman Catholic Church; and Accelerator's struggle to protect Last Order, as he fights against his former mentor Kihara Amata.

In-universe it is called the 0930 Incident, an event that would influence several other events and story arcs to come later in the series, and would be the primary trigger for the final arc of the Toaru Majutsu no Index series before New Testament. This is most notably due to the now apparent hostility between the two sides after the events of the arc as well as the acknowledgment of the existence of "magic", and the ever increasing presence of Kamijou Touma and his Imagine Breaker in magic side affairs.

Investigation of Kamijou Touma
After several incidents of having their plans thwarted such as the Book of the Law incident, the Croce di Pietro fiasco, and most recently the Adriatic sea disaster, as well as steadily having their strength decrease, the Roman Catholic Church finally decided to investigate one common factor in all of these events, Kamijou Touma. After the destruction of La Regina del Mare Adriatico, an investigation was set-up by the Pope under the command of Vento of the Front to investigate if Kamijou Touma is an enemy of God (and by default the Roman Catholic Church), and if so have him executed.

The document for authorization of the investigation was handed to the Pope on September 26 of the timeline, and was later approved shortly; the investigation lasted for five days and confirmed Kamijou Touma as an enemy of God.

Invasion plan
The Roman Catholic Church's plan to invade Academy City is to have Vento of the Front cripple the city's defenses and populace through the use of Divine Punishment, at which point the support units outside would use Wooden Stake magic to stab the unconscious masses, as a way to mitigate losing scores of their forces if they try to invade the city head-on. This is due to the limited number of forces the church deployed, as such they are using Vento of the Front's Divine Punishment at full advantage.

However, the invasion plan in itself is just an accessory to Vento of the Front's true mission, which is to kill Kamijou Touma which takes priority over other targets such as Index and Aleister Crowley and would even destroy Academy City itself just to get it done.

A Day in the Life in Academy City
Accelerator and Last Order are finally released from a certain hospital after an entire month of being confined. Here, they move into the Yomikawa Residence in the Family Side after Yomikawa Aiho becomes their guardian. Meanwhile, Academy City begins the season of autumn with a mandatory change of all summer uniforms with their winter counterparts. Here, Touma is forced to accompany Misaka Mikoto on her Penalty Game that they agreed upon during the events of the Daihasei Festival, though with notable disturbances in excursions with him such as Touma's unwillingness and Shirai Kuroko's incessant invasion of their privacy.

Things get awry as Last Order accidentally locks herself outside Yomikawa's apartment and meets Misaka 10032. She becomes jealous of Misaka 10032's goggles and steals it away from her, she then taunts Misaka 10032 and runs away shortly which forces Misaka 10032 to give chase. While looking for Last Order, Misaka 10032 meets an exhausted Kamijou Touma who is still waiting for Mikoto to finish her gawking at Gekota products. Here, Touma could not tell Misaka 10032 from her sister because she was missing her goggles.

To remedy this problem Touma buys Misaka 10032 a cheap necklace. Though grateful and affectionate of his gesture, Misaka 10032 would've preferred a ring. This is because she remembers from an earlier conversation regarding Misaka 19090's behavior with the other clones, regarding rings being put in the ring finger for good fortune; however, Touma vetoed this because it was not noticeable enough, much to her disappointment. Touma upsets Misaka 10032 even more after consuming a chick-shaped treat, which enamored Misaka 10032 believing the treat is a true animal. However, this little incident is then interrupted by the arrival of the original – Misaka Mikoto – who becomes irritated at the sight of Touma being with Misaka 10032 instead of her for their promised Penalty Game, with this however, they begin to argue with Touma unfortunately being caught in the middle. The incident reaches its climax when Misaka 10032 shows to Mikoto on how she is more forward and honest on her feelings towards Touma than her, and embraces her arm. The situation takes on an incredibly confusing turn, as Last Order embraces Touma as well, forcing Misaka 10032 to pursue her as to retrieve her goggles, leaving both Mikoto and Touma befuddled.

With Last Order gone, Accelerator is forced to search for her with the help of Yomikawa Aiho as a member of Anti-Skill. While searching for her, Aiho confronts Accelerator's reluctance at reciprocating other people's good will that they have shown to him, especially that of Last Order, and believes it to be based on his fears of being unable to do it naturally on his own. Aiho continues to talk and opens an old wound of Accelerator's – the Special Ability Institute. A place where he was kept in until he was nine, and was part of the horrific experiments made there. Aiho states that her unit was the one that dismantled the facility, which Accelerator is thankful for. Accelerator continues by saying on how he was a monster, and because of this, repaying the debt through him showing goodwill is impossible now. Aiho tells him however, that even if he believes it is impossible to pay back his debts, he shouldn't stop from trying to pay back as much as possible, since he himself despises the fact that he is powerless in paying it. Aiho gives an example to Accelerator regarding her own debt that she wants to pay back and compares it to his: that she will not point a gun at a child even if they are espers. Hearing this, Accelerator begins to understand her own situation. Finally, Aiho states that with his own strength he can repay it in his own way. Regarding this, Accelerator thought of what would have happened if he had saved the Sisters from the experiments instead, though Accelerator simply mocks this thought, to which Aiho responds that what he is feeling right now would eventually pay back that debt of his.

Exchange of partners
Mikoto shortly leaves Touma to try and calm herself down after the whole ordeal, here, Touma meets Last Order. Here, she introduces herself to Touma and explains to him on how she is the control center of the Sister clones. Last Order then tells Touma on how she came to him to thank him for his help with stopping the Level 6 Shift experiments. However, Touma is believes she did not just entered the School District 7 Underground Shopping Center for the sole intention of thanking him, this infuriates Last Order which forces Touma to try to calm her down similar to his actions with Misaka 10032 earlier, by mimicking his interactions with Index, which is by feeding her.

At the same time as this, Accelerator while still looking for Last Order bumps into Index who is exhausted herself after trying to find Touma. Accelerator reluctantly takes Index to a nearby restaurant as a good deed, after being reminded by Aiho's lecture. Even after Index squandered his money due to her insatiable appetite, Accelerator asks her if she knows where Last Order is after showing Index her picture, to which she replies that she does not know (due to her perfect memory), much to his dismay. However, being grateful for Accelerator's hospitality Index decides to help him in his search for Last Order despite his protests.

After a while, Last Order states to Touma that she has to leave, though she would have preferred to at least spend a little more time with Touma. Last Order continues by saying that she truly is thankful even though they met by chance, however, it was time for her to go since "that person" (Accelerator) would become worried and would start looking for her and troubling him. Last Order says that that person is weak, and that not only is he unable to protect what he held in his hands but worn those hands in the process, however, Last Order says that she would be the one to protect him, as so to not cause any more strain on him. Last Order leaves, and at that same moment Touma notices Index coming in his way. Back with Accelerator and Index, Index notices Touma from afar as well though is reluctant to leave Accelerator. However, Accelerator tells Index that he has found the person he was looking for as well, and with that the two girls walk past by each other in a crowded path to reunite with their respective important person.

During the storm – Start of the invasion
At exactly 6:33 in the evening, Vento of the Front breaks into Academy City's Gate No. 3 immediately incapacitating the Anti-Skill and Judgment members on patrol due to Divine Punishment, which quickly spreads throughout the communication lines of the city trying to report about the intruder. With the city's defenses down, Vento of the Front manages to kill three of the General Board Directors.

With no one to stop her, Vento of the Front literally just walks into the city and later taunts Aleister Crowley who is monitoring normal communication channels as well. Introducing herself as Vento of the Front a member of God's Right Seat, she taunts Aleister regarding the weakness of his city's defenses, however, he warns her not to underestimate the city. Vento of the Front's conversation with him ends with her declaring the destruction of Academy City, Aleister Crowley, Index and the Imagine Breaker.

Academy City response
Immediately after his conversation with Vento of the Front, Aleister Crowley orders Kihara Amata – commander of the Hound Dogs – to carefully capture Last Order alive as so they can use the Imaginary Number District and activate Fuse Kazakiri (with Kazakiri Hyouka already manifesting her form earlier in the afternoon) to destroy the enemy forces.

Accelerator vs. Kihara Amata
While heading for home in the rain with Last Order, Accelerator is suddenly attacked by a group of Hound Dogs, regardless however, Accelerator makes short work of the armed group destroying a couple of their vehicles. Kihara Amata arrives shortly thereafter and is dismayed at their failure. Accelerator meets up with his former mentor and exchange some colorful insults and banters toward each other, before Kihara lunges towards Accelerator and punches him in the face, much to the surprise of Accelerator thinking that the switch to his collar that activates his esper mode is off. In his state of confusion, Kihara Amata is once again able to make a blow on Accelerator, knocking him down.

After implying his objective in capturing Last Order, Accelerator tries to attack in a different approach, using his vector powers he uses wind to smash down upon Kihara Amata. However, after a sound is heard the winds that were formed by Accelerator instantly dissipate and allowing Kihara Amata to attack him again. After revealing to Accelerator that he did not get any form of ESP development himself, Accelerator destroys Amata's gloves believing it was how Amata was bypassing his vector redirection abilities. However, for all Accelerator's trouble Amata was still able to attack him with physical blows. Continuing to pummel Accelerator, Amata reveals on how him being his ability developer allowed him to know every detail about his powers, especially his weaknesses. Amata says that he simply needs to pull back before hitting Accelerator as so his redirect will reverse the vectors that were pulling away from him and instead go towards Accelerator instead. Amata also shows on how he can disrupt Accelerator's control over the wind using a sound that would throw his calculations out of order. With this and him being in a bloody mess, Accelerator is utterly defeated.

Failure and renewal of the operation
Amata shares one small secret to Accelerator regarding on why the Level 5 Railgun was cloned instead of him. With the Hound Dogs successfully detaining an unconscious Last Order, Amata opts to finally kill Accelerator. Fearing for Last Order's life, Accelerator musters one final effort, using his vector powers to control the wind and carry Last Order away from their location, mindful of her landing. Greatly inconvenienced by this, Kihara Amata orders the Hound Dogs to split into groups and search for Last Order while he kills Accelerator. Beaten and bruised, Accelerator in his most desperate hour begs for someone to give him a miracle.

Almost immediately, Accelerator's request is fulfilled by the appearance of Index in front of the Hound Dogs, completely unaware of what's going on. With her appearance distracting, Accelerator is able to create an escape plan. Accelerator propels himself into a Hound Dog van, skewers the Hound Dog member in the driver seat with metal and threatens him to drive to a certain hospital. With this, Accelerator takes away Index from the scene before being shot at by the Hound Dogs.

With Accelerator retreating, Amata decides to destroy the vehicle instead with a missile, however, his view is blocked by the arrival of Vento of the Front. Irritated by her appearance, Amata fires the missile on Vento of the Front, however much to his surprise she survives. Vento of the Front converses with Kihara Amata regarding his apparent immunity towards her Divine Punishment as well as their missions overlapping (regarding Amata trying to kill Amata). Seeing Vento of the Front as a waste of time, he orders units to form groups and do specific tasks, one of which is to kill Vento of the Front while he and one unit of Hound Dogs will wait for them in their designated rendezvous point.

Kamijou Touma
While trying to find Index who left him to go return the tissue packet Accelerator gave to her, Touma discovers a mysterious malady has befallen the security forces of Academy City and realizes that an intruder has infiltrated Academy City, worried of Index, Touma once again tries to find her, however, he bumps into Last Order at exactly 7:02 PM, who pleads to Touma to save Accelerator.

Touma goes with Last Order to the location of where Accelerator was beaten, however, they discover that there are only debris and Hound Dogs there. They are later forced to hide as Hound Dogs start their clean up operation of the location. With the Hound Dogs slowly cornering them, Touma is forced to take Last Order and make a run for it, with Hound Dogs firing their weapons and in close pursuit. Touma and Last Order later breaks into a restaurant, deciding that a place with many witnesses, however, they soon discover that the people inside the restaurant has been stricken with the mysterious malady affecting Academy City. They are however, suddenly attacked by Hound Dogs which forces Touma and Last Order to take cover not knowing what move he should do.

Accelerator
Meanwhile, Accelerator gets rid of Index by lying to her about the battery pack that is needed for his collar to work and leaves her in the care of the Heaven Canceller. Here, Accelerator discovers from the driver of the black van he commandeered that the Hound Dogs can track him using their Scent Sensor. He takes the shotgun left in the van and uses it as a make-shift crutch, and later spares the life of the driver of the Hound Dog of the van after having a little talk with him.

Near the 5th School District, Accelerator calls Heaven Canceller regarding the condition of Index and Last Order, as well as to warn him of Hound Dogs, suggesting to evacuate the hospital. Heaven Canceler says that based on the information retrieved from the Misaka Network, Last Order is still alive and is with a ordinary person, unfortunately they are being chased by a squad of Hound Dogs, though the exact details are unknown. Heaven Canceller then scolds Accelerator for his lack on focus on a single goal, stating that it is impossible for him to destroy Hound Dogs, kill Kihara Amata and save Last Order without a scratch on her, and advises Accelerator to just return Last Order alive, for if she is alive then Heaven Canceller will save her. Accelerator later heads for the Third Resource Recycling Processing Facility to find a detergent that will remove his scent from being detected by the Hound Dog's Scent Sensor.

Tsuchimikado Motoharu
After determining the invasion and mysterious malady that struck Academy City was caused by God's Right Seat. Motoharu knowing full well that he is totally outclassed by them, he instead decides towards the outside of Academy City specifically through the same gate that Vento of the Front broke into. Motoharu realizes that the supporting invasion force by the Roman Catholic Church has yet to move into the city, he decides to head them off and prevent the force from entering Academy City, in order to protect the city where his sister lives.

Kamijou Touma vs. Vento of the Front
Kamijou Touma discovers that the Hound Dogs that were him and Last Order have become unconscious due to the work of a mysterious magician introducing herself as Vento of the Front, who has come to kill him for reasons unknown. Touma is forced into an extremely disadvantageous battle in an enclosed space against Vento of the Front, as he is forced to defend himself as well as protect the unconscious civilians and Last Order from Vento of the Front's attacks. After receiving a few attacks from Vento of the Front, Touma manages to determine Vento of the Front's attack pattern, using the chain pierced on her tongue to trace the trajectory of the attacks she conjures using her hammer. However, within a small timeframe he is still in a disadvantageous position due the confusing pattern she works with. It is not until Vento of the Front tries to attack Last Order that Touma is forced to leave her on her own. Here, Touma tells Last Order to leave and find help, she reluctantly leaves her side leaving her cellphone behind. Continuing his battle with Vento of the Front the restaurant is brought into ruin from all her attacks, as Vento uses them to injure Touma through the debris. Here, Touma is exhausted from trying to defend himself and the unconscious civilians. Vento of the Front taunts Touma and later reveals to him the reason of her arrival, here, she states that he is her main target and shows her the document signed by the Pope himself that makes him the enemy of God and the entire Roman Catholic Church. Vento of the Front decides to make Touma more serious after seeing him being astonished by this discovery, she threatens to kill every person inside the restaurant. Seeing the urgency of the situation, Touma tries to stop Vento of the Front, however, before she could launch the attack she start coughing up blood for reasons unknown. Touma tries to launch an attack on her, however, she quickly retreats from the restaurant before he could do so.

Accelerator vs. Hound Dogs
As predicted by Accelerator, a squad of Hound Dogs (headed by Nancy) tracked his scent and infiltrates the Third Resource Recycling Processing Facility. Here, he decides to get rid of the Hound Dogs first before trying to rescue Last Order, however, due to the structure and the machinery of the facility, Accelerator is unable to use his power.

With this in mind, Accelerator is forced to use his wits instead against the upcoming Hound Dogs. Sowing fear and confusion through the Hound Dog ranks via deception, and managing to utilize the environment as well as the Hound Dogs inexperienced in drawn-out combat scenarios, Accelerator is able to kill the Hound Dog units after him with little to no trouble at all. Finally, Accelerator sows the seeds of abject terror into the Hound Dogs by using increasingly creative and horrific ways of killing them, which is experienced first hand by one of the members, Accelerator manages to clear the facility of the Hound Dogs. Free from any present danger, Accelerator is finally able to use the detergent that will disable the Scent Sensor's tracking of him.

Accelerator later finds an injured Hound Dog member trying to escape the facility and most importantly Accelerator's wrath. However, poor judgment overcomes in as Anti-Skill authorities arrive to aid him, the Hound Dog member taunts Accelerator regarding Last Order, which naturally greatly enrages him. With Accelerator outside of the recycling facility, he is able to use his powers again which he uses against the unfortunate Hound Dog member, who he kills and turns him into a bloody stain on the pavement. In Accelerator's rampage, he manages to destroy the squad card that Saigou Ryouta and his partner Sugiyama Edao were using. Here, due to the smoke from the explosion of their vehicle, they barely witness Accelerator murdering the Hound Dog, however, this was enough just cause for him to label Accelerator as a suspect to an attempted murder, which he later forwards to other Anti-Skill members.

Tsuchimikado Motoharu vs. Roman Catholic Church forces
Motoharu arrives at the Academy City Outer Zone and enters an abandoned bus maintenance bay. He discovers that the Roman Catholic forces are planning to use Wooden Stake magic to skewer the people who have fallen unconscious due to Divine Punishment. He later finds the spell caster, who attacks Motoharu with the stakes. However, Motoharu manages to dodge them all and later discovers the pattern and composition of the spell, which is based on Pythagoras.

He discovers that he only needs to destroy one stake from the seven stakes that serves as the nucleus to nullify his opponent's magic. The opponent's attacks become relentless, and Motoharu is forced to use magic to survive, injuring him. Knowing that he can't win in a drawn-out battle, and with other Roman Catholic forces that needs tending to, Motoharu finds one of the seven stakes and destroys it, nullifying the spellcaster's magic.

Reorganization of efforts
Hound Dog members later infiltrate the hospital Heaven Canceller works in to eliminate one of their own (the Hound Dog that Accelerator spared) and Index, and quite possibly everyone else in the hospital. Here, they discover that the entire facility's patients and personnel has been evacuated most likely into it's basement parking grounds. Here, the Hound Dogs (one of which was one of the Heaven Canceller's former patients) get a call from Heaven Canceller who warns them of the Accelerator's wrath and just quit Hound Dog and forget Kihara Amata. However, they do not heed his warnings, to which the doctor tells them not die as so he can save them as long as they are not dead. After the call they are immediately destroyed by the Accelerator in ten minutes.

Still worrying about Last Order, Accelerator later receives a call from Kamijou Touma through the cellphone Last Order dropped a while ago during his fight with Vento of the Front, however, both of them are unable to recognize the other's voice. Here, Touma states on how Accelerator was the only who was able to answer his calls. They exchange information regarding Last Order's last whereabouts. Near the end of their conversation, Accelerator urges Touma to return to his normal as he doesn't want him to be involved any longer. However, Touma outright refuses and decides he wants to help Accelerator as well. Knowing that he would only be weighed down if he had assistance, Accelerator lies to Touma regarding where they would meet to throw him off. Before the end of the call, Touma warns Accelerator regarding the mysterious invader that has infiltrated Academy City and has taken down Anti-Skill, (which both surprises and confuses Accelerator) and tells him to be careful. Finally, both Touma and Accelerator apologize to each other for leaving Last Order alone.

Attack on the Windowless Building
Following Touma's instructions as to where Last Order's final whereabouts were, Accelerator comes upon a piece of clothed ripped from Last Order's clothes. He immediately gets a call from Kihara Amata himself, where he confirms Accelerator's worst fear, that he has acquired Last Order. In his call, Kihara Amata taunts Accelerator regarding the Testament machine inputting a virus into Last Order and the suffering that was induced on her because of it. However, Accelerator realizes that someone is controlling Kihara Amata for him to not risk hurting Last Order when retrieving her, because of this Accelerator calls out Amata's bluff and enrages him, ending their call.

Accelerator realizes that Academy City and the General Board of Directors are the ones pulling the strings behind Kihara Amata, and can easily pick one of them to find where Kihara Amata is. Angered by the fact that Academy City is using him, Accelerator once again uses esper mode which had barely four minutes of power left. Here, he set his sights on the main base of the General Chairman of Academy City – the Windowless Building – and using his esper powers launches a powerful attack on it that should be capable of obliterating any regular building. However, when he comes to after attacking the building, he realizes that the building remains intact and caught not a single scratch. This severely demoralizes Accelerator as his attack did nothing but squandered his batteries, however, he is forced to carry on and find Last Order.

Preparatory Stage
With Last Order in Kihara Amata's clutches, he uses the Testament machine on Last Order to install a program that would force her to use the brainwave network of the Misaka clones (which renders them immobile) to help her manifest and control Fuse KAZAKIRI from Kazakiri Hyouka the manifestation of all of the AIM dispersions of espers in Academy City. Inside the Windowless Building, Aleister Crowley is unperturbed by Accelerator's attack on his base and continues to observe the Sisters from around the world, Vento of the Front and Kazakiri Hyouka. With the Imaginary Number District already materializing itself and creating pressure inside Academy City, all magicians that use magic inside the city will overload and injure themselves.

Ever since the installation of the virus, the changes are slowly becoming more tangible and continues to expand at an alarming rate.

Initiation Stage – Fuse KAZAKIRI
Suddenly, an explosive burst of light and sound occurs in the 7th School District with the shockwave that can be felt from afar. From the epicenter of the explosion a powerful energy begins to form, eventually creating an innumerable number of enormous streams of light that destroys anything that touches. Suddenly another phenomenon occurs, one of the enormous streams of light performs a destructive movement towards the outside of Academy City, destroying it and anything in its path.

Kamijou Touma, Index, Accelerator, Misaka Mikoto, Tsuchimikado Motoharu, Vento of the Front and Kihara Amata bear witness to the unusual phenomena that has occurred in the city. Touma, Index, Motoharu and Vento of the Front immediately recognize the power that has materialized in Academy City as an angel.

Effects and response to the counteroffensive
With the summoning of Fuse KAZAKIRI and its subsequent annihilation of the supporting forces outside of Academy City as well as Vento of the Front's prioritization of stopping the angel that has appeared in Academy City, the invasion of Academy City has essentially ceased. Meanwhile, Kamijou Touma is forced to halt his search for Last Order in order to deal with the angel that has appeared in Academy City, he calls Accelerator to apologize to him and to tell him that he is own his own from now on (though he himself is aware and apathetic to that), their last words to each other is not to die.

Meanwhile, Index emerges from the underground parking area of a certain hospital after realizing that there is no battery pack for Accelerator's collar to try and find Kazakiri Hyouka, who she realizes is the one causing the distortion happening in Academy City. At the same time as this, the immobilized Sister clones try their best to counter the command Last Order has sent them through their network due to the virus installed on her, but is unsuccessful at doing so.

Preparations for the final battles
Knowing that the General Board of Directors have a hand in controlling Kihara Amata, Accelerator breaks into the office of Thomas Platinaburg and severely injures him in the process. Here he discovers Amata's location as well as information regarding the operation.

Meanwhile, Index, Touma and Mikoto run into each other on the streets and end up hiding together from the Hound Dogs patrolling the area. Index reveals to Touma that the angel manifestation is actually Kazakiri Hyouka, and begs Touma not to intervene, as she fears that his Imagine Breaker will kill Kazakiri Hyouka. Touma convinces Index, that he will not kill Hyouka and will save her. After a brief conversation, Mikoto decides to help them out and attacks the Hound Dogs, catching their attention and allowing Touma and Index to escape the area.

Before leaving, Mikoto states that due to the Penalty Game she can still give him orders. She stipulates that she must save his friend and to come back alive no matter what, Touma accepts the order and tells Mikoto to come back as well.

While moving to the center of the angel manifestation together, Index explains the nature of Vento of the Front's Divine Punishment magic to Touma, as Misaka is still locked in combat with the Hound Dogs. After Index states that she has no idea of the exact structure of Kazakiri Hyouka's angelic structure, Touma knowing that Hyouka is composed of AIM calls – Mikoto one of the most knowledgable person he knows regarding such topics – in order for her (in the heat of battle)to help Index to figure out Hyouka's structure. Index separates from Touma in order to find the source of the angel.

Final battles
Both Touma and Vento arrive at the epicenter of the angel manifestation. Touma is horrified at what has happened to Kazakiri Hyouka who seems unable to recognize him. Realising that there is nothing he can do to help Kazakiri Hyouka, Touma prepares to fight Vento of the Front to protect Hyouka from her. With Vento of the Front as a member of God's Right Seat, who intends to destroy the artificial angel due to its nature as a heresy against God.

Meanwhile, Accelerator arrives at the building where Last Order is kept, quickly wiping out the Hound Dogs stationed there, though at the cost of his weapon, and is forced to confront Kihara Amata once again.

Kamijou Touma vs. Vento of the Front II
Vento the Front and Touma engage in a violent battle as Kazakiri Hyouka grows more and more unstable. Due to the nature of the Imaginary Number District, Touma is able to have an advantage against Vento of the Front. To compensate for this as well as knowing Touma would try to protect anyone, Vento of the Front begins attacking civilians again, much to Touma's anger. However, Hyouka suddenly releases some sort of glittering scales that protect the civilians around them, much to both Touma and Vento of the Front's surprise. Realizing that it was Hyouka's doing, Touma is relieved that Hyouka is still with him regardless of her current form and promises that Index will save her. With Hyouka protecting the civilians Touma is now able to fight Vento of the Front without any worries.

As the glittering scales produced by Kazakiri Hyouka snow forth on the ground of Touma and Vento of the Front's battlefield protecting the innocent people around them, Touma and Vento of the Front go all-out at one another as their fight continues. As their battle heats on and as Vento of the Front receives damage from using magic, she repeatedly states her hatred for science, due to creating the fallen angel, due to injuring her. However, reasons finally become more personal as she states that she hate science due to making her in this current form and finally for killing her brother.

In a lull in their battle, Vento of the Front reveals her reason for fighting against science. Here, she states on how she and her brother was involved in an experimental amusment park ride. Having only a limited supply of their rare blood-type, her brother sacrificed his life in order for his sister to receive treatment. Because of these events Vento of the Front began hating science.

Hearing this, Touma states that her reason is foolish and an affront to the sacrifice her brother made. For hating science that tried to make them happy and for hating the science that her brother gave up in order for her life to be saved. Vento of the Front remains stubborn until the end even though she knows in the wrong path, Touma becomes resolute in making Vento of the Front live her life appropriately once again. Touma charges towards Vento of the Front who continues to attack, although she is repeatedly affected by the suppresive force produced by the Imaginary Number District as she continues to suffer internal injuries from using magic. However, eventually Touma is able to break through Vento of the Front's attacks to land a powerful blow on Vento of the Front's face, knocking her out and breaking her illusions.

Accelerator vs. Kihara Amata II
After securing Last Order, Accelerator fights his former mentor once more, but is unable to land a single hit on Kihara Amata, who continue to land blows on Accelerator. Despite this however, Accelerator remains resolute in defeating Amata even he continues to taunt Accelerator while beating him up and dodge his attacks at the same time. As Accelerator makes one final lunge at Kihara, his collar batteries die out after squandering it from all his excursions throughout the night, because of this his powers and motor functions disappear, rendering him powerless.

However, even after losing his motor functions and abilities, Accelerator remains resolute in his state and rises again in a zombie-like state and manages to surprise Kihara Amata and severely injuring him. Despite his efforts in stopping him, Amata is unable to create a counter against Accelerator's unpredictable and relentless assault on him. This enrages Amata off so much that he destroys the cure (more like the original script of the virus) that would save Last Order. In his darkest hour, Accelerator is given hope by the arrival of the girl he had met just a few hours ago, Index.

Even though she recognizes Accelerator from earlier, Index preoccupies herself with Last Order. Determining her to be the core of Kazakiri Hyouka's angelic form and compares the manifestation of Fuse KAZAKIRI as forcing telesma into a container with human form, similar to what the Hermetic Order of the Golden Dawn used to do. She asks Mikoto (who is still fighting the Hound Dogs) regarding science side topics such as the Brain-wave networks as well as the AIM Dispersion field in Academy City. Index determines through their combined knowledge that Last Order's mind is being restrained in order for her to become the core of the mysterious power that the city has (AIM dispersion field) and to distort it to create an angel.

With this Index need only to remove the knot that is restraining Last Order's mind so to speak. Index concludes that a song would be the apt choice, as a song's rhythm, pitch and musical intervals can create multiple interactions with the mind and incite a multitude of emotions from a person. With this she could free Last Order from the shackles that restrain her mind, and save Hyouka and all of Academy City.

Meanwhile, after seeing Index enter the office they were in, Kihara Amata tries to intervene but is however stopped by Accelerator who tries desperately to protect Index from Amata. Without his powers and motor fuctions, Accelerator simply turns into a moving target for Amata to pummel into submission, however, despite Amata's efforts Accelerator continues to take on the punishment and not allow himself to yield against Amata. In the end Index begins singing an aria, that even Accelerator understood was for Last Order's well-being. Hearing her song, Accelerator strengthens his resolve in order for Index to continue his song and brands himself as a villian who will protect them in his own way.

Accelerator stands up one final time and screams the name of his creator, Kihara Amata and begins his assault against him anew. Accelerator attacks Amata and gets a hit on him, but his efforts are quickly extiguished. With Accelerator now down, Amata is now truly enraged at Accelerator. Amata uses a grenade and throws it directly onto Accelerator's face where it quickly explodes presumably killing him.

However, Amata removes his guard after presuming himself to be the victor against Accelerator; here, he is caught off-guard by Accelerator who has managed to survive the grenade blast without a scratch. Accelerator shows himself before a restrained Amata, with a grotesque expression and with black wings emanating from his back, Accelerator has awakened during Index's song. In his final hour, Amata rationalizes Accelerator's transformation, skeptical that Accelerator has somehow inputted new values for his Personal Reality and believing that the AIM wings on his back and the true nature of his powers to be that of an angel.

With one seemingly undecipherable word that Accelerator uses, Kihara is sent flying by Accelerator into the atmosphere as a literal railgun projectile, obliterating him completely with only the plasma trail left in his wake.

Kamijou Touma and Acqua of the Back
With Vento of the Front defeated, Touma need only to wait for Index to finish her part of the mission knowing that his right hand could only destroy Hyouka if he was to come close to her. Touma is also concerned for Vento of the Front, due to her Divine Punishment spell sending people unconscious as well as for her own well-being, knowing her position as a member of God's Right Seat who attacked Academy City and sent it into crisis. The silence however, is broken by the arrival of Acqua of the Back of the God's Right Seat, who has taken Vento of the Front away. Acqua of the Back introduces himself to Touma after he demanded to know his identity. Here, he states that their is no longer a reason to fight as they are now retreating. Touma however, demands the release of Vento of the Front knowing the true nature of her reason for becoming a member of God's Right Seat, Acqua of the Back rebukes him regarding this as Vento of the Front chose to become a part of God's Right Seat and use it for her own reasons.

Finally, Acqua of the Back gives Touma her Cross of Divine Punishment, and states that due to his right hand touching it, the spell has been negated and making the spell no longer useable by Vento of the Front, and that all the people that were affected would now start regaining consciousness. Acqua of the Back later leaves with Vento of the Front, but not before warning Touma not to cross him for he is a Saint.

Terra of the Left and Acqua of the Back
After getting outside of Academy City while carrying Vento of the Front, Acqua of the Back opted to go to the supporting Church forces stationed outside of the city, although they were annihilated. However, Acqua of the Back later receives a call from Terra of the Left. Here, Terra of the Left tries to confirm with Acqua of the Back if his business in the city, and confirms to him the defeat of Vento of the Front and the failure of the mission.

Terra of the Left later tells Acqua of the Back to leave Academy City as is and not to take on Kamijou Touma even if Acqua of the Back is prepared to take on Academy City on his own. As he states that they should plan for their next move into taking down Academy City, and that the fallen angel that appeared in the city might be of use to them. Acqua of the Back concedes even though he disagrees with Terra of the Left's methods, and is later told by Terra of the Left to return with Vento of the Front as those are the orders of Fiamma of the Right.

Return of Kazakiri Hyouka
With Index singing her Aria for Last Order, she fulfills her mission as after Touma's confrontation with Acqua of the Back, Hyouka's wings start slowly disappearing one-by-one. Touma immediately rushes towards her to check up on her condition, careful not to touch her using his right hand. However, when Touma arrives by her side, he finds a very distraught Hyouka who realizes that moments before she was turned into a monster and destroyed her surroundings.

She begins blaming herself for the destruction and once again labels herself as a monster that needs to be destroyed and asks Touma to destroy her. However, does not acquiesced to her and states that he will not use the power of his right hand for the purpose of destroying his friends. Touma says that when Hyouka was in her angelic form you helped people protect people from harm, and for doing that she is human and encourages her to be proud of the fact.

Touma tells her that they'd need to check on the injured first, but then that they should meet up with Index again afterwards before she disappears, because they are friends.

A call from the dark side of Academy City
Index leaves Accelerator to call help for him, but not before stating that the black wings have appeared were similar to telesma. Accelerator waits alone in the now-ruined office with the unconscious but safe Last Order, when Accelerator notices the arrival of some unexpected guests. Here, a mysterious figure using the abilities of telepathics is able to communicate with Accelerator to make a negotiation with him. Here, the mysterious figure discusses with Accelerator on how he might be of use to Academy City after the greatest crisis it has faced (and the fact that Accelerator has caused a significant amount of damage during the event). As reparations for this, the figure suggest that Accelerator be put to work for Academy City due to his powers' usefulness in military affairs, which makes Accelerator believe that Academy City is starting a war.

Despite his reluctance (as Accelerator wants him and Last Order to not get involved), Accelerator accepts the figure's offer and is shot to unconsciousness by the figure, taking him away and destroying all evidence of the battle that had occured in the office.

Effects and implications in future events
The events of the arc would fuel events in the Toaru Majutsu no Index timeline, some more direct than others, however inevitably, the arc proved to be the prelude to World War III.

Effects in the world stage
The effects of the invasion proved to be too widespread for both sides to contain, with Academy City revealing its angel to the world, as well as the Roman Catholic Church's revealing of its Magic though covered up as an esper development program. Both sides criticize each other's claims, and later demands of concessions and compromises could not be reached.

With obvious hostilities, Academy City and the Roman Catholic Church prepare themselves for an invetable clash. These preparations and hostilities however, were not unnoticed by other factions, because of this, both the Russian Orthodox Church and the Anglican Church would be forced to make a decision side to ally themselves in, which would later result in their inconclusive conference a few days later.

Effects in Academy City
Due to the presence of hostilities, parents and guardians become greatly concerned for their children's safety and have started wanting to have their children recovered from the city.

Meanwhile, immediately after the invasion the Skill-Outs of Academy City take advantage of the strained security of Academy City (due to the preparations of an armed conflict with the Roman Catholic Church) to cause an error on the communications network, allowing them to attack their targets as they please.

Other factions take advantage of the result of the invasion as well, such as BLOCK who has lost their faith on the higher-ups and are now planning to kill Aleister Crowley.

Finally, the effects of the invasion, more specifically Aleister Crowley's use of Heaven Canceller's patients such as, Kamijou Touma, Accelerator, Last Order and the clones for his plans has greatly strained the relationship between the two founders of Academy City. With Aleister Crowley unyielding in changing his methods, Aleister Crowley severs his ties with the Heaven Canceller, his doctor.

Trivia

 * With seven episodes used for the adaptation, this would make the Academy City Invasion arc the longest story arc in the anime adaptation of the Toaru Majutsu no Index Light Novels to date.
 * This is one of the few Toaru Majutsu no Index story arcs where Touma does not end in Heaven Canceller's Hospital.