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 Crested Ibis stakes 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 is 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 couterparts. 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 ineccessant 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 Radio Noise 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 Underground Mall 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 mimicing 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 squadered 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.

Last Order retrieval operation
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.

Battle Preparation
While trying to find Index who left him to go return the tissue packet Accelerator gave to her, Touma discovers a mysterioust 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.

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 Canceler. 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.

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.