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.

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.