The mysterious white Sister leaves Touma's room despite willingly allowing her to take shelter there, while Touma goes to his remedial classes. As he returns home, he finds Index lying in a pool of her own blood in front of his room. It was the work of a magician who has been following her, while Index tried to recover her lost nun cap. A tall red-haired man who wears a bar code under his eye appears, calling himself Stiyl Magnus. The man suddenly casts rune magic towards Touma...! After Touma escapes, he encounters another trick up the man's sleeve, Innocentius, at the same time as this, Index wakes up from her coma, and though gives a hint to the mysterious origins of the man's magic to the desperate Touma.
Touma discovers Index in front of his doorstep lying in a pool of her own blood, though alive, she is severely injured. Touma wonders who did this to her, when a man with red hair and long black robe appears before him, telling him that it was their doing. The magician tells him that they may have overdone it a bit, and the reason that she returned was because she wanted to get the headdress or hood back from Touma's room. The magician tells him that his partner did not intend to injure her, as the Walking Church is supposed to protect Index – which was destroyed by Touma.
Touma asks why they did this to her, and the magician states that she contains within her brain the 103,000 volumes of grimoire, and needed to recover and protect it (Index) to prevent magicians from using her, by using any means necessary. This enrages Touma and tries to attack the magician, but he simply dodges it. He also introduces himself as Stiyl Magnus and then says his magic name - Fortis931, which he says is like a murderer's nickname - and proceeds to show to Touma his power over fire.
Stiyl then summons flames into his hands and uses it to attack Touma, however, he surprises Stiyl as he is left unscathed by his attack. Touma realizes that his right hand can also affect magic and becomes more confident that he can take on Stiyl. Stiyl is surprised by this and attacks Touma again with his fire magic, but Touma simply negates it again. Stiyl realizes that Touma was the one who destroyed Index's Walking Church, knowing this; he chants a spell and summons Innocentius, the Witch Hunting Pope.
Innocentius' heat is powerful enough to melt the surrounding metal near him, and proceeds to attack Touma. Touma, knowing that it can be cancelled by his right hand, simply swept Innocentius away from his sight; however it is revealed that it recovered and attacks Touma again with a mystical flaming cross. Touma notices that Innocentius is still technically negated by his right hand, but recovers every time his right hand takes effect. At that moment Index speaks, she tells them those mystical runes that were applied in the building. Touma asks her if she is Index, to which she answers that indeed that she is Index, but her proper name is Index Librorum Prohibitorum, and right now she is in John's Pen Mode. Stiyl uses Touma's preoccupation in blocking Innocentius to attack, which prompts Touma to retreat and run. Touma later finds the area where Stiyl applied the runes, however, his discovery is cut-short after Innocentius continues his pursuit on him and he once again retreats; he fumbles and falls several storeys into a roof shed and then on several bicycles. Touma realizes that Innocentius can only move in the area where the runes where applied, and uses the opportunity to try and contact help. However, he soon questions himself and keeps on telling himself that he will not run away, and later asks himself on why would anyne would follow a complete stranger into hell (referring to Index's remark in the previous episode).
Back in the apartment, Stiyl tries to recover Index but is later surprised to see the sprinkler system activated. He is enraged that Touma has gotten him wet for nothing – as Innocentius will still be able to survive in the wet environment. Touma returns to the apartment and states to Stiyl on how he would've won if he instead engraved the rune markings on the wall instead of sticking them on paper. He is enraged for a moment after thinking that Innocentius has been defeated; however he smiles as Innocentius returns and orders it to kill Touma. However, Innocentius soon disappates after Touma uses his right hand on it. Touma tells to a surprised Stiyl that even if the paper could not be washed away, the ink will. Stiyl is shaken by this, and tries to use another fire attack on him; however, Touma charges towards him and knocks him out with a single punch to the face.
After the battle, members of Anti-Skill barricade the perimeter around Touma's apartment as so to let the fire department can do their duties and to keep civilians out of the way. We see Misaka Mikoto in the crowd wondering what's going on, when a girl who calls Mikoto "Onee-sama" runs up to her. She asks Mikoto if she is having some late night fun and not actually attending extra lessons, Mikoto rebutes her (calling her Kuroko) however and suddenly realizes that Kuroko is wearing her Judgment armband, implying that she is on duty. Kuroko states that the fire maybe esper related.
Meanwhile, Touma rests Index on a bench and asks her if she has any magical books inside her head that can heal her injury. Index states that even if there is, his power would just negate it and even if he was capable he is unable to do it. Index explains the origins of magic Touma. She tells him that magic was not meant for espers, as it was intended for the people who wanted the abilities like those of espers. Touma realizes that there are no students in Academy City that could help Index; however, he remembers that students are not the only persons that reside in the city.
Touma visits Tsukuyomi Komoe's apartment, where he barges in after she opens the door. Touma lays Index down on the tatami mat, after Komoe cleaned it of empty cans and cigarette butts. Index glows and returns to John's Pen Mode. Index states that she in critical condition and asks them to follow her instructions carefully. Touma asks Komoe to take care of Index, and leaves after Index tells him that his right hand will negate the magic that will be performed in the room. Touma obliges and leaves Komoe's house. However, on a tower that overlooks the city, a woman with long hair, holding a long sword, is calmly observing him.
By order of appearance
- Imagine Breaker (not named) - Kamijou Touma Level 0
- John's Pen Mode - Index
- Fire magic - Stiyl Magnus
- Rune magic - Stiyl Magnus
- Innocentius - Stiyl Magnus
- Touma references Index's question of if he was willing to follow her in hell, twice in the episode.
- Touma's cellphone that was broken in episode 1 is thrown away during the episode.
- Index references Stiyl's use of rune magic. Rune is derived from the Old Norse word, rún, which means "secret lore".
- Index Librorum Prohibitorum, literally meaning "List of Prohibited Books", is referenced by this episode by Index and is her full name. In the real world it is a publication of a list of books that were prohibited by the Catholic Church, that lasted well into the middle of the 20th century before being abolished by Pope Paul IV in 1966.
- The runic markings that Stiyl used are ᚲ and ᚨ, which means "torch" and "one of the Æsir (gods)" respectively.
- Innocentius is referred in this episode as a witch hunting Pope. It may refer to several Popes named Innocentius or Innocent, especially Pope Innocent VIII, well known for instigating severe measures against witches and magicians.
- The heat that came off of Innocentius was powerful enough to melt metal surrounding him, however it seemed that it did not not burn the flammable objects that were near it as well.
- When Innocentius was in pursuit of Touma in the hallway, where Stiyl applied his runes, the papers did not burn when Innocentius passed through it.
- When Stiyl came to pick-up Index after Touma run-away from Innocentius, Index's eyes were closed, however, in the scene where Touma was about to punch Stiyl after defeating Innocentius, her eyes are both open, as if she was in John's Pen mode.
- When Komoe asked Touma if he disliked women who smoke, her lips does not move and only smiles.
- What exactly occurs when an esper uses magic?
- How did Index know Touma's name?
- Seeing Komoe's apartment implies that she is within legal age to smoke and drink alcoholic beverages, it is unknown whether or not Komoe's current state is natural or not.
- Who is that long-haired woman near the end?
- Where did Touma go after he left Komoe's apartment?
- Touma: "I don't believe in this fairy tale of magic...Neither can I understand beings like you magicians...But...Don't you guys know things like justice and evil?" -said to Stiyl.
- Touma: "Chasing a little girl like this through the crowds...Covering her with blood...With all this in front of you, can you still call yourself just?!" -said to Touma.
- Stiyl: "Among our people, this magic name is more like a murderer's nickname." - said to Touma, referring to his magic name.
- Sityl: "One of the five major elements which make up this world, the great fire of genesis, the light of blessing which nurtures life, and the light of judgment which punishes evil. While it brings a gentle fortune, at the same time, it is the frosty misfortune which annihilates the cold darkness. It's name is fire, it's role, the sword. Show yourself by devouring my body and show your might!" -incantation to summon Innocentius.
- Touma: "I'm not running away...I'm not running...Who in the world would accompany a complete stranger he just met...to the depths of hell?"
- Touma: "Dammit! That's right. If I don't want to accompany her down to hell...I just need to...drag her out of hell!"
- Komoe: "I know it's weird to be saying this now but...Do you dislike women that smoke?" -said to Touma.