Tōma Kamijō is chased by hooligans after he stops one of them from disturbing a girl. In reality he was trying save them as the girl is Level 5 Psychic Mikoto Misaka, who can control and generate electricity. After losing them, he meets Mikoto who wants a duel but he refuses citing that he's just a Level 0 psychic. Nevertheless, she shoots an electrical bolt at him but it is stopped by the power of Tōma's right hand which nullifys it. Angered, she attacks with a powerful lighting strike which only ends up causing a citywide blackout. The next morning, after lamenting his recent bad luck, he finds a young nun hanging outside of his veranda. After feeding her spoiled food, she introduces herself as Index, a nun from the Church of England and is being chased by magicians because she has memorized 103,000 grimoires. After both of them explain about their own worlds, Index doesn't believe that Tōma's right hand can nullify other powers while he doesn't believe magic exist. To test their proofs, Tōma use his powers on Index's magical garb, The Walking Church which has the power to stop physical and magical attacks, which is unfortunately blown into pieces. After biting Tōma in revenge and fixing her garb, Index concludes that his powers are the cause of his bad luck, leaves and thanks him. He tells her to come again if she needs help. After coming back from summer classes, he meets Mikoto again who wants a rematch but when he refuses again, she stomps her foot in anger causing nearby electronics to go haywire including cleaning bots who sounds the alarm which forces both of them to quickly runaway. When he returns home, he finds Index laying on the ground bleeding and behind him a man who calls himself a magician.

The magician reveal himself as Stiyl Magnus and explain that his partner Kaori unintentionally hurt Index as her Magical garb was suppose to stop the blow and his mission to 'protect' Index or actually the Index-Librorum-Prohibitorum, the 103,000 books implanted in her mind as she possess photographic memory. Tōma, angered by Stiyl's ill treatment of Index attacks him and he counterattack by using Fire magic but is surprised when Tōma nullifys the spell. Stiyl then summons a fire creature named Innocentius which Tōma can't stop as the creature keeps regenerating itself from his attacks. It is only when Index's other personality, John's pen mode, reveals the creatures powers comes from Runes placed around the building that Tōma is able to improvise and defeat Innocentius and Stiyl. Tōma uses the sprinklers to destroy the Runes ink and rescue Index. When he learns from Index that he can't help heal her wounds using magic as it can only be use by normal people, Tōma brings her to the only normal person he knows for help, his teacher, Komoe Tsukuyomi. Meanwhile, a young woman with a sword is watching Tōma.

Komoe helps Index in healing her wounds using an ancient magic ritual and is successful. Later the next morning, Komoe ask Tōma about Index which he lies that she is her sister. Komoe is obvious about the lie but decides to let it go, believing it's something he has to solve on his own. While Komoe is out, Tōma learns about the organization that Index belongs. Necessarius, The Church of Necessary Evil was formed by Church of England Puritans who were stances Anti-Magic, who wanted to destroy Britain's Magic culture since Britain was a magical country. Ironically, they took a 'Fight fire with fire' policy by learning and using magic to defeat magic thus explaining the organizations name. The Index-Librorum-Prohibitorum was put into Index mind so she would a living library for the church since reading the originals cursed people. Tōma scolds her for not telling him but promise to protect her from the magicians. Meanwhile Stiyl and his partner, Kaori Kanzaki, the swordswoman from the previous episode, are watching Toma and Index from afar and comments how happy Index is and wonders how long they’ll have to continue tearing that happiness up. While Tōma and Index goes to a public bathhouse, he learns that she doesn't remember her past or her life at England for a year except the knowledge of the grimoires. Both of them get into a fight and Index leaves him, where Tōma suddenly finds himself in an empty street and meets Kaori.

Kaori explain she uses a Rune to repel people from coming here and asks Tōma to hand over Index which he refuses. He is easily beaten by Kaori's swordsmanship and wire techniques and wonders why she didn't kill him in the first place. Backing off a little, Kaori admits that she’s not doing this because she likes to, and she explains, to Tōma surprise, she belongs to Necessarius, just like Index. In fact, Kaori calls Index a dear friend and claims that she didn’t intend to hurt Index - she only wanted to secure Index as she didn't know her magical garb was destroyed, so that Index can live. The reason for all this is Index’s perfect memory ability. She explains that the capacity of human brains are small, but forgetting unneeded memories is part of organizing the brain. Index can’t do that, so her memory is quickly filled with trivial stuff. With 85% of her memory devoted to the 103,000 magic volumes, the other 15% fills up quickly and needs to be erased or else Index will die from information overload. They do this every year, and there are only three more days before it needs to happen again. She asked Tōma to hand over Index again since she's not gonna remember him but Tōma refuse citing if Kaori care about Index that much, shouldn't she tell her about everything to end the misunderstanding between the two. However this only angers Kaori who starts beating Tōma as she lashes out on how he doesn’t understand how she and Stiyl feel. They try everything to ensure Index always remember them including giving her a diary but no more how much they try, it still didn't work to the point it was unbearable for them to see her smile. Nevertheless, he tells her they were inconsiderate of Index feelings as they were leaving a scare young girl who had no idea what was going and they did nothing to help and feels that if they have given her even happier memories in the next year, and let her know that there’s happiness waiting for her, she won’t be afraid of losing her memories, then there’s no need to run away anymore before he loses consciousness and questions Kaori why she became strong and who she wanted to protect with her strength. Three days later, Tōma wakes up in Komoe's apartment and finds Index taking care of him. Index feels responsible for what happen to Tōma but he ease her mind. Kaori and Stiyl arrives at the apartment, but Index tries to make them go away and attempts to protect Tōma by saying that she’ll do whatever they want.

Tōma, sitting next to a sleeping Index, is aware that he can't do anything to stop the erasure of Index's Memory. Then he gets a call from Kaori, who tells him that the spell will be performed at exactly midnight. Tōma, who refuses to give up, tries to convince Kaori in finding another way to help Index which she tells him to try before midnight. He calls all the hospitals he knows until, but with each no one answers until it is already midnight. Styil and Kanzaki finally arrive to perform the spell. While Styil is preparing the erasure and brushing the seal on the wall, he tells a desperate Tōma (which he angrily calls a mutant) that if he really wants to try out his luck, he should touch the holy cross, an ornament which is needed to make the memory loss complete. Tōma tries to touch it but hesitates due to uncertainty. After some small talk, Kanzaki and Styil wait a few minutes outside so Tōma can finally say goodbye to Index. While talking to himself for failing to save her, he suddenly realizes something. Kaori's statement about the grimoires consuming 85% of Index memory and the remaining 15% reserved for daily life doesn't make sense. He calls Komoe to confirm. His suspicions are confirmed when Komoe reveals humans, even those with photographic memory will never suffer or die from information overload since the human brain is capable of storing large amount of information. Realizing that the Church erased Index memories to ensure her loyalty to them and lied to Styil and Kaori about her condition, Tōma is determined to save her. When he finds a rune in her throat, he touches it which end up activating John's Pen mode. The light and sound of the activation make Styil and Kanzaki rush into the room, where they see Index in her Pen Mode. After the Pen mode attempts to analyze what happened and reverse the process, it states that there is absolutely no way to reverse it. It then chooses the most "effective" way of eliminating the threat (Tōma), and activates the spell "St. George's Sanctuary", ending the episode.

Kaori and Stiyl are shocked to see Index using magic since she supposedly doesn't know how. Tōma reveals the lies Necessarius told them as he tries to stop St. George's Sanctuary spell using his right hand. Styil at first wants to stop Tōma, but Tōma manages to convince him that destroying the magic responsible for her pain will finally give Index a normal life without erasing her memories. When Index's spell almost breaks Tōma hand, Kaori uses her wires to push Index away which cause the spell to shoot into space, hitting the Academy's Surveillance Satellite and dropping magical feathers called Dragons Breath. With the help of Styil's Innocentius, Tōma manages to touch Index head thus disabling John Pen mode but is knocked out by one of the magical feathers that struck the side of his head. At a hospital, Index, now her normal self, reads a letter from Styil meant for the recovering Tōma. Styil, while hating Tōma for what he did, is thankful for saving Index and reveals the Church has decided to leave Index alone for the time being to be monitored he and Kaori question their superiors on why they lied about Index's condition. Index learns some sad news from the doctor who is taking care of Tōma; he is suffering from brain damage (because of the feathers) and no longer remembers his past life. She meets him and tries to make him remember all the times they had done together but he has no clue what she is talking about. As she is about to cry, Tōma suddenly tells her he's joking. He tells her that because Dragons Breath was a magical power, the negation power in his right hand was able to reverse the effects of the spell. Index is relieved, but angry and leaves after biting Tōma. Afterwards, the Doctor reveals in a conversation with him, that Tōma is lying, since he truly lost his memories. When he asks why, Tōma explains he lied to ease her mind, because he didn't want to see her cry. The Doctor then asked where his memories were now, if they were destroyed. To this, Tōma responded: "That's easy, isn't it? They now reside in my heart."