A Certain Magical Index is set in a world where supernatural abilities are a reality. Individuals who possess special powers acquired via science are called Espers (超能力者 Chōnōryokusha?). They possess their powers from birth, but most only awaken them during the Power Curriculum Program. Those Espers who awaken their abilities without the aid of special scientific instruments, whether at birth or through meditation, are referred to as Gemstones (原石 Genseki?). Others, known as Magicians (魔术师 Majutsushi?), gain their powers upon mastering the power of magic, either from obtaining knowledge from special books known as Grimoires (魔道书 Madōsho?) or by using mystical artifacts, though the existence of magicians is a secret to the public. While Magicians align themselves with ancient religions, Espers are aligned with scientific institutions. This leads to a power struggle between the magic and science factions for control of the world.
The story is set in Academy City (学园都市 Gakuen Toshi?), a technologically advanced city located in western Tokyo that is known for its educational and research institutions. Tōma Kamijō is a student in Academy City whose right hand, the Imagine Breaker, has the ability to negate any supernatural power, but also negates his own luck, much to his chagrin. One day, Tōma meets a young English girl named Index - a nun from Necessarius, a secret magic branch of the Church of England, whose mind has been implanted with the Index Librorum Prohibitorum - 103,000 forbidden magical books that the Church has removed from circulation. His encounter with her leads him to meet others from the secret worlds of science and magic. Tōma's unusual power places him at the center of conflicts between the Magicians and Espers in Academy City who try to unravel the secrets behind Academy City, Index, and Tōma's own special power.
Besides its own manga adaptation, the series also has two manga series which are side stories focusing on other main characters. One of them is A Certain Scientific Railgun, which focuses on Mikoto Misaka, an Electromaster and one of the most powerful Espers in the city. The second, A Certain Scientific Accelerator, focuses on Accelerator, a teenager who can control vectors, known as the most powerful Esper in Academy City.

A Certain Magical Index (2008–2009)[edit]
No. Episode title Original air date on MBS
1 "Academy City""Gakuen Toshi" (学园都市) October 4, 2008
Tōma Kamijō, a Level 0 student living in Academy City, has a unique esper ability that allows him to nullify psychic, magical and divine powers, but it also negates his own good luck. He survives a reluctant duel with said ability against Mikoto Misaka, a powerful Level 5 psychic capable of controlling and generating electricity, ending with Mikoto causing a citywide blackout. The next morning, Tōma wakes up to find a young nun from the Church of England hanging off his balcony. Introducing herself as Index, she reveals that she is being chased by magicians because she carries 103,000 grimoires. The two become friends after an embarrassing incident, involving Index proving the existence of magic and Tōma proving the power of his right hand, and they part ways. However, when he returns home from remedial class, Tōma finds Index laying on the ground bleeding and, behind him, a man who calls himself a magician.
2 "The Witch Hunting King (Innocentius)""Majo-Gari no Ō (Inokentiusu)" (魔女狩りの王 (イノケンティウス)) October 11, 2008
The magician introduces himself as Stiyl Magnus and explains that his partner Kaori Kanzaki unintentionally hurt Index as her magical garb was supposed to stop the blow. His mission was actually to protect Index, who possesses photographic memory of the 103,000 grimoires implanted in her mind called the Index Librorum Prohibitorum. Angered by Stiyl's ill treatment of Index, Tōma attacks him, to which Stiyl responds by using fire magic and is surprised when Tōma nullifies the spell. To stop Tōma, Stiyl summons a fire creature known as Innocentius. When Tōma finds himself unable to negate the creature, Index activates John's Pen, her self-protection system personality, to reveal that Innocentius' power comes fromrunes placed around the building. Tōma defeats Stiyl and Innocentius by setting off sprinklers to wash away the runes. However, because of Index's wounds and Tōma's inability to use magic, he brings Index to the only non-esper he knows, that being his teacher Komoe Tsukuyomi.
3 "The Church of Necessary Evil (Necessarius)""Hitsuyōaku no Kyōkai (Nesesariusu)" (必要悪の教会 (ネセサリウス)) October 18, 2008
After Tōma leaves, Komoe successfully helps Index heal her wounds using an ancient magic ritual but asks Tōma the next morning who she is. When he lies that she is his sister, Komoe spots the fib immediately but decides not to press the issue since she believes it is something he must solve on his own. While Komoe goes out to shop, Tōma learns that Necessarius, the organization that Index belongs to, implanted the Index Librorum Prohibitorum into Index's mind so that she would be a living library for the Church, since reading the originals would curse and taint people. Meanwhile, Stiyl and Kaori continue to watch Index and comment on how her happiness will be short-lived. When Tōma and Index get into a fight and separate, Tōma finds himself in an empty street and meets a girl wielding a nodachi, which so happens to be Kaori.
4 "Perfect Memory Ability""Kanzen Kioku Nōryoku" (完全记忆能力) October 25, 2008
Tōma refuses to hand Index over to Kaori, who reveals that she is also a member of Necessarius and a dear friend to Index. Kaori never intended to hurt Index when attempting to secure her the day before, unaware that Index's magical garb was previous damaged by Tōma. While eighty-five percent of Index's memory contains the entire Index Librorum Prohibitorum, the remaining fifteen percent needs to be annually erased to avoid any strain with any unnecessary memories, and there is only three days left before the limit is reached. Even though Index would not be able to recall him, Tōma asks Kaori why she does not explain everything to Index. Stiyl and Kaori had tried everything to restore Index's memories, but it became unbearable to see her smile with each successive failure. Tōma criticizes that Index's feelings were not taken into account each time, questioning why Kaori was hiding this from her. After Tōma is severely injured by Kaori, he wakes up three days later in Komoe's apartment in the care of Index. When Stiyl and Kaori arrive, Index tries to protect Tōma by promising to do as they ask.
5 "12 o'clock (Limit)""Jūni-ji (Rimitto)" (十二时 (リミット)) November 01, 2008
Tōma learns that Stiyl and Kaori will come at exactly midnight to perform the spell to erase Index's memory. Despite Tōma's attempts to find another way to save Index, midnight arrives and he is helpless as Stiyl and Kaori arrive to prepare the spell. The duo give him time to say goodbye to Index. In this time, Tōma becomes suspicious of Kaori's statement that Index's memory only has fifteen percent for daily life in a year. Calling up Komoe, he learns that humans can never suffer or die from being overloaded with information and realizes that the Church regularly erased Index's memory to ensure her loyalty to them and tricked Stiyl and Kaori. Determined to save Index, Tōma tries to dispel a magical rune in her throat, only to activate her John's Pen mode. Unable to analyze and devise a means of countering Tōma's ability, John's Pen activates St. George's Sanctuary, a spell it has determined as the most effective way of eliminating Tōma.
6 "Fantasy Killer (Imagine Breaker)""Gensō-Goroshi (Imajin Bureikā)" (幻想杀し (イマジンブレイカー)) November 11, 2008
After Tōma convinces Stiyl and Kaori that they were tricked by Necessarius about Index's condition and that destroying the magic responsible for Index's pain will allow her to live a normal life, Tōma is able to disable her John's Pen mode with help from Stiyl and Kaori. However, St. George's Sanctuary remains in effect and Tōma is rendered unconscious when a feather from the spell touches his head. At the hospital, Index discovers that Necessarius will leave her alone for now since Stiyl and Kaori are now questioning why the Church lied about her condition and that Tōma's memories have been erased since the spell destroyed his brain cells. At first, Tōma says that he is unable to recognize Index when she goes to see him, but brushes it off as a joke and explains that he canceled the spell with his right hand's ability, now called Imagine Breaker, before she leaves. What Index does not know is that Tōma really was unable to remember anything but did not want to burden Index with his condition, though feeling that his memories still remain in his heart. Two weeks later, Stiyl meets Aleister Crowley, the ruler of Academy City, and to keep the status quo of non-interference between science and magic, Aleister lends Tōma to Stiyl for an assignment to rescue "Deep Blood", someone capable of killing vampires, from a magician in Academy City.
7 "Misawa Cram School (Science Cult)""Misawa-juku (Kagaku Sūhai)" (三沢塾 (かがくすうはい)) November 15, 2008
Tōma continues to keep his memory loss a secret and inadvertently upsets Index when he meets with his two friends, Motoharu Tsuchimikado andPierce Aogami, who both inadvertently insult her. Forced to buy them all lunch, they go to a fast food restaurant, where Index gets into an argument with a girl dressed like a miko, who says that she is a magician and leaves before Index can get any answers concerning which magical organization the girl belongs to. On the way home, Index chases after a kitten she names Sphinx and is separated from Tōma. She then runs into Stiyl, who needs Tōma to rescue Aisa Himegami, a girl codenamed "Deep Blood", from Aureolus Izzard, an alchemist leading a secret science-worshiping cult at the Misawa Cram School after three years in hiding. When Tōma refuses, Stiyl coerces him with threats that Necessarius will take Index away. When they arrive at the cram school, Tōma is surprised to learn that "Deep Blood" is the girl he met earlier and finds a dead corpse in a suit of armor.
8 "Gold Transmutation (Ars Magna)""Ōgon Rensei (Arusu Maguna)" (黄金练成 (アルス＝マグナ)) November 22, 2008
Stiyl explains the dead knight was from the 13 Knights of the Roman Catholic Church and that a magical barrier is concealing all magical occurrences inside the school from the public. Tōma and Stiyl are forced to separate when the students, under the control of a spell, cast an imitation of a Gregorian choir to attack. When Stiyl destroys the spell's source, he finds Aureolus while Tōma runs into Aisa, who reveals that she came to Aureolus willingly because the Misawa Cram School is able to repel vampires, who are otherwise ordinary people. Aureolus had agreed to help her with her powers if she used her blood to lure vampires to the Misawa Cram School in order to save someone important to him. When Aureolus finds them, Aisa confronts him about his objectives and threatens to leave if he continues to kill people. However, Aureolus seals Tōma and Stiyl's memories, and the two awaken outside the school without any recollection of their mission until Tōma uses his Imagine Breaker to nullify the spell. Meanwhile, Index has followed Stiyl's mana trail to the school, but is put to sleep and captured by Aureolus. The remaining 13 Knights attack the school with a true version of a Gregorian choir, but it is restored by Aureolus's true power, Ars Magna. Tōma finds Sphinx outside with Index's habit and realizes that Index is now inside the school.

15 "Angel Fall (Angel Fall)""Otsukai Oroshi (Enzeru Fōru)" (御使堕し (エンゼルフォール)) January 15, 2009
Komoe sends Tōma, with Index tagging along, off to a beach resort until things calm down with the superiors of Academy City, due to his interference with the experiment. Tōma is anxious because his parents will be coming to see him for the first time since his memories were destroyed. Although relieved to see his father Tōya Kamijō, he is convinced that his cousin Otohime Tatsugami and his mother Shiina Kamijōrespectively resemble Mikoto and Index, as if were some sort of prank. Moreover, he becomes confused to see that the townspeople have been changed to familiar faces or just unmatched personalities, yet he seems to be the only one who notices the difference. Tōma later encounters a strange blonde girl, who then holds a saw to his neck, questioning if he is a spell caster. Luckily, Kaori and Tsuchimikado arrive to explain that Tōma is not responsible for a spell known as Angel Fall. The blonde girl, calling herself Misha Kruezhev, a magician from Annihilatus of the Russian Orthodox Church, along with the two, conclude that Tōma is unaffected since he is at the center of this spell, which has changed the appearance of everyone, but the spell will end if the ritual site is destroyed or if the spell caster is defeated. It is revealed that Tsuchimikado is a member of Necessarius working as a spy, much to Tōma's surprise.
16 "Father (Tōya Kamijō)""Chichioya (Kamijō Tōya)" (父亲 (かみじょうとうや)) January 22, 2009
Kaori, Tsuchimikado and Misha, all suggesting that the spell caster must be someone close to Tōma, join him at the beach resort at night to investigate the source of the spell. Tsuchimikado reveals he used to be an onmyōji before becoming an esper. It is explained that Tsuchimikado and Kaori were able to cast a spell against Angel Fall, but they remain affected, appearing to others as a famous pop singer named Hajime Hitotsui and Stiyl, respectively. Kaori was formerly a priestess of the Amakusa Church, a Japanese Catholic organization, and was a Saint with the gift of stigma, the ability to temporarily use holy powers. However, she left the organization due to her resenting both her fate as a priestess and the concept of luck and fortune. When Tōma later gives Misha some gum using his right hand, she hesitantly takes it, but somehow knowing more about Angel Fall firsthand. The next day, Misha insists on accompanying Shiina back to her new home, since she forgot to lock the door, but Tōma and Tsuchimikado decide to get there first due to suspicion. Upon inspecting the contents of the house, Tōma realizes that Tōya's appearance has not changed upon seeing his family photos. Racing back to the resort, Tōma confronts his father, deduced as the spell caster.
17 "Archangel (The Power of God)""Daitenshi (Kami no Chikara)" (大天使 (かみのちから)) January 29, 2009
It turns out that Tōya knows absolutely nothing about Angel Fall, but when Misha appears to them, she is revealed to be an impostor taking advantage of her appearance as Sasha Kruezhev, a member of Annihilatus. Misha subsequently unveils herself to be the Archangel Gabriel, the fallen angel who was cast down from Heaven by the spell, who now plans on destroying Tōma (believing him to be the caster) in order to grant her return. While Kaori holds Gabriel off, Tsuchimikado tells Tōma and Tōya that the ritual site is actually the family's new home, since Tōya accidentally cast the spell from coincidentally arranging occult souvenirs around the house in a Feng shui arrangement. Tsuchimikado plans to destroy Tōya, technically being the source of source of Angel Fall. However, when Tōma tries to stop Tsuchimikado, the latter beats up the former then knocks Tōya out. In a sudden twist, Tsuchimikado casts a spell to destroy the ritual site, despite knowing his life is at risk from using magic, which allows Gabriel to return to Heaven. Tōma returns to the hospital again, surprised to see Tsuchimikado alive and well, all thanks to his psychic healing ability, Auto Rebirth. Tsuchimikado is actually a freelancer for many organizations for espionage. Tōya and Shiina visit Tōma, who is outraged to learn that his family's new house was completely destroyed by Tsuchimikado's spell. However, Tōma must suffer Index's wrath for mistreating her while she was under the spell, appearing as Aogami the whole time.
18 "Impostor (Replica)""Nisemono (Repurika)" (伪者 (レプリカ)) February 5, 2009
Mikoto is being stalked by Mitsuki Unabara, the Tokiwadai Middle School principal's grandson, ever since the last week of summer vacation. When she sees Tōma passing by with his friends, she pretends to go on a date with Tōma. After an embarrassing mix-up with hot dogs, Tōma learns that less than ten of the Sisters remain at Academy City while the rest went overseas for treatment. Mikoto later goes to a restaurant to get food while Tōma converses with Unabara outside. Tōma sees an identical Unabara running into the restaurant, injured and warning Mikoto about an approaching danger, which means Tōma was talking to an impostor, who hits him from behind. As Tōma flees, Index reveals by phone that the impostor duplicated Unabara's appearance by using Aztecan sorcery, wielding an obsidian spearhead replicating the lance of Tlahuizcalpantecuhtli. When Tōma is forced to fight him at a construction site, the impostor reveals that his mission was to become close to Tōma's friends to prevent the formation of the Kamijō Forces, in which Tōma would ultimately lead a group of mages and espers who fear will destroy the truce between them. The impostor, who had fallen in love with Mikoto, decided to protect her by killing Tōma. However, after being defeated and severely injured by falling steel beams, the impostor asks Tōma to promise him to protect Mikoto since Tōma and his friends will continue to be targeted. Unknown to both of them, Mikoto is listening nearby and is embarrassed to hear Tōma's answer.

19 "The End (Last Order)""Uchidome (Rasuto Ōdā)" (打ち止め (ラストオーダー)) February 12, 2009
Since his defeat, Accelerator is no longer feared by others, though he remains powerful enough to get rid of troublemakers. During the last day of summer vacation, he is approached by a younger Misaka clone capable of showing emotions, who introduces herself as Misaka 20001, nicknamed Last Order, and begins to follow him around, much to his annoyance. Because she is hungry, Accelerator takes Last Order to a restaurant and sees Ao Amai, a former researcher for The Sisters Project, but does not pursue him. As Last Order eats, she converses with Accelerator on the Sisters and how she believes that Accelerator was an unwilling participant of Project Level 6 Shift. Tired of her comments, Accelerator leaves her at the restaurant to confront Kikyō Yoshikawa, a researcher in charge of Project Level 6 Shift. She informs him that Last Order was not created for The Sisters Project but for administrating the Misaka Network and that Amai injected a virus into Last Order, which could spread to the other Sisters and cause them to go berserk and attack humans. To stop the virus before activating by midnight, she gives Accelerator the choice of finding Amai to explain how to stop the virus or returning Last Order to her incubator, so Accelerator chooses the latter.
20 "Final Signal (Virus Code)""Saishū Shingō (Wirusu Kōdo)" (最终信号 (ウィルスコード)) February 19, 2009
Accelerator returns to the diner only to find that Last Order has been kidnapped by Amai. Accelerator manages to track down Amai and knocks him out before he can escape with Last Order. However, the virus in Last Order activates earlier than expected and Yoshikawa is still en route with Last Order's incubator. To stop the virus, Accelerator uses his powers and a clean copy of Last Order's data to remove the virus. However, nearing the end of the process, Amai awakens and shoots Accelerator in the head. Accelerator is unable to fully stop the bullet, having chosen to finish removing the virus instead of protecting himself, and collapses afterward. Amai tries to finish him off but is shot by Yoshikawa, who has arrived to put Last Order into her incubator. After discussing their roles as researchers and her dream of wanting to become a teacher, she and Amai shoot each other. When Yoshikawa awakens in the hospital, she learns from Heaven Canceller, who is none other than Tōma's frog-faced doctor, that Accelerator saved her but suffers from brain damage from the shot he took while saving Last Order and needs rehabilitation.
21 "Identity Unknown (Counter Stop)""Shōtai Fumei (Kauntā Sutoppu)" (正体不明 (カウンターストップ)) February 26, 2009
Tōma returns to school after summer break but is followed by Index, who thinks she will not have anything to eat for lunch while he is away at school. Arriving at school, he learns that Komoe is doing research on AIM (An Involuntary Movement), a diffusion field of power that espers emit. When Index arrives in class, Komoe sends her away and then introduces Aisa as the new transfer student. Instead of leaving, Index runs into another transfer student, Hyōka Kazakiri, and befriends her. When Tōma finds them later, Komoe catches Tōma skipping the opening ceremony and Hyōka mysteriously vanishes. Aisa becomes suspicious of Hyōka, recalling her as the top student at her old school but was never seen, and warns Tōma and Komoe about her. Meanwhile, Tsuchimikado meets with Aleister concerning the illegal arrival of a Necessarius mage named Sherry Cromwellin Academy City and, despite Tsuchimikado's offer to take care of Sherry discreetly to preserve the peace between Necessarius and Academy City, Aleister wants Tōma to defeat her, as his involvement will help the "key" to the Five-Element Agency. As Tōma, Index and Hyōka head to an underground mall for lunch, Kuroko finds Sherry and attacks her unsuccessfully when the latter summons a golem. Though Kuroko is saved by Mikoto, Sherry escapes and casts a spell to send eyeballs throughout the city.
22 "Statue (Golem)""Sekizō (Gōremu)" (石像 (ゴーレム)) March 5, 2009
Sherry begins her assault on Academy City to start a war between it and Necessarius. As a result, Tōma, Index and Hyōka are locked in the underground mall before they can be evacuated with everyone else. Mikoto and Kuroko find them and Kuroko then teleports Mikoto and Index away first. When Tōma hears an explosion, he goes to confront Sherry, who has defeated the Anti-Skills led by one of his school teachers, Aiho Yomikawa, and leaves Hyōka to wait for Kuroko to return. As he tries to fight Sherry's Golem Ellis, Hyōka arrives but her face is cracked, and Tōma ends up seeing a prism-like object in her head. When she flees, Sherry decides to pursue her, while Tōma gets a call from Komoe, who explains that Hyōka's is an artificial being created from the AIM diffusion fields. Meanwhile, Hyōka manages to regenerate her face, but Sherry, who knows Hyōka is not human, insults her by calling her a monster and is about to crush her, but Tōma appears and saves her.
23 "Hyōka Kazakiri (Friends)""Kazakiri Hyōka (Tomodachi)" (风斩氷华 (トモダチ)) March 12, 2009
Tōma stops and successfully destroys Sherry's golem with Imagine Breaker. When she summons another one, Tōma coordinates with the Anti-Skills to put her on the defensive. However, when Sherry suddenly decides to flee, Tōma realizes that her target is not Hyōka specifically but anyone valuable enough to trigger a war between Necessarius and Academy City, so Index is now Sherry's intended target. Hyōka, acknowledging how she came into being, chooses to save Index and escapes the underground mall without Tōma. Meanwhile, Index separates from Mikoto in order to pursue a runaway Sphinx and is attacked by Golem Ellis. Though Index is able to hold her own against Golem Ellis by interfering with its remote-controlled mechanism, the tables are turned against her when it is switched to automated control and she is about to be crushed until something unexpected happens.
24 "Imaginary Number School District - Five-Element Agency""Kyosū Gakku · Gogyō Kikan" (虚数学区・五行机関 (きょすうがっく ごぎょうきかん)) March 19, 2009
Tōma pursues Hyōka but encounters Sherry instead and is forced to fight her. He learns Sherry once had a friend named Ellis who was an esper involved in an experiment between Necessarius and Academy City twenty years ago to create the first esper-magician hybrid but suffered from the experiment and was killed by the Knights as the experiment was a violation of the truce between science and magic. To prevent this tragedy from occurring again, Sherry intends to divide both sides forever through conflict. Outraged that Sherry does not believe that people who are different like Index and Hyōka could be friends, Tōma successfully defeats Sherry. However, doing so results in Golem Ellis above ground losing control, and Index is cornered until Hyōka suddenly appears and destroys the golem each time it reforms. After Tōma arrives to deliver the finishing blow, Index and Hyōka reconcile, and Hyōka later fades away to the Imaginary Number School District. Meanwhile, Tsuchimikado confronts Aleister upon realizing the latter was behind the whole incident all this time to test the Imaginary Number School District and warns him that Tōma will be his enemy if he keeps using him. As each of the characters settle back into their daily lives, Stiyl meets with the Archbishop of Necessarius, Laura Stuart, who decides that Necessarius will need Index and Tōma's help for an upcoming problem as Kaori is missing in Japan after the events of Angel Fall.

A Certain Magical Index II (2010–2011)[edit]
No. Episode title Original air date on AT-X
1 (25) "August 31st (The Last Day)""Hachigatsu Sanjūichi-Nichi (Saigo no Hi)" (8月31日 (さいごのひ)) October 8, 2010
Tōma Kamijō is struggling to complete his summer homework at home, but Index is just being a distraction to him. While Tōma takes Index to a restaurant for a change of location, they are attacked by a magician named Ōma Yamisaka, who kidnaps Index and runs off. As Tōma tries to find her, running into Mikoto Misaka along the way, Ōma prepares a ceremony that will allow him to access the grimoires inside Index's head in order to find a cure for a curse inflicted on a woman he has fallen in love with. As the ceremony begins, Ōma's body and mind is put through excruciating pain trying to access the grimoires. Thanks to Index discreetly using her new cellphone, Tōma is able to find her and stop the ceremony. Tōma gets Ōma to snap out his depression and offers to cure the woman's curse using his Imagine Breaker. Meanwhile, Motoharu Tsuchimikado witnesses Kaori Kanzaki fighting and defeating the Knights of England in Japan before parting ways.
2 (26) "The Book of the Law""Hō no Sho" (法の书) October 15, 2010
Archbishop Laura Stuart informs Stiyl Magnus that The Book of the Law has been stolen and a skilled decoder named Orsola Aquinas has been kidnapped both by the Amakusa Catholics. She sends him, along with a group of Catholic battle nuns known as the Agnese Forces, to Japan to search for this grimoire as well as Orsola. In order to get Tōma's assistance, Stiyl pretends to kidnap Index. While Tōma coincidentally runs into Orsola on the way to save Index, the Amakusa Catholics appear and abduct her via a hole in the ground. After determining that the goal of the Amakusas Catholics is to use a special teleport magic to escape with Orsola before midnight, Tōma, Index, Stiyl and the Agnese Forces set up camp at the required location, where Tōma gets into a lot of awkward situations with the group's leader, Agnese Sanctis. Because Kaori was once an Amakusa Catholic, Stiyl knows he may have to fight her if necessary. Meanwhile, the Amakusa Catholics prepare to make their move.
3 (27) "The Amakusa Church""Amakusa-shiki" (天草式) October 22, 2010
The Agnese Forces face off against the Amakusa Catholics as a diversion while Tōma, Stiyl and Index sneak inside an amusement park. While escaping from some of the Amakusa Catholics, Tōma manages to find Orsola and gives her a crucifix necklace that Styil gave him earlier. The two are reunited with Stiyl and Index, who are facing against the leader of the Amakusa Catholics, Saiji Tatemiya. Working together, Tōma and Stiyl defeat Saiji and the rest of the Amakusa Catholics are captured by The Agnese Forces. However, the captured Saiji reveals to Tōma and Index that the Amakusa Catholics have never stolen The Book of the Law, as the real reason the Catholic Church wanted Orsola was to kill her to prevent the secrets of the grimoire from being abused. The Amakusa Catholics only got involved as Orsola sought them for protection but ran away as she did not trust them. Troubled by this revelation, Tōma asks Lucia and Angelene, two of the Catholic battle nuns, to see Orsola again but he accidentally angers Lucia, who tries to kill him, Index and Saiji. However, she and Angelene are forced to retreat when Index uses spell interception on Angelene's magic and counters Lucia's attack.
4 (28) "Voice of the Magicbane (Sheol Fear)""Mametsu no Koe (Sheōru Fia)" (魔灭の声 (シェオールフィア)) October 29, 2010
Stiyl explains that the Amakusa Catholics will not kill Orsola until they can prove her to be a heretic. As Saiji leaves to free his comrades, Stiyl tells Tōma and Index to go home, since they have no further stake in this matter. Tōma, however, goes by himself to where Orsola is being held and tortured by Agnese, who reveals that her battle nuns deceived Necessarius to assist them. He is later joined by Stiyl, who reveals the crucifix necklace Tōma gave to Orsola means she is under protection of the Church of England, followed by Index and the Amakusa Catholics. While Tōma is put in charge in protecting Orsola, the others fend off the battle nuns, with Index utilizing Sheol Fear, the power to deafen and paralyze some of the battle nuns. However, Lucia brings another force of battle nuns, who willingly stab their ears to protect themselves from Sheol Fear.
5 (29) "Lotus Wand""Hasu no Tsue (Rōtasu Wando)" (莲の杖 (ロータスワンド)) November 5, 2010
As Tōma, Index, Stiyl, Saiji and Orsola barricade themselves from the battle nuns, Tōma and Index come up with an idea that Orsola could help them decipher The Book of the Law in Index's head to their advantage. When Orsola mentions her deciphering method, Index reveals her translations would be false, revealing Orsola was never able to really decode the grimoire all along. While the others fend off against the battle nuns, Tōma confronts Agnese, who attacks him with her Lotus Wand. However, Tōma manages to learn its attack patterns and lands a hit on Agnese. As Agnese tries to bluff that Tōma sacrificed his friends as decoys, they arrive with Innocentius, who Stiyl managed to summon thanks to the Amakusa Catholics. With her confidence broken, Agnese is knocked out by Tōma, breaking the battle nuns' morale, before Tōma himself falls unconscious. Waking up in the hospital in Academy City, Tōma is greeted and taken care by Kaori, who thanks him for helping and tells him that Orsola and the Amakusa Catholics are now under the protection of the Church of England. Meanwhile, back in London, Laura reveals to Stiyl that the true reason she got involved with the Orsola incident was to get the Amakusa Catholics under her control and use them as leverage to ensure Kaori's loyalty to Necessarius.
6 (30) "Wreckage (Remnant)""Zangai (Remunanto)" (残骸 (レムナント)) November 12, 2010
Kuroko Shirai goes out shopping with Mikoto, only to be interrupted her partner, Kazari Uiharu, who reports about robbers stealing an aerospace travel case. Kuroko subdues the thieves but is then attacked and wounded by their leader, another teleporter named Awaki Musujime. She reveals to Kuroko about Tree Diagram's destruction and how various factions are gathering of its remnants, the contents of the travel case being one of them. Kuroko manages to escape, but becomes concerned over what Awaki had told her, particularly concerning how Mikoto had been trying to stop them for reasons she had kept from her, namely being that if Tree Diagram were rebuilt, the Level 6 Shift experiment would start over again. As Mikoto goes out that night to confront Awaki, Kuroko decides to follow her and overhears their conversation before Awaki escapes. As Kuroko decides to take matters into her own hands, Misaka 10032 decides to take action.
7 (31) "Coordinate Relocation (Move Point)""Zahyō Idō (Mūbu Pointo)" (座标移动 (ムーブポイント)) November 19, 2010
Kuroko finds Awaki at a nearby building and uses the latter's trauma of self-teleportion to make the first strike, but during their battle, Kuroko's injuries make her unable to concentrate on teleporting and she is trapped under a pile of furniture. Awaki explains to Kuroko that she and her organization, the Science Syndicate, plan to build a new Tree Diagram in order to create other species of espers. Believing that Kuroko wants to find the answer for having acquired her esper abilities, Awaki tries to persuade Kuroko to join her in the cause, but Kuroko rejects her offer, verbally abusing Awaki for making excuses for her own behavior. Kuroko breaks loose and tries to attack Awaki, only to be shot by her. After a brief traumatic loss of control over her powers, Awaki attempts to kill Kuroko by dropping the building on top of her, but she is saved by Mikoto and Tōma, who came to rescue her after he was alerted by Misaka 10032. As the Anti-Skills stop the Science Syndicate, Awaki tries to escape but is confronted by Accelerator, who uses the Misaka Network to utilize his powers in order to defeat her and destroy the Tree Diagram remnant. As everyone recovers, Mikoto gives her thanks to Kuroko.
8 (32) "The Daihasei Festival""Daihaseisai" (大覇星祭) November 26, 2010
Academy City is hosting the Daihaisei Festival, a sports competition between the various schools of the city, during which visitors from outside the city are allowed entry. While Tōma's parents, Tōya Kamijō and Shiina Kamijō, as well as Misuzu Misaka, assumed to be Mikoto's older sister, get to know each other, Tōma and Mikoto decide to make a bet in which the loser does anything the winner wants. Meanwhile, Laura contacts Aleister Crowley to inform him that magicians have infiltrated Academy City in order to make a transaction with a magical weapon called the Stab Sword, which has the power to kill a Saint. Meanwhile, Tōma has several troubles with a hungry Index and awkward situations with the class representative, Seiri Fukiyose. Later, Tōma runs into Stiyl and Tsuchimikado, who tell him about the intruding magicians and asks him not to get Index involved. While getting scolded by Seiri after an awkward incident with Index and Komoe Tsukuyomi, Tōma runs into a woman named Oriana Thomson. When his Imagine Breaker reacts to her, he realizes she is one of the magicians in question and starts to follow her.

15 (39) "Queen's Fleet""Joō Kantai" (女王舰队) January 21, 2011
Agnese explains they are on a fleet of magic ships called the Queen's Fleet, where she and her battle nuns are being punished. She agrees to let Tōma and Orsola escape in exchange for rescuing Lucia and Angelene, who are at risk of having their brains restructured to prevent them from casting a spell that would allow them to escape. As Agnese goes to the fleet's flagship to confront Bishop Biagio Busoni, the fleet's commander, Tōma and Orsola manage to find and rescue Lucia and Angelene, who say that Agnese is in danger of being used for a spell that would destroy her brain. Just then, the other ships start shooting at them, causing them to fall into the sea, but they are rescued by Index and the Amakusa Catholics using a magical submersible boat. After learning that the spell Biagio intends to use Agnese for has the power to destroy cities and erase their culture, the Amakusa Catholics agree to help Tōma rescue Agnese. They launch an attack on the fleet, where Tōma and his group face up against the battle nuns. But when the other ships try to sink the ship where both Tōma's group and the battle nuns are, Angelene gets injured saving one of the nuns.
16 (40) "Rosary of the Appointed Time""Kokugen no Rozario" (刻限のロザリオ) January 28, 2011
Lucia and the Amakusa Catholics hold off the battle nuns while Tōma, Index and Orsola continue onwards to the flagship. While Tōma distracts an army of ice golems, he soon encounters Biagio, who uses his magic enlarging crosses and gravity magic to defeat him. Meanwhile, Orsola manages to find Agnese, but is soon found by Biagio, who reveals he needs Agnese so he can use the Queen Fleet's powers to destroy Academy City. As Biagio subdues them, Tōma arrives and knocks him down. With his plans foiled, Biagio activates the Queen Fleet's self-destruction spell that will cause a large explosion. Tōma orders Orsola to escape with Agnese and the others while he fights Biagio one more time, finally defeating him and stopping the spell despite the flagship sinking. As Tōma wakes up in a hospital, he gets a call from Heaven Canceller who informs him that he is being flown back to Academy City and reminds him of Mikoto's bet for him. In London, after being informed of the recent events by Tsuchimikado, Kaori greets Orsola, who has returned with Agnese. Meanwhile in Vatican City, a nun with a pierced face from God's Right Seat forces the Pope to sign an order to investigate Tōma and eliminate him if he is seen as an enemy.
17 (41) "Penalty Game""Batsu Gēmu" (罚ゲーム) February 4, 2011
Autumn arrives at Academy City and the students change into their winter uniforms. Accelerator, Last Order and Kikyō Yoshikawa move out of the hospital into Aiho Yomikawa's apartment, while Misaka 10032 and three other Sisters begin rehabilitation in the city. Meanwhile as promised in their bet, Mikoto has Tōma do whatever she wants, dragging him to a mobile phone shop, which is offering a Gekota phone strap for those who take out a couples plan. However, in order to qualify for the offer, they have to take a photo of themselves as a loving couple, which is ruined when a jealous Kuroko intervenes. Elsewhere, Last Order gets herself locked out of the apartment, which leads to Misaka 10032 making fun of her situation. Last Order is jealous that she is the only Misaka clone which does not have goggles, so Last Order steals and run off with Misaka 10032's goggles, which she does not take too kindly.
18 (42) "Specimen Number (Serial Number)""Kentai Bangō (Shiriaru Nanbā)" (検体番号 (シリアルナンバー)) February 11, 2011
In London, the ladies of Necessarius have trouble learning how to use a new washing machine. Back at Academy City, Mikoto finally claims her phone straps, while Tōma encounters Misaka 10032, who is searching for Last Order, and buys her a necklace so he can distinguish her from Mikoto. As Mikoto rejoins them, Misaka 10032 starts teasing her and clinging onto Tōma, attracting the attention of Last Order before Misaka 10032 chases after her again. Elsewhere, Hyōka Kazakiri appears from the Imaginary Number School District and is apprehended by the Anti-Skills. Accelerator heads to the underground mall to look for Last Order and ends up encountering Index, who decides to help search for Last Order after he treats her to a meal. Meanwhile, Last Order approaches Tōma to thank him for stopping the Level 6 Shift experiment, mentioning how she hopes to protect Accelerator. Tōma and Last Order soon part ways and join up with Index and Accelerator respectively, though Tōma and Accelerator do not actually see each other, and start making their ways home.