Tōma Kamijō is chased by hooligans after he stops one of them from disturbing a girl. In reality he was trying save him 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 refuse citing he just a Level 0 psychic. Nevertheless, she "shoots" an electrical bolt at him but it is stop by Tōma right hand which has a power called Imagine Breaker. 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 chase by magicians for she "possess" 103,000 grimoires. After both of them explain each other 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 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 and 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 refuse 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. Toma, angered by Stiyl's ill treatment of Index attacks him and he counterattack by using Fire magic but is surprised when Toma nullify s the spell. Styil then summons a fire creature named Innocentius which Toma can't stop as the creature keeps regenerating itself from his attacks. It is only when Index other personality, John's pen mode, reveals the creatures powers comes from Runes place around the building that Toma is able improvise and defeat Innocentius and Stiyl using the sprinklers to destroy the Runes as they were on paper and rescue Index.

While Komoe helps Index in healing her wounds using magic, Toma meets Stiyl's partner, Kaori Kanzaki and learns from her why they are hunting Index and the organization, Necessarius, The Church of Necessary Evil.

Touma learns the truth about Index's perfect memorization and her loss of memories.

Touma tries desperately to save Index's memories before it is too late.

Following the events of last episode and the activation of Index's defense mechanism Touma struggles to hide his amnesia from Index.

Stiyl and Touma join forces to investigate the mysterious Misawa Cram School.

Touma encounters Ars Magna the leader of Misawa Cram School and a man with his own connection to Index.

Touma confronts Ars Magna in a dangerous battle to rescue both Index and Deep Blood.

Touma spends some time with Misaka Mikoto and makes a strange discovery.

Touma goes in search of Misaka to investigate the clone experiment.

Touma discovers the reason behind the experiment and appears to grow closer to Misaka.

Misaka and Touma hatch a plan to defeat Accelerator and end the experiment.

Touma faces off against Accelerator for the sake of Misaka and her 'sisters'.

Touma and Index head to the beach to avoid the fallout from Touma's fight with Accelerator. They also plan to meet Touma's Family but when they arrive they aren't quite what Touma was expecting.

The Angel Fall spell remains in effect with only Toma, Kanzaki, Misha and Tsuchimikado relatively unaffected. However, the person responsible for casting the spell remains a mystery. Misha quickly becomes the prime suspect after a strange conversation with Toma. But when Toma follows up on his hunch he discovers that the real culprit is not Misha but his own father. As such he hurries to reach his father before Misha and the other mages can confront him.

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After figuring out the truth of Misha’s real identity, Kanzaki sends Kamijo and Toya to destroy the ritual spot. When Tsuchimikado suggests that Toya must die for the spell to end, a violent – and seemingly fatal – encounter ensues.

In order to shake off the unwanted attention she’s getting from Unabara, Misaka asks Kamijo to pretend to be her boyfriend. Things get complicated when the faux-couple discovers that Unabara is hiding a magical secret.

Accelerator meets the last of Misaka’s clones – Last Order – who explains the special role she played in the Sister experiment. Later, Accelerator learns what steps he’ll have to take to keep Last Order safe.

After Accelerator frees Last Order of the virus infecting her brain, he’s attacked by gun-wielding Amai. Just as all appears lost for Accelerator, Yoshikawa arrives to help – but Amai isn’t going down without a fight.

School’s back in session and that means new transfer students – one of which is Index! In class, Komoe offers more insight into the realities of life as an esper – and a powerful new magical presence is detected in Academy City.

Panic ensues in Academy City upon the arrival of the sorcerer Sherry Cromwell, who makes no secret of her plans to destroy Kazakiri! Kamijo steps up to ruin Sherry’s plot – but the situation is more complex than he knows.

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. Sherry attempts a simultaneous summoning of Ellis, destroying the ground beneath her and escaping. Wondering why Sherry would turn to escape so quickly when her target, Hyōka, was right in front of her causes Tōma to realize that her true target was Index all along. Chasing after a runaway Sphinx, Index is attacked by Ellis. At first she is able to hold her own against the remote controlled Ellis by interfering with the control mechanism, when Ellis switches to automated control things turn worse. Index can only call Tōma's name as Ellis prepares to crush her.

Kamijo, Index and Kazakiri join forces to take on Ellis. When the battle ends, and with the support of Index, Kazakiri returns to the place of her origin. Later, Tsuchimikado ponders Aleister’s role in recent events.

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As summer ends, Toma desperately tries to catch up on homework—but that’s totally out of the question once a magician named Yamisaka kidnaps Index. As Toma tries to rescue his friend, he finds there may be more to her captor’s motives than just malice.

The Book of Law is an encrypted grimoire that only one nun has the skills to decipher—and it’s gone missing! If its magic is ever used, it will bring about all sorts of ruin. Now, the church just has to keep the gifted nun safe. How hard can that be?

The battle over Orsola, the only nun who can read the Book of Law, continues as Toma is forced to act as an unwitting decoy. The Amakusa clash with church representatives, but the real culprit behind the plot might not be who Toma expected.

With Orsola taken hostage, Toma and his gang take the battle to the church. There, Index unleashes a mighty spell. Things look bleak for the Roman Orthodox, but their willingness to sacrifice themselves might just give them the upper hand.

The Roman Orthodox nuns continue their attack as Orsola risks everything to have Index decipher the Book of Law. The infamous grimoire could help them finally defeat their enemies—but that’s only if it works like it's supposed to.

A high-tech suitcase is stolen from couriers, and Kuroko is on the job! But the contents of the package may prove to be more dangerous than any robbers or petty crooks. Also, what is up with all the strange weather in Academy City?

Mikoto’s clones use their telepathic network to enlist Misaka 10032 to aid them in stopping Musujime from rebuilding the Tree Diagram in an effort to find out why humans are the only beings with esper powers.

It’s the Daihasei Festival, and everyone’s parents are in town! As Toma and Mikoto compete against each other in various events, a Roman Orthodox magician and her assistant negotiate to purchase a powerful relic from the English Puritan Church.

As Toma and his group try to track down Oriana, they discover that a “Shorthand”—a specialized spell that operates on its own once being cast—is shorting out their magic. But before they can deactivate it, an incident happens at the middle school.

With the Shorthand cancelled, Stiyl uses his magic to locate Oriana, causing a fight to erupt. In London, Laura learns that Oriana’s deal might not be for the Stab Sword, but for something else entirely.

Tsuchimikado’s location spell backfires and leads Oriana straight to him, resulting an epic showdown. But he’s not the only one exposed to Oriana’s magic: Himegami feels the force of the spell caster’s power, and may not survive.

Toma and Tsuchimikado investigate the history of a sacred artifact as they try to figure out what Oriana’s plan is. When they discover they have only until nightfall to stop her from enacting an evil plot, the battle for the future of Academy City begins!

As Toma and the others come close to beating Oriana, the motivations behind her actions are finally revealed. But taking out Oriana might not be enough to stop her plot from reaching a catastrophic completion!

After winning a trip to Italy, Toma and Index run across a few old acquaintances. But wherever these two go, disaster is sure to follow—this time in the form of assassins!

Agnese makes a deal with Toma and Orsola that guarantees their safe escape from the Roman Orthodox ship—so long as they take Sisters Angelene and Lucia with them. As they search for the nuns, they uncover more about the ship’s terrible true purpose.

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Toma goes head-to-head with Bishop Biagio during an attempt to rescue Agnese. As the battle rages, the Queen of the Adriatic Sea is revealed to be a ship that can completely destroy Academy City.

Mikoto convinces Toma to sign up for a couples cell phone contract with her so she can get an adorable promotional item—but how far are the two willing to take the ruse before they get, well, maybe a little too close.

Laura is confronted with a confidential memo during her bath time, Toma buys Mikasa 10032 a piece of jewelry, and many old enemies come together in the search for Last Order.

Accelerator attempts to make amends for his past by doing a few good deeds, but ends up attacked by a group led by someone from his past. Meanwhile, Toma discovers strange goings-ons in the police force and overhears talk of an intruder in Academy City.

Accelerator manages to escape from Kihara, taking Index with him. Elsewhere, Toma and Last Order are on the run from Hound Dog—but the real threat to their lives may come from Vento.

When Accelerator deduces who is pulling all the strings in Academy City, no person—or building—is safe from his rage. Meanwhile, Toma goes on a mad dash through the city looking for Last Order, but what he finds is an angel.

In order to save Last Order, will Accelerator sacrifice himself? Vento’s past is revealed, Toma delivers a very Toma speech, and Index sings a song as the battle rages on in Academy City.

Accelerator is injured, but even in that state he’s approached by a city-employed organization that wants to recruit him. As rumors of an impending war spread throughout Academy City, the students in Toma’s class decide to throw a party.

GROUP continues to order Accelerator around by giving him an assignment to kill Misuzu—which leads to Accelerator protecting the woman just to spite the organization when Skill Out attacks.

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Since the September 30 attack on Academy City by The Right Seat of God's Vento of the Front, tensions grows between the Catholic Church and Academy City, with the latter's tightening their security. Tōma has an unlucky day where he gets bitten by a hungry Index, hit by a ball on the head by Seiri, accidentally sees his teacher Suama Oyafune removing her skirt and gets attacked by Mikoto after the latter discovers a selfie of him and her mother Misuzu in his phone. As he heads home, Tōma is forced to follow an old woman named Monaka Oyafune, Suama's mother, to an empty park. Monaka reveals to Tōma that she is one of Academy City's Board of Directors and fears the upcoming war and wants him to investigate whether the recent world wide protest against Academy City are really the work of the Catholic Church. Tsuchimikado appears and shoots Monaka, which the latter explains she ordered the former to shoot her to protect her family and satisfy the rest of the Pro-War Board of Directors for talking with Tōma behind their backs. Agreeing to work with her, Tōma follows Tsuchimikado as they head to Avignon, France via a supersonic jet.

Tōma is parachuted into a river and almost drowns but is saved by Itsuwa of the Amakusa Catholics. He explains to Itsuwa that he and Tsuchimikado are trying to find Constantine's Document, also known as the C Document, a magical item that was long ago given by Emperor Constantine to the Pope which allowed whatever the user believes, the people living on Papal Lands also believed it, which Tsuchimikado believes is responsible for the world wide anti-Academy City protest. Bringing him to a cafe, Itsuwa explains the C Document is in Avignon and not in Rome due to the events of the Avignon Papacy and the city's ley lines allows the document to spreads it's magic throughout Europe. However, Tōma and Itsuwa are forced to abandon the cafe after rioters reazlies Tōma is from Academy City. Meanwhile in London, Stiyl and Agnese interrogate Lidvia and Biagio over information on who God's Right Seat are and their goals which Lidvia reveals they are four special individuals who sacrificed their ability to use normal magic in exchange for divine powers so they can rid themselves of Original Sin and become closer with God. As they avoid the rioters, Tōma and Itsuwa gets a call from Tsuchimikado that they need to find one of the city's ley lines so Tōma's Imagine Breaker can destroy the effects of the C Document. Just before Tōma and Itsuwa disrupts one of the site of the ley lines, they are attacked by God's Right Seat, Terra of the Left.

Tsuchimikado appears and joins forces with Tōma and Itsuwa against Terra, who flees when a platoon of powered suits sent by Academy City interfere with their fight. Tsuchimikado then stays behind to stop the suits while Tōma and Itsuwa chase after Terra at the Palais des Papes. Once there, Tōma contacts Mikoto by phone and learns from her that according to the media, Academy City launched an attack on Avignon in retaliation against a plan to attack it, but their conversation is cut short when Terra, having the C Document in his hands, attacks him. During their fight, Terra realizes that Tōma still has not attained the full power of Imagine Breaker because he lost his memory, but nevertheless, Tōma takes advantage of a weakness in Terra's abilities to defeat him and destroy the C Document. Just as Tōma is about to inquire Terra about what he knows about Imagine Breaker, a squad of stealth bombers led by Accelerator attack the palace, allowing Terra to escape. However, at St. Peter's Basilica, Terra is killed for involving civilians in the conflict by Acqua of the Back who decides to take the war against Academy City personally after Terra and Vento's failures.

Team GROUP captures a blackmarketter for questioning who is later killed by an esper wearing a steel helmet. Etzali investigates the blackmarketter's home but a black ops team arrives. Etzali disguises himself as one of the operators but not before leaving some clues to his team. GROUP learns the blackmarketter sold a weapon to a sniper named Sunazara whose target is Monaka and Accelerator stops the assassination attempt after Awaki teleport him to Monaka's location. GROUP soon learns the assassination attempt was a distraction for another darkside team named SCHOOL, lead by the 2nd Level 5, Teitoku Kakine, and their real target was the particle engineering laboratory. To further complicate matters, the other teams like MEMBER, BLOCK and ITEM are getting involved as well. Meanwhile, the former Skill-Out Shiage is now working with Team ITEM, led by the 4th Level 5, Shizuri Mugino and her teammates, Rikō Takitsubo, Saiai Kinuhata and Frenda Seivelun, who treat Shiage with no respect. Learning about Monaka's assassination attempt, ITEM reazlies SCHOOL's real goal and heads to the particle engineering laboratory only to fight with the steel helmet esper. Despite killing the esper, Teitoku escapes with the device he stole, forcing ITEM to split up while Shiage runs away from SCHOOL's Pink dressed Assassin. Elsewhere, GROUP learns Team BLOCK is planning to steal Biological weapons from the city's virus vault but Etzali reveals the vault is a decoy as their real target is Satellite control center which controls the Hikoboshi 2 orbital laser weapon in space. Accelerator heads to the Satellite control center alone to fool BLOCK that they are falling for their trick.

While Kazari takes a lost Last Order home, Accelerator arrives at his location and faces Saraku, a teleporter of MEMBER and defeats him after realizing Saraku can only teleport behind his opponents. Elsewhere, MEMBER's leader "The Professor" confronts Teitoku only to be killed by the latter after using his power, Dark Matter. Meanwhile, BLOCK starts their real goal, to shut down the city's surveillance system and help 5000 mercenaries invade the city. However, one of their members is actually Etzali in disguise, who alerts the city's drone helicopters to head to their location and stop the mercenaries. Despite their heavy loses, the remaining BLOCK members, Saku Tatsuhiko and Megumi Teshio, continues their next part of the plan, bringing the mercenaries to Academy City's detention facility and kidnap Awaki's gang to use as leverage to make her help them enter the Windowless building and kill Aleister. GROUP heads to the detention facility where Accelerator stays back to hold off the remaining mercenaries while Etzali faces off against Xochitl, a MEMBER agent and his colleague from the Aztec organization who has come to Academy City to kill Etzali for treason. Tsuchimikado and Awaki confronts Saku and Megumi trying to free Awaki's gang but Megumi kills Saku for endangering the hostages and decides to forcefully get the information from Awaki instead. Despite Megumi knocking out Tsuchimikado, Awaki is able to defeat Megumi after getting over her trauma of teleporting herself. With the hostages safe and Etzali saving Xochitl's life from the grimoire she was using, GROUP heads back home. However, Teitoku arrives at ITEM's apartment after torturing Frenda for information.

While Hamazura is out running errands for Mugino, SCHOOL stages an attack on ITEM. When Mugino runs from Kakine, Takitsubo offers to protect Hamazura, but ends up needing his help instead. Kakine issues a challenge to Accelerator.

Itsuwa reveals to Tōma she has come to Academy City as his bodyguard to protect him from Acqua, who is now targeting him for ruining God's Right Seat plans. While Itsuwa's Amakusa comrades watch from afar and plan to have she and Touma to get close and be a couple, Mikoto is still dealing with the revelation of Tōma's amnesia. Tōma brings Itsuwa to his home, where Index accidentally destroys the bathroom, which Itsuwa decides to bring Tōma and Index to a spa located in 22th District's underground city. After an awkward meeting between Itsuwa, Index and Mikoto in the spa, Tōma and Itsuwa takes a walk at a park. However, Acqua appears, having defeated the rest of the Amakusas, demands Tōma hand over his right arm which contains Imagine Breaker. Tōma and Itsuwa tries to fight back but are unable to hit him due to Acqua's Saint powers. After beating Tōma to a pulp, Acqua gives him one more day before he gets his right arm while Itsuwa feels guilty for failing her mission.

With Kamijo unconscious, Itsuwa is guilt-ridden, and receives a pep talk from Tatemiya. As Orsola researches Acqua's past, the Amakusa Church members make their stand against Acqua, at which Itsuwa reveals their new secret weapon.

Kanzaki battles Acqua under Academy City, but finds herself overpowered by his might. Mikoto runs into Kamijo after he sneaks out of his hospital room. Kanzaki works with the Amakusa Church members to find a way to beat Acqua.

Itsuwa and Kanzaki both up the ante in their pursuit of Kamijo. Index and Kamijo are summoned to Britain to deal with a magic issue, but while en route, their jet falls victim to a terrorist plot that threatens the lives of everyone aboard.

After being escorted to London, Kamijo and Index have an audience with the queen and three princesses to discuss the threats facing Britain. Upon dividing into separate teams, Kamijo assists with tracking down the members of New Light.

As the coup continues, even the sisters of the puritan church are targeted, while the queen and princesses find their lives in danger. Index analyzes the evidence of the Eurotunnel blast. Knight Leader is confronted by a former colleague.

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Acqua and Knight Leader continue their fateful showdown in the forest. Princess Carissa reveals a devastating new technique using Curtana Original. When Kamijo and Index's lives are endangered, an unexpected ally comes to their rescue.

Kamijo, Kanzaki, Index, and Vilian head toward Buckingham Palace to stop Carissa. The palace is bombarded from the floating fortress Coven Compass, and others join the battle when Carissa calls in her own cruise missile strike.

Accelerator and the other members of GROUP are assigned to eliminate the members of Spark Signal, a terrorist group which has taken hostages. Hamazura and Kinuhata find themselves on the run when they defy the city's higher-ups.

Hamazura desperately tries to rescue Takitsubo when the building she is in falls under terrorist attack. Stephanie hunts down Kinuhata to exact revenge for Sunazara. Accelerator seeks out assistance from an unlikely benefactor.

Técpatl and Unabara square off in Shiokishi's chambers, while Accelerator and Sugitani face each other in the hallway outside. Kinuhata discovers the true reason for the current assault against herself, Takitsubo, and Hamazura.

Tensions escalate as Russia threatens military action against Academy City, while French sorcerers storm the English Channel. Kamijo and Lessar's search for Sasha Kruezhev leads them to the Elizalina Alliance of Independent Nations.

After dealing with the sorcerers at the Russian airbase, Accelerator has a Misaka clone skydive down to confront him. Vento challenges Fiamma while Kamijo and the others watch on. Hamazura gets some disturbing news from Digurv.

Kamijo begins second-guessing himself after Fiamma's rebuke. Hamazura fights to protect the village from privateers. The fighting between Britain and France ramps up. Accelerator lashes out at Kamijo over Last Order's condition.

Accelerator begins finding clues about the parchment he is carrying. Hamazura and Digurv find an unexpected ally in Acqua. Takitsubo receives some welcome news from Elizalina. Kamijo and Lessar attempt to infiltrate Fiamma's base.

Kamijo runs into Sasha Kruezhev, and he continues to formulate a plan to stop Fiamma. Hamazura and Takitsubo discover an imminent threat to Digurv's village. The archangel Gabriel rains havoc upon the Russian and Academy City forces.

As Kamijo and Sasha look on, Hyoka rushes in to stop the archangel's rampage. Accelerator joins the battle as well, with a newfound purpose. Acqua has his own strategy to weaken the archangel's power, though at great cost to himself.

Kazakiri advises Accelerator about the song Index once sang to treat Last Order. Hamazura has a surprise encounter. Lessar offers a proposition to Sasha. The long-awaited showdown between Kamijo and Fiamma takes a drastic turn.

Hamazura must defend the members of ITEM against a new threat from Academy City. Accelerator acquires the final piece of the puzzle to a cure for Last Order. The showdown between Fiamma and Kamijo becomes even more intense.

An overjoyed Accelerator gains a new perspective on the world. The duel between Kamijo and Fiamma concludes, and the doomed Star of B'Tselem begins its crash landing. The ITEM members are tracked down by an old acquaintance.

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