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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