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.

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.

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.