Kamijo meets Index, who is on the run from a magic society that wants the library of forbidden knowledge stored in her memory. Later, Kamijo is shocked to find Index at his house – bleeding and accompanied by a strange man.
Touma Kamijou is a student living in Academy City, a highly advanced place in terms of technology. Despite being gauged as a level zero esper (no powers), he possesses on his right hand the Imagine Breaker, an ability that negates any power whatsoever. Touma finds a young girl named Index who is trying to run away from Necessarius, a powerful magic organization that she is member of. Blessed with the skill of memorizing any sort of information, she holds 103,000 forbidden magical books within her head. As science and magic cross paths, Touma must face several dangers amid espers and magicians who appear in the exciting scientific town.
Kamijo meets Index, who is on the run from a magic society that wants the library of forbidden knowledge stored in her memory. Later, Kamijo is shocked to find Index at his house – bleeding and accompanied by a strange man.
Kamijo tangles with Stiyl, upset with the magician’s rough behavior toward Index. When quick thinking allows Kamijo and Index to escape, they head to the one person that might be able to help them.
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.
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.
Kamijo chases Sherry away only to discover the sorcerer now has designs on Index! Meanwhile, with her secret revealed, Kazakiri takes advantage of her new situation and sets out to fight Ellis.
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.
