Set in Academy City, a city of scientifically advanced superhuman students, located to the west of Tokyo, in a world where magic is also real. Kamijou Touma's right hand, the Imagine Breaker, can negate all magic, psychic, or divine powers, but not his own bad luck. One day he finds a young girl, Index, hanging on his balcony railing. She turns out to be a nun from the Church of England, and her mind has been implanted with the Index Librorum Prohibitorum — all the magical texts the Church has removed from circulation. His encounter leads him to meet others from the secret world of science and magic and right into an adventure where science and magic collide.
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.
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.
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.
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.
During a trip the bathhouse, Komoe offers insight on the awakening of esper powers to Index and Himegami. Later, Mikoto is skeptical when Kamijo volunteers to take on Accelerator in battle.
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.
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.
Kamijo fights Accelerator to gain a better life for Mikoto and her clones. When the battle ends, Misaka 10032 visits Kamijo in the hospital to discuss the steps that must be taken for the clones to adapt to life in Academy City.
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, 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.
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!
Kamijo succeeds in eliminating the magical threat to Index’s life. Unfortunately, his memory is erased in the process! Later, Stiyl’s boss orders him to work with Kamijo. Their assignment: Find “Deep Blood.”
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.
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?
Aureolus finds his plan to turn Index into a vampire thwarted and learns that Kamijo has already saved Index’s memory. Overwhelmed by anger and jealousy, the alchemist attacks Kamijo in a fit of murderous rage.
Kamijo senses something odd about the relationship shared by Mikoto and Misaka, who appears to be Mikoto’s twin. Later, after a friendly meeting with Kamijo, Misaka has a much more intense encounter with Accelerator.
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.
Kamijo learns that thousands of Mikoto clones were created for one simple, violent reason. Now that her look-alikes are dying off, the real Mikoto vows to save the rest of her doppelgangers by making the ultimate sacrifice.
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.
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.
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.
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!
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.
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?
Kaori Kanzaki confronts Kamijo, demanding that he hand over Index. Kamijo is wounded in the ensuing scuffle – and when he wakes up a few days later, Index offers to take drastic measures to protect him from further harm.
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