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.

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?

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.

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.

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

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!

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.

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.

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.

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.

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!

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

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.

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.

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.

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.

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 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?

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.