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.

Tōma is parachuted into a river and almost drowns but is saved by Itsuwa of the Amakusa Catholics. He explains to Itsuwa that he and Tsuchimikado are trying to find Constantine's Document, also known as the C Document, a magical item that was long ago given by Emperor Constantine to the Pope which allowed whatever the user believes, the people living on Papal Lands also believed it, which Tsuchimikado believes is responsible for the world wide anti-Academy City protest. Bringing him to a cafe, Itsuwa explains the C Document is in Avignon and not in Rome due to the events of the Avignon Papacy and the city's ley lines allows the document to spreads it's magic throughout Europe. However, Tōma and Itsuwa are forced to abandon the cafe after rioters reazlies Tōma is from Academy City. Meanwhile in London, Stiyl and Agnese interrogate Lidvia and Biagio over information on who God's Right Seat are and their goals which Lidvia reveals they are four special individuals who sacrificed their ability to use normal magic in exchange for divine powers so they can rid themselves of Original Sin and become closer with God. As they avoid the rioters, Tōma and Itsuwa gets a call from Tsuchimikado that they need to find one of the city's ley lines so Tōma's Imagine Breaker can destroy the effects of the C Document. Just before Tōma and Itsuwa disrupts one of the site of the ley lines, they are attacked by God's Right Seat, Terra of the Left.

Tsuchimikado appears and joins forces with Tōma and Itsuwa against Terra, who flees when a platoon of powered suits sent by Academy City interfere with their fight. Tsuchimikado then stays behind to stop the suits while Tōma and Itsuwa chase after Terra at the Palais des Papes. Once there, Tōma contacts Mikoto by phone and learns from her that according to the media, Academy City launched an attack on Avignon in retaliation against a plan to attack it, but their conversation is cut short when Terra, having the C Document in his hands, attacks him. During their fight, Terra realizes that Tōma still has not attained the full power of Imagine Breaker because he lost his memory, but nevertheless, Tōma takes advantage of a weakness in Terra's abilities to defeat him and destroy the C Document. Just as Tōma is about to inquire Terra about what he knows about Imagine Breaker, a squad of stealth bombers led by Accelerator attack the palace, allowing Terra to escape. However, at St. Peter's Basilica, Terra is killed for involving civilians in the conflict by Acqua of the Back who decides to take the war against Academy City personally after Terra and Vento's failures.

Team GROUP captures a blackmarketter for questioning who is later killed by an esper wearing a steel helmet. Etzali investigates the blackmarketter's home but a black ops team arrives. Etzali disguises himself as one of the operators but not before leaving some clues to his team. GROUP learns the blackmarketter sold a weapon to a sniper named Sunazara whose target is Monaka and Accelerator stops the assassination attempt after Awaki teleport him to Monaka's location. GROUP soon learns the assassination attempt was a distraction for another darkside team named SCHOOL, lead by the 2nd Level 5, Teitoku Kakine, and their real target was the particle engineering laboratory. To further complicate matters, the other teams like MEMBER, BLOCK and ITEM are getting involved as well. Meanwhile, the former Skill-Out Shiage is now working with Team ITEM, led by the 4th Level 5, Shizuri Mugino and her teammates, Rikō Takitsubo, Saiai Kinuhata and Frenda Seivelun, who treat Shiage with no respect. Learning about Monaka's assassination attempt, ITEM reazlies SCHOOL's real goal and heads to the particle engineering laboratory only to fight with the steel helmet esper. Despite killing the esper, Teitoku escapes with the device he stole, forcing ITEM to split up while Shiage runs away from SCHOOL's Pink dressed Assassin. Elsewhere, GROUP learns Team BLOCK is planning to steal Biological weapons from the city's virus vault but Etzali reveals the vault is a decoy as their real target is Satellite control center which controls the Hikoboshi 2 orbital laser weapon in space. Accelerator heads to the Satellite control center alone to fool BLOCK that they are falling for their trick.

While Kazari takes a lost Last Order home, Accelerator arrives at his location and faces Saraku, a teleporter of MEMBER and defeats him after realizing Saraku can only teleport behind his opponents. Elsewhere, MEMBER's leader "The Professor" confronts Teitoku only to be killed by the latter after using his power, Dark Matter. Meanwhile, BLOCK starts their real goal, to shut down the city's surveillance system and help 5000 mercenaries invade the city. However, one of their members is actually Etzali in disguise, who alerts the city's drone helicopters to head to their location and stop the mercenaries. Despite their heavy loses, the remaining BLOCK members, Saku Tatsuhiko and Megumi Teshio, continues their next part of the plan, bringing the mercenaries to Academy City's detention facility and kidnap Awaki's gang to use as leverage to make her help them enter the Windowless building and kill Aleister. GROUP heads to the detention facility where Accelerator stays back to hold off the remaining mercenaries while Etzali faces off against Xochitl, a MEMBER agent and his colleague from the Aztec organization who has come to Academy City to kill Etzali for treason. Tsuchimikado and Awaki confronts Saku and Megumi trying to free Awaki's gang but Megumi kills Saku for endangering the hostages and decides to forcefully get the information from Awaki instead. Despite Megumi knocking out Tsuchimikado, Awaki is able to defeat Megumi after getting over her trauma of teleporting herself. With the hostages safe and Etzali saving Xochitl's life from the grimoire she was using, GROUP heads back home. However, Teitoku arrives at ITEM's apartment after torturing Frenda for information.

While Hamazura is out running errands for Mugino, SCHOOL stages an attack on ITEM. When Mugino runs from Kakine, Takitsubo offers to protect Hamazura, but ends up needing his help instead. Kakine issues a challenge to Accelerator.

Itsuwa reveals to Tōma she has come to Academy City as his bodyguard to protect him from Acqua, who is now targeting him for ruining God's Right Seat plans. While Itsuwa's Amakusa comrades watch from afar and plan to have she and Touma to get close and be a couple, Mikoto is still dealing with the revelation of Tōma's amnesia. Tōma brings Itsuwa to his home, where Index accidentally destroys the bathroom, which Itsuwa decides to bring Tōma and Index to a spa located in 22th District's underground city. After an awkward meeting between Itsuwa, Index and Mikoto in the spa, Tōma and Itsuwa takes a walk at a park. However, Acqua appears, having defeated the rest of the Amakusas, demands Tōma hand over his right arm which contains Imagine Breaker. Tōma and Itsuwa tries to fight back but are unable to hit him due to Acqua's Saint powers. After beating Tōma to a pulp, Acqua gives him one more day before he gets his right arm while Itsuwa feels guilty for failing her mission.

With Kamijo unconscious, Itsuwa is guilt-ridden, and receives a pep talk from Tatemiya. As Orsola researches Acqua's past, the Amakusa Church members make their stand against Acqua, at which Itsuwa reveals their new secret weapon.

Kanzaki battles Acqua under Academy City, but finds herself overpowered by his might. Mikoto runs into Kamijo after he sneaks out of his hospital room. Kanzaki works with the Amakusa Church members to find a way to beat Acqua.

Itsuwa and Kanzaki both up the ante in their pursuit of Kamijo. Index and Kamijo are summoned to Britain to deal with a magic issue, but while en route, their jet falls victim to a terrorist plot that threatens the lives of everyone aboard.

After being escorted to London, Kamijo and Index have an audience with the queen and three princesses to discuss the threats facing Britain. Upon dividing into separate teams, Kamijo assists with tracking down the members of New Light.

As the coup continues, even the sisters of the puritan church are targeted, while the queen and princesses find their lives in danger. Index analyzes the evidence of the Eurotunnel blast. Knight Leader is confronted by a former colleague.

Acqua and Knight Leader continue their fateful showdown in the forest. Princess Carissa reveals a devastating new technique using Curtana Original. When Kamijo and Index's lives are endangered, an unexpected ally comes to their rescue.

Kamijo, Kanzaki, Index, and Vilian head toward Buckingham Palace to stop Carissa. The palace is bombarded from the floating fortress Coven Compass, and others join the battle when Carissa calls in her own cruise missile strike.

Accelerator and the other members of GROUP are assigned to eliminate the members of Spark Signal, a terrorist group which has taken hostages. Hamazura and Kinuhata find themselves on the run when they defy the city's higher-ups.

Hamazura desperately tries to rescue Takitsubo when the building she is in falls under terrorist attack. Stephanie hunts down Kinuhata to exact revenge for Sunazara. Accelerator seeks out assistance from an unlikely benefactor.

Técpatl and Unabara square off in Shiokishi's chambers, while Accelerator and Sugitani face each other in the hallway outside. Kinuhata discovers the true reason for the current assault against herself, Takitsubo, and Hamazura.

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.

After dealing with the sorcerers at the Russian airbase, Accelerator has a Misaka clone skydive down to confront him. Vento challenges Fiamma while Kamijo and the others watch on. Hamazura gets some disturbing news from Digurv.

Kamijo begins second-guessing himself after Fiamma's rebuke. Hamazura fights to protect the village from privateers. The fighting between Britain and France ramps up. Accelerator lashes out at Kamijo over Last Order's condition.

Accelerator begins finding clues about the parchment he is carrying. Hamazura and Digurv find an unexpected ally in Acqua. Takitsubo receives some welcome news from Elizalina. Kamijo and Lessar attempt to infiltrate Fiamma's base.

Kamijo runs into Sasha Kruezhev, and he continues to formulate a plan to stop Fiamma. Hamazura and Takitsubo discover an imminent threat to Digurv's village. The archangel Gabriel rains havoc upon the Russian and Academy City forces.

As Kamijo and Sasha look on, Hyoka rushes in to stop the archangel's rampage. Accelerator joins the battle as well, with a newfound purpose. Acqua has his own strategy to weaken the archangel's power, though at great cost to himself.

Kazakiri advises Accelerator about the song Index once sang to treat Last Order. Hamazura has a surprise encounter. Lessar offers a proposition to Sasha. The long-awaited showdown between Kamijo and Fiamma takes a drastic turn.

Hamazura must defend the members of ITEM against a new threat from Academy City. Accelerator acquires the final piece of the puzzle to a cure for Last Order. The showdown between Fiamma and Kamijo becomes even more intense.

An overjoyed Accelerator gains a new perspective on the world. The duel between Kamijo and Fiamma concludes, and the doomed Star of B'Tselem begins its crash landing. The ITEM members are tracked down by an old acquaintance.