Accelerator é abordado pelo clone de Misaka. Entretanto, vê Ao Amai, líder do projeto responsável pela criação das irmãs.

Accelerator captura Amai num centro de investigação e recupera o clone de Misaka, mas o vírus que existe nela é ativado antes do que era esperado.

Enquanto vai às compras com Mikoto, Kuroko recebe informações sobre uma mala que foi roubada e dirige-se, hesitante, aos escritórios do comité.

Kuroko persegue Musujime, uma jovem capaz de se teletransportar, e acaba por se ver em apuros. Musujime conta o seu plano a Kuroko.

Os colegas de Kamijo ficam gravemente feridos depois do ataque de Oriana. Kamijo persegue-a e acaba por perceber qual é o seu plano.

Accelerator e os companheiros saem do hospital e ficam com Yomikawa. Ao regressar da sua desastrosa viagem a Itália, Kamijo é contactado por Mikoto.

Orsola e o grupo não se conseguem entender com a nova máquina de lavar. Kamijo depara-se com uma sucessão de problemas ao ser conduzido por Mikoto.

Accelerator e Last Order festejam o seu reencontro quando são interrompidos pelos Hound Dogs. Uma figura suspeita chega a Academy City.

Accelerator encontra-se com Index e espera pelo melhor momento para contra-atacar. Depois de escaparem aos Hound Dogs, Last Order e Kamijo deparam-se com um novo inimigo.

À medida que os protestos contra Academy City se intensificam, Misaka embebeda-se e começa a "aterrorizar" os alunos. Quem será a sua primeira vítima?

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.