The day arrives for Accelerator's bandages to come off after he is shot in the head, and Last Order is eager to celebrate. A secret weapon is stolen from an atmospheric research facility, and the culprits seem to be targeting Accelerator with it.

A high-school-age girl attempts suicide, but finds herself at the mercy of a fanatical group calling themselves "DA." When a young woman carrying a photo of Last Order is pursued through the hospital, Accelerator determines to find out why.

Esther leads Accelerator to the warehouse where she was once held, where they encounter a more advanced "coffin" controlled by Hishigata. Accelerator tries to learn more about DA. Esther reveals more about how her necromancy works.

Accelerator takes on the two DA members in the hospital morgue, and receives assistance from an unexpected source. When DA once again messes up a mission at the hospital, plans go into motion to have them removed from the operation.

As Accelerator is sidelined while his Misaka Network electrode recharges, Antiskill leads a raid on a supplement factory being used as a front for DA. Meanwhile, the members of Scavenger carry on their mission to eliminate DA.

Yomikawa attempts to defend Esther, Huotou, and the Sisters clone from Scavenger's attacks, and learns why they are so hostile to the city's teaching staff. Huotou fights back against Naru, with help from Esther, but will it be enough?

Having failed to obtain Last Order, Hishigata instead directs his efforts toward securing the kidnapped Sisters clone to gain the memories of their 10031 deaths to complete his formula. Esther begs Accelerator to take her under his wing.

Unable to discover the secret to reaching Level 6, Hishigata tries a new approach by recruiting Esther Rosenthal, a necromancer. Esther and Hishigata's sister, Hirumi, become fast friends, but Hirumi's secret may jeopardize that friendship.

As Hishigata's coffins are en route to his lab with the Sisters clone, Accelerator manages to throw a monkey wrench into their operation. Hishigata completes his formula, providing a boost to the coffins' abilities, which are turned on Accelerator.

While Hishigata continues to bleed out from his stab wound, Hirumi opens her eyes and seems to be her normal self. However, as her Level-6 transformation progresses, it becomes clear that not everything about Hirumi is as it appears.

Hirumi's body continues its horrific transformation, assimilating the facility and growing larger. Esther is confronted with the question of what she wants to do about her situation, and whether she can step up to become a hero.

Accelerator, Esther and the others finally arrive near Isaac's main body, and ready themselves for the final conflict. However, with the charge in Accelerator's electrode nearly spent, do they stand a chance of defeating Isaac and saving the city?