Misaka’s electro-manipulation abilities – and delightfully destructive Railgun projectile move – make her a rock star in Academy City. The techno-metropolis is packed with supernaturally powered students known as espers, including Misaka’s flirty friend and roommate, Kuroko. She uses her teleportation skills as a member of the Judgment law enforcement team, fighting crime alongside her fellow agent Uiharu. Joined by their friend Saten, a spunky Level 0 esper, Misaka, Kuroko, and Uiharu have a blast taking on danger whenever and wherever it arises.
Academy City's Daihasei Festival is approaching, and the festival's steering committee is charged with recruiting at least two Level 5s to take the athlete's pledge during the opening ceremonies. However, getting volunteers proves to be a challenge.
As the Daihasei Festival begins, Uiharu and Saten enjoy themselves, while Kuroko sees to her Judgment duties. Mikoto and Kongo run an eventful three-legged race against teams from other schools. A plot involving MEMBER begins going into motion.
The Tokiwadai team competes in the Balloon Hunter event, but due to a case of mistaken identity, one of the Sisters substitutes for Mikoto. Yoshio Baba feeds the other school's team with data on the Tokiwadai competitors, with surprising results.
Saten's quest for Shadow Metal ends up landing her in trouble. Uiharu notices something amiss with the website Saten was browsing. Mikoto learns that Wannai did not get her gym uniform returned, prompting her to go track down her Sister.
With her closest friends now giving her the cold shoulder, Mikoto feels isolated and helpless, but finds a surprise ally in Kongo. Kongo tries to track down any clues that will lead her to the whereabouts of Mikoto's missing "twin sister."
Saten carries an injured Kongo to safety, while Awatsuki and Wannai tackle Yoshio Baba and his robotic Great Danes. Mikoto spots Saten with Kongo in an ambulance, blames herself for getting Kongo hurt, and determines to set things right.
With Kongo out of danger, Awatsuki finishes the task of having her psychometrist friend probe the kitten's memories. What Saten hears gives her pause, and she turns to Kuroko for advice. Kozaku confronts Mikoto, asking her about the Sisters.
With the assistance of her friends, Mikoto identifies the location from the website data that Uiharu recovered. Upon arriving at the location, Mikoto finds Shokuho waiting for her, and reveals her side of the events that have led up to this point.
Mikoto and Shokuho continue pursuing Gensei Kihara using their own individual methods. Kuroko attempts to identify the girl who abducted Uiharu and Misuzu. Saten decides to investigate an abandoned factory that may be connected to the case.
Shokuho and Mikoto find themselves in a traffic jam, and Shokuho demonstrates a tremendous example of her ability. The background behind the Exterior project is revealed, as well as Shokuho's connection to one of the original Misaka clones.
Kozaku uses Exterior to make her way into Mikoto's mind, convincing her to attack the building without windows. Before she can go after Gensei, Shokuho must contend with Kozaku's puppet, until help arrives from an unexpected source.
Kamijo and Sogiita find that at best, they can only slow down Mikoto's transformation. Kuroko continues to search for Kozaku while dodging her puppet. Gensei pursues Shokuho for the access code that will let him unlock Exterior's potential.
Kuroko continues searching for Kozaku, but after exhausting every possible hiding spot in the building, she must reexamine her situation. When Mikoto's transformation hits a critical threshold, it is time for Gensei to unlock Exterior's limiter.
Gensei has fallen victim to Shokuho's cunning, but Mikoto is still struggling to contain her power. Kamijo decides that he must help her at any cost.
A young Kozaku grins and bears her way through her youth in an Academy City research institution, where she befriends Dolly, one of the other girls there. But when Kozaku learns the grim truth about Dolly, it sets her on a life-altering course.
Mikoto is introduced to Indian Poker, a new fad that is sweeping Academy City, which allows people to share their dreams, by Shokuho Clique member Hokaze. Saten tells Uiharu about a new app that seems to predict accidents before they happen.
To demonstrate the authenticity of his predictions, Miyama sends Kuroko out with foreknowledge of several incidents that are about to take place. But when two cases occur in close proximity, Kuroko decides to call in additional help from Judgment.
After Saten demonstrates skills she acquired through Indian Poker, Mikoto comes upon a Trader who happens to have a card she is keenly interested in. However, ITEM operative Kinuhata is also eager to obtain the card for herself, to the same end.
When Saten buys the last of the mackerel at the supermarket, Frenda pesters her to let her have them, eventually leading to an unexpected friendship. However, when her seemingly innocuous text message is intercepted, Saten finds herself in danger.
Frenda and Saten find themselves under fire from an unknown assailant, and duck into a department store to find cover. When none of Frenda's usual tricks seems to work against their pursuer, she has no choice but to resort to drastic measures.
Shokuho approaches Mikoto to ask her to break into a research facility and determine the results of a unique experiment. But before Mikoto can enter the building, she has an encounter that raises serious questions for her, demanding good answers.
Kuriba explains to Mikoto and Shokuho how she fears that the Doppelganger's "soul" might pose a threat to the city. The members of Scavenger move in to incapacitate and capture the Doppelganger, but find their task more difficult than expected.
Shocked by the arrival of the Level 5 Mikoto, the members of Scavenger must keep their dark side affiliation a secret from her. Scavenger's Leader proposes that Mikoto teams up with them, since they share the goal of stopping the Doppelganger.
To counter the Doppelganger's giant monster form, Mikoto creates a giant magnetically-induced monster of her own. As the two do battle, it becomes evident that the Doppelganger has an ultimate objective other than combat in mind.
As the fight atop the airship draws to a close, the Doppelganger's true intentions become clear. Following the battle, the members of Scavenger seek to regain their former glory, while the circle of Mikoto's friends becomes more interconnected.