ข้อมูลอนิเมะA Certain Scientific Railgun S

Ruiko is chased by some thugs in an alleyway until she is rescued by Mikoto who deals with them. The next day, as she waits for her friends to arrive at Tokiwadai, Mikoto has an uncomfortable run in with Tokiwadai's other Level 5 esper, Misaki Shokuhou, who warns Mikoto that she and her friends should not mess with her clique. Later Mikoto, Kuroko, Kazari, Ruiko and Erii visits Banri in the hospital who is undergoing physiotherapy. While Erii rekindles with Banri, Mikoto reveals to the others she brought a present for Banri and wants to give to her with a surprise but realizes she left her bag containing the present in Banri's ward. Just then, a criminal patient that was under watch by AntiSkill is broken free by some of his companions and takes Erii as a hostage. Upon learning of the situation from Yomikawa and Tsuzuri, Mikoto heads to the rooftop to try and prevent the culprits escaping via helicopter. They throw Erii off the side of the building in order to break free, but she is saved thanks to Ruiko and Kuroko. Learning that her bag is onboard the fleeing helicopter, Mikoto has Kuroko teleport her to the skies where she deals with the culprits using her railgun and culprits surviving thanks to Kuroko. With the incident dealt with, Banri finally opens her present from everyone, revealed to be a Sakugawa Middle School uniform for her to wear once she recovers.

Mikoto recalls in a dream of how, when she was younger, she was approached by scientists wanting to use her DNA map to help cure Duchenne muscular dystrophy. The next day, Kuroko tries to take Mikoto through an alleyway to get to the mall, only to find it filled with people. They discover this is due to someone hiding envelopes containing money cards within the alleyways, piquing people's curiosity to search for them. After running into Ruiko, who is also on the hunt for the money cards, Mikoto overhears some SkillOuts who have managed to locate the source of the envelopes and decides to follow them. Meanwhile, Ruiko grows curious as she allegedly seen Mikoto at the mall, despite Mikoto never actually getting there, with Mii explaining to Kazari about a rumor of there being clones of her. The SkillOuts eventually trace the envelopes back to a Nagatenjouki Academy student named Shinobu Nunotaba, demanding she hand over the other envelopes. Things get tense, however, when it appears the SkillOuts are getting killed off one by one, which she claims to be an ability called "Critical" that allows her freely kill anyone she's touched. As Mikoto arrives on the scene, where the SkillOuts hadn't really been killed but were instead brought to the height of their fear and knocked out with a paper fan, Shinobu refers to her as 'the original'.

Mikoto is reminded of rumors about there being a clone of her and attempts to question the girl, who was distributing the envelopes in order to fill the alleyways that security cameras can't reach with human eyes, but she leaves after inadvertently setting the building on fire whilst burning the evidence, simply stating Mikoto would be unable to stop what was happening with her power. After saving the Skillouts and curious about what the girl said, Mikoto looks up for information on her, whose name is Shinobu Nunotaba. Mikoto learns Shinobu worked at the medical facility where she had given the scientists her DNA. Mikoto decides to infiltrate this facility by disguising herself and using her electricity to get past the security. Reaching a room that is separate from the rest of the building's network, Mikoto hacks into database and is shocked to learn that the scientists did tricked her into giving them her DNA for Project Radio Noise, which aimed to create clones of her. However, the project was canceled when the Supercomputer Tree Diagram discovered the clones won't match Mikoto's level of power. Feeling some relief from this, believing there weren't any clones of her after all, Mikoto leaves the facility whilst a similar-looking girl arrives later to delete the database.

Three months earlier, in an unknown facility, a pair of scientists mentor the birth of a clone of Mikoto, labelled Misaka 9982, installing memory functions via Testament. Back in the present, Mikoto, who is feeling cheerful with the clone rumors being seemingly debunked, goes shopping with Kuroko and the others at the mall, helping Kazari and Erii buy a rice cooker whilst also picking out things for an upcoming school trip. The next day, as Mikoto ends up having nothing to do, some young children, including the girl whose bag she previously found, pick up on this and have her play with them. Noticing one of the kids wearing a Gekota badge, Mikoto frantically goes through a whole bunch of gumball machines in order to try and win one for herself. As the day comes to an end, Mikoto suddenly senses a power identical to her own and, upon chasing after its source, comes across Misaka 9982.

After unwillingingly helping her rescue a kitten from a tree, Mikoto tries to question Misaka 9982, but is unable to learn much due to being unable to decipher a codeword. She instead decides to follow her around in case she returns to her base of operations, where they end up doing some surprisingly sisterly activities. Later that evening, as Misaka 9982 points out that she isn't returning to her point of origin, Mikoto takes her leave after inadvertently giving her the badge she won earlier. After receiving some help from Kazari in deciphering the code she was told about, Mikoto is horrified to learn of the Level 6 Shift Project, in which 20,000 Sisters are to be killed in 20,000 battles in order to evolve Academy City's most powerful Level 5 esper, Accelerator, into a Level 6 esper. Whilst learning of this, Misaka 9982 engages in her assigned battle with the aforementioned Accelerator, finding herself helpless against his reflective abilities. Fleeing to a railway yard, she attempts a sneak attack on Accelerator using a planted mine, only for him to survive and tear off her leg. Mikoto arrives on the scene, only to look in horror as Misaka 9982 is crushed to death by a train, clutching onto the badge she received from her sister. Enraged at Misaka 9982's death, Mikoto charges at Accelerator head-on.

Mikoto unleashes her anger at Accelerator, who quickly deduces she is the original, becoming further enraged upon seeing Misaka 9982's torn leg and hearing Accelerator's selfish reasons for participating in the experiment. However, even her most powerful attacks are simply reflected back at her. Just then, the fight is halted by the arrival of dozens of other Sisters, who request that Accelerator stop fighting Mikoto to avoid throwing off the experiment's calculations. As Accelerator takes his leave, Mikoto feels no comfort in hearing the Sisters acknowledge themselves as nothing more than guinea pigs. After a restless night, Mikoto is approached by Shinobu, who explains why she chose to oppose the experiment. Having been called back from the Radio Noise Project to assist in the Level 6 Shift Project, Shinobu got to see the sensitive side of one of the Sisters and become unable to see them as anything other than human. Upon hearing this, Mikoto takes it upon herself to destroy the facilities involved in the experiment, keeping it a secret from Kuroko and the others.

As Mikoto secretly lays waste to each of the labs involved in the Level 6 Shift project, Kuroko continues to cover for her disappearances, but she grows increasingly concerned and starts to miss her friend. While on patrol she encounters a child called Minori searching for Shinobu's cash cards along with some friends, acting on an urban legend that the cards with certain serial numbers are lucky. Kuroko scolds them and confiscates the card they found, but later finds Minori continuing the search alone and saves her from getting hit by a car. Minori reveals that she is looking for the cards as a special gift for a close friend who is moving away, and so reminded of her partner, Kuroko decides to supervise her search along with Kazari and Ruiko, even while knowing that as members of Judgement they could not let Minori keep the card. Mii comes across them and offers a more 'analogue' suggestion- that they search for a four-leaf clover instead. During their search, Kuroko's concerns for Mikoto are revealed, and Ruiko and Kazari remind her that her efforts are appreciated, not just by Mikoto but by her other friends as well. Kuroko and Minori each find four-leaf clovers, and Kuroko decides to keep hers, resolving to continue her loyalty and hard work. Meanwhile, the engineers of the Level 6 Shift project discover Mikoto's sabotages and prepare to respond.

With only two facilities remaining, the higher ups behind the Level 6 Shift project call upon the services of the underground group, ITEM. As Mikoto infiltrates one of these facilities, she finds herself against one of its members, Frenda Seivelun, who causes trouble for her using flammable tape and stuffed toys containing bombs. Meanwhile, Shinobu arrives at the other remaining facility, where they are attempting to transport the data whilst the other facility is being attacked. Mikoto chases down Frenda who, after a series of failed attacks, fills the room up with nitrogen, bluffing that it is an explosive gas, preventing Mikoto from using her electricity and putting her at a huge disadvantage. However, Mikoto, refusing to simply give up and be killed, manages to fight back against Frenda, leading to her bluff becoming exposed and a prompt electrical payback. As Mikoto tries to interrogate Frenda, who is unable to respond due to being shocked, she is suddenly attacked by ITEM's leader and the 4th ranked Level 5 esper, Shizuri Mugino.

Mikoto attempts to escape from Shizuri's attacks, which proves difficult due to ITEM's third member, Rikō Takitsubo, using her AIM Stalker ability to help Shizuri and Frenda home their attacks on her position. Meanwhile, Shinobu, who felt Mikoto shouldn't have to carry her burden alone, sneaks into the basement of her facility where the incubated Sisters are being held. There, she intends to install emotions into all of the remaining Sisters via the Misaka Network in the hopes it may move the organizers to suspend the experiments. However, she is apprehended by ITEM's fourth member, Saiai Kinuhata, who was guarding the facility in case a second party was involved in the attacks. Shinobu somehow manages to get the program installing, but it is suddenly blocked by an unforeseen error code, labelled "Breach code no. 20001". She attempts to use violence to save herself, but her attack proves futile against Saiai's Offense Armor ability and she is taken into custody. Back at the other facility, a weakened Mikoto is forced to use her ability to deflect Shizuri's Meltdowner attack, clueing her in on her true identity. Learning of this, Shizuri decides to send Frenda and Rikō away so she can settle things with Mikoto herself.