In a battle royale to determine the rankings of second-year Pandoras, Satellizer el Bridget, The Untouchable Queen, is the strongest-ranked Pandora. During class, physics teacher and training instructor Yumi Kim talks about her experiences as a Pandora during the last war against the Nova, in which one battle against a powerful Nova was ultimately won thanks to the sacrifice of her squadmate, Kazuha Aoi. Meanwhile, Kazuha's brother, Kazuya, is transported to the West Genetic Academy by student president Chiffon Fairchild and is given a rundown about the nature of Pandoras and Limiters. Kazuya arrives while Satellizer is in a battle against the second-ranked Pandora, Ganessa Roland, Kazuya mistakes Satellizer for his late sister and hugs her, provoking an embarrassing reaction from her and leaving her open to attack.

Because of Kazuya's interference, Satellizer lost the battle against Ganessa, who is now the number-one-ranked second-year Pandora. Kazuya wants to apologize to Satellizer, but Chiffon advises him against it due to Satellizer's aphephobia and her propensity toward attacking anyone who touches her. Soon, Satellizer arrives, and Kazuya tries apologize to her. Despite Kazuya holding her arm, Satellizer does nothing but tell him to leave her alone. Just then, a gloating Ganessa arrives and insults Satellizer, which starts a fight between the two despite Chiffon's warnings. When Satellizer manages to knock her down, Ganessa goes into Pandora Mode and proceeds to beat and torture Satellizer. Kazuya tries to stop the fight, but Ganessa slaps him away which causes Satellizer to react and go into Pandora Mode as well, and defeats Ganessa. Yumi and Medical Officer Eliza Schmitz soon arrive to stop the fight, and they punish both girls with detention. After getting to know the headmistress and his dorm neighbor, Arthur Crypton, Ganessa's Limiter, Kazuya still wants to apologize properly to Satellizer. Meanwhile, a Pandora named Miyabi Kannazuki takes an interest with Kazuya and wants to make him her newest Limiter.

After introducing himself to his class and having lunch with class representative Kaho Hiiragi, Kazuya spots Satellizer and decides to apologize to her.properly He finds her on the rooftop, and through their conversations, he is glad to find that she is a shy and nice person. Both Arthur and Kaho are shocked to find that Kazuya can talk to her normally. However, third-year Pandora Miyabi and her three Limiters arrive and Miyabi wants to make Kazuya her newest Limiter, but when he rejects her offer, she threatens Kazuya, which prompts Satellizer to raise her weapon against Miyabi. As the two Pandoras fight, Miyabi uses Accelerating Turn to increase her speed, but she is surprised to learn that Satellizer can also use Accelerating Turn. After taking a strike to her face, which angers her, Miyabi orders her Limiters to freeze both Kazuya and Satellizer and beat them. As Miyabi and her Limiters humiliate and sexually harass Satellizer, Kazuya activates his Freezing powers to stop them. By the time Yumi, Eliza and Chiffon arrive to stop the fight, Satellizer has brutally beaten Miyabi and her Limiters and is about to deliver a deadly blow when Kazuya pleads with her to stop, which she does. As Yumi and Eliza learn the secrets of Kazuya's abilities, Chiffon warns him again to stay away from Satellizer because she is now the target of the other third-years, who do not take lightly of those who disrespect the Academy's hierarchy. At the same time, Attia Simmons informs Ingrid Bernstein of what just happened.

After spending a week in solitary confinement for her actions, Satellizer faces Ingrid, who challenges her to a duel to punish her for going against the third-years and tells her to get a Limiter ready for it. Upon hearing about it, Kazuya begs Satellizer to let him be her partner, but she refuses. Instead, Sattelizer attacks Ingrid before their match, but Ingrid is well-prepared and gets the upper hand thanks to her Tempest Turn. When her Limiter, Leo, arrives, Ingrid gives Satellizer one more chance to get a Limiter, for which Kazuya volunteers despite being warned of the consequences of associating with Satellizer. Thanks to his powerful Freezing ability, Satellizer is able to knock down both Leo and Ingrid, but, hellbent on punishing Satellizer, Ingrid refuses to give up and goes into Pandora Mode, leaving Kazuya confused as to why Ingrid takes hierarchy discipline so seriously. Ganessa reveals to Kazuya that a year ago during an outdoor training session, Ingrid's best friend Marina died when she fought a Nova alone, and she believes Marina would have survived had the younger students not run away due to a lack of discipline in their ranks. Hearing this, Kazuya freezes Ingrid and tells her that he understands her pain just like he had when he lost his sister. He tells her her actions are tainting her late friend's memories, that Marina didn't die in vain as she was actually sacrificing her life to protect the younger students. With Ganessa confirming it as well, Ingrid realizes this isn't what Marina wanted, and breaks down in tears at the truth.

Satellizer finally accepts Kazuya as her Limiter as she doesn't feel uncomfortable when he touches her and he can do Freezing without performing a baptism. Arthur and Kaho are shocked by this development and even more so when they learn Satellizer has invited Kazuya into her room tonight. Meanwhile, a new student from Tibet named Lana Linchen has arrived at West Genetics Academy. As Kazuya, Arthur and Kaho head to the girls' dormitory, they are confronted by the 3rd to 5th-ranked Second-year Pandoras, Audrey Duval, Tris Mackenzie and Aika Takeuchi, whom all lost to Satellizer at the battle royale and wants to take it out on Kazuya, and tortures Arthur and Kaho for interfering. In anger, Kazuya activates his Freezing powers but soon lose consciousness as Lana arrives to rescue them and defeats the second-year Pandoras. Informed on what just happened, Satellizer visits the hospitalized Kazuya. As she has a chat with Arthur and a hospitalized Kaho, Lana believes Kazuya is her chosen one (a Limiter) but Arthur and Kaho advise her not to as Kazuya is Satellizer's Limiter. Meanwhile, Attia, Elizabeth Mably and the other third-years discuss about these recent developments.

Lana enrolls into Satellizer's class where she is shown to be a formidable fighter when she defeats Ganessa during a practice bout. Despite being warned, Lana makes her moves on Kazuya, hoping to make him her partner much to Satellizer's jealousy. Arthur and Kaho continue to warn Kazuya not to be with Satellizer after telling him how she was held back a year and expelled from East Genetics for seriously injuring a Limiter who was a playboy. Later, Attia lies to Lana that Satellizer hasn't performed a baptism with Kazuya as she is only using him for his Freezing powers, which Lana brings Satellizer to a training facility where they fight over who should be Kazuya's partner. After a brutal fight, Kazuya intervenes to clarifty Lana about his relationship with Satellizer but Attia, along with two other third-years, Arnett McMillan and Cleo Brand, arrives.

After Kazuya is knocked unconscious, Satellizer starts fighting against Arnett while Lana, who seeks revenge for being used, goes against Cleo. Arnett manages to use her Double Accel technique to take advantage of Satellizer, allowing her to slit her neck while Lana is similarly overwhelmed by Cleo's Tempest Turn. As she tries to remain conscious while the third-years argue on what to do with her, Satellizer recalls when she and her mother were brought into the El Bridget household. Because her mother was her father's mistress, Satellizer was treated harshly by her younger half-brother, Louis, who even sexually abused her, and she was forced to bear it for her mother's sake until her older half-sister Violet learns about it and stops it. On her deathbed, Satellizer's mother apologizes to Satellizer for what she had gone through and encourages her to never lose to anyone. Remembering those words, Satellizer stands up and defeats Arnett with a Triple Accel technique while Lana uses Cleo's Tempest Turn together with her fighting style to defeat Cleo. However, all four girls refuse to give up but the fight is stopped when Chiffon and Ticy arrive and orders the third-years to stand down after Chiffon quickly subdues Arnett. As Satellizer and Lana bring Kazuya to the hospital, Chiffon meets Elizabeth at the swimming pool and tells her to stop targeting Satellizer as it is useless and their peaceful days are about to be over soon.

The West Genetics Academy decides to hold a prom where both Satellizer and Lana crosses eyes over who will Kazuya go to the dance with which he chooses the former. Meanwhile, Elizabeth decides to take Chiffon's advice and tells the third-years to stop targeting Satellizer but Attia still wants to humiliate Satellizer. On the night of the prom, Attia challenges Satellizer to compete in the Pandora Queen beauty contest which the latter agrees out of pride. When she's about to go on stage soon, Satellizer becomes nervous but Lana who is also competing, encourages her to withstand it for the sake of her partner. Despite being shy on stage, her timidness appeases the crowd and she wins the crown. Angry about her loss, Attia arranges for Satellizer to wear a skimpy outfit which becomes transparent under the spotlight, but Kazuya uses his Freezing ability to freeze the crowd and helps Satellizer escape from embarrassment.

Kazuya is invited to East Genetics Academy to meet the #1 ranked third-year Pandora, Cassie Lockheart, who possesses Stigmata from his late sister, Kazuha. Despite her potential, she explains she plans to retire after graduating to become a novelist. As Kazuya returns home, Sister Margaret reveals that Satellizer also possesses six of Kazuha's Stigmata, but showed little compatibility with them. Cassie reveals to her teacher Milena that the reason she doesn't want to join the Chevaliers, the Pandora elite, was because she was there when Satellizer attacked the playboy Limiter when she was still a student at East Genetics, and Satellizer's resolve to never give up no matter how many times Cassie put her down made her scared and realize how weak she was. Just then, East Genetics is attacked by a group of Type S Nova who exhibit abilities that have never been seen before, overwhelming the students and absorbing some of the Pandoras, including Cassie and Milena. Meanwhile, Satellizer overhears Kazuya talking with Arthur and Kaho, believing that Kazuya only chose her because she reminded him of his sister.

As West Genetics sends their fourth-year Pandoras to reinforce East Genetics, the West Genetics Academy is soon attacked and surrounded by the Nova. With the fourth-years too far to help them, Yumi and Eliza leads the remaining fourth-years and the Military to the front lines while the rest of West Genetics' Pandoras and Limiters are ordered to guard the Academy. However, the Nova soon release Nova Forms, Pandoras they absorbed earlier at East Genetics who are now infected and under their control. Meanwhile, Satellizer is angry that Kazuya sees her as a replacement for his sister, but before he can explain, both of them, along with Lana, Ganessa and Arthur, are called by Sister Margaret to defend the underground Ravensborne Nucleohede facility which holds the body of Maria Lancelot, the first and mother of Pandoras. As the Nova Forms attack the Academy, a small group of them lead by Cassie and Milena manage to breach into underground facility. Sister Margaret realizes the Nova Forms target is Maria's body and laments the fact the same Stigmas that gives a Pandora their power comes from the Nova and are also responsible for turning them into a Nova Form.

As the Nova Forms head towards the Ravensborne Nucleocheode, they are held back by Ingrid, Cleo, Arnett, Attia and their Limiters. Cassie and Milena manage to evade them only to encounter Elizabeth and her Limiter, whom the latter learns the Nova Forms weak point is the Nova Stigma between their collarbones which will destroy the infection and release them from Nova control. However, Cassie breaks into the lower levels where Satellizer and the others are. After defeating Lana and Ganessa, Cassie goes after Satellizer who refuses Kazuya's help, where they both get into a fierce battle using all of their Tempest Turn and Accel techniques. As Cassie prepares a finishing blow to Satellizer, Kazuya summons up all of his Freezing abilities to stop Cassie and tells Satellizer how important she is to him which the latter realize how much Kazuya cares about being her partner.

Milena is stopped by Chiffon and Ticy from approaching Maria's body. Meanwhile, Cassie shoots an energy beam at Satellizer but Ganessa sacrifices her life to shield her. Traumatized from Ganessa's death who considers Satellizer her comrade, Satellizer goes berserk and turns into Nova Form where she brutally beats Cassie, cutting both her arms and ripping off her infected Stigma. Free from Nova control, Cassie begs Satellizer to kill her but she is stopped by Kazuya, who manages to hold her back and calm her, which turns her back to normal. With Ganessa revealed to have survived and Milena defeated, the Pandoras believe it is over, but the last remaining Nova uses Milena's Stigma as a beacon to teleport into Ravensborne Nucleotide, forcing Satellizer, Lana, Ingrid, Cleo, Arnett, Attia, Elizabeth, Chiffon and Ticy to fight it. However, the Nova uses Cassie's infected Stigma to infect Satellizer into a Nova Form and uses her to cast a powerful Freezing ability to stop the Pandoras as it goes after Maria's body. Hearing her cries for help, Kazuya activates his Freezing on Satellizer and thanks to Kazuha's spirit, she breaks free of the Nova's control and stops its Freezing which finally allows the Pandoras to finish off the Nova. After recovering and returning to East Genetics, Cassie, influenced by both Kazuya and Satellizer's ideals, tells Milena that she decided to join the Chevaliers and still be a novelist. And with her change of personality, the other Pandoras comment how much Satellizer has changed thanks to Kazuya. In the epilogue, Sister Margaret has a talk with a "Professor Aoi" over the Stigmata as a double-edged sword, but he warns the fight with the Nova is far from over.