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 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.

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.

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.

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.

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.

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.

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.

Satellizer, Kazuya and Rana are en route to a Chevalier base in Alaska when they are called for help to defend an oil field from a Type S Nova. As the three of them fight the Nova, their battle is watched by a female scientist. Together with Chiffon, Elizabeth and their Limiters, they destroy the Nova which they discover is a robot Dummy Nova, realizing the whole thing was set up to test their skills. Since the incident at West Genetics, the Nova are coming into their dimension at a shorter time. In response, the Chevalier have approved the E-Pandora Project by Scarlett Oohara, which aims to make young woman who aren't genetically compatible with Stigmata into Pandoras despite oppositions by others including Professor Gengo Aoi, Kazuya's grandfather. At the Alaskan base where the world's top Pandoras have gathered, Chiffon introduces the others to Roxanne Elipton, Charles Bonaparte and Julia Munberk, the top Pandoras of Genetics America, France and Germany respectively. Together with Cassie and Chiffon, the five of them are the top five Pandoras of their generation. After trying their new uniforms, Scarlett explains she gathered the top Pandoras in collecting data to help the E-Pandora Project. When Roxanne comments Scarlett may have performed human experiments before the E-Pandora Project was approved, she is angrily confronted by a trio of E-Pandoras.

Rana is to displeased when she discovers Satellizer and Kazuya will be sharing a room. Later, a mock battle between the Pandoras and E-Pandoras is held to test their strengths. In the first two rounds, E-Pandoras Gina Papleton and Rattle are defeated. Amelia Evans, the strongest E-Pandora, battles Elizabeth in the third round. Despite being badly beaten by Elizabeth, Amelia refuses to give up even when it becomes clear her body cannot take it. It is only after when her friends and Scarlett persuades her that she gives up the fight. The E-Pandoras feel down with their defeat but Amelia cheers up her comrades by telling them they will defeat the Pandoras, who they consider uppity elites due to coming from rich families, while they themselves came from even worse backgrounds. The next day at lunch, Amelia, Jina and Rattle are surprised to find Elizabeth having lunch with them. Elizabeth assures the E-Pandoras they only lost because the regular Pandoras had longer training and experience than them so she and others Pandoras will help them to be strong as the Pandoras, cheering the E-Pandoras. Meanwhile, Secretary Spencer orders Scarlett to administered "Mark IV" despite her opposition.

Scarlett reveals the Mark IV proposition to the E-Pandoras and original Pandoras explaining it to be a nanomachine infusion containing original Pandora data to enhance the E-Pandora's compatibility with their Stigmata. Afterwards, the original Pandoras discuss the timing of Mark IV and its viability. While Satellizer and Rana train competitively, Amelia meets with Scarlett to discuss her concerns about the Mark IV wherein Scarlett reveals that due to the E-Pandoras willing agreement to join the project, they have no say in the matter but somewhat manages to allay Amelia's concerns. Back in training, Satellizer manages to diffuse a confrontation between Rana and Jina over Rattle's eating habits. Amelia confronts Jina about volunteering for the Mark IV but Jina rebukes her stating its only fairly her turn. Later, Jina thanks Satellizer revealing that it's Satellizer's data she'll be using and that'll allow her to defeat Satellizer for their practice match. During the administration, a problem arises before a flash forward to the match wherein Jina appears to be holding her own as shown in a promotional video to the public. Spencer is briefed in Jina's increasing unusual Stigmata activity, but he considers it to be expected and necessary to the point of her being a living corpse for the public's support. At the administration lab, a helpless Jina is shown to be becoming a Nova and consciously aware of it. Desiring to see Amelia and Rattle again, Jina breaks free of the lab while Spencer orders the mobilization of selected Pandora to stop her.

Satellizer departs as she remembers the match with Jina while Jina in Nova Form engages Elizabeth. Barely conscious, Jina reveals to Amelia that the Mark IV is s sham as Charles starts to engage Jina as well, ultimately killing her. Later, the other E-Pandoras hold a memorial service for Jina by burning her mementos. Scarlett interrupts the service ordering the others to stop the fire as she reveals the Mark IV experiments will continue whether the E-Pandoras choose to or not. Elizabeth, overseeing the service visits Satellizer after being turned away by Dr. Ohara while investigating and warns her to stay away. Outside the facility, Elizabeth consoles Amelia. Pursuing the matter, Elizabeth attempts to enlist the aid of Chiffon but is denied while being overheard by Satellizer. Curious about Elizabeth's methods while attempting to forcible assist and intervene, Satellizer is shot by Elizabeth who continues on her own.

As Kazuya accompanies Satellizer, who is confined to a wheelchair, to West Genetics for treatment, she has a change of plans and heads to Bali instead. Meanwhile, Elizabeth, as her Noblesse oblige duty, sends information about the E-Pandora project to her family, hoping their influence will lead to an investigation into Chevalier's shady activities and save the E-Pandoras. However, Spencer and the Chevaliers discovers the leak and has Elizabeth tortured with electroshock as punishment. Three days later, Chiffon, Eugene, Andre and Rana are worried over Elizabeth, but much to their shocked, the Chevaliers return a catatonic Elizabeth to them. At the same time, the Mably Conglomerate are hit with a series of scandals which ruins the company's reputation. Andre and Chiffon realizes this was the work of the Chevaliers in retaliation of Elizabeth's leak as she discovered the Mark IV experiment is incomplete and the Chevaliers were trying to cover up the truth to the public. Amelia is sadden on what has happen to Elizabeth. Elsewhere, Elizabeth reveals to Kazuya she came to Bali to ask her family for help to stop the E-Pandora project. Arriving at a hotel owned by the el Bridget family, Satellizer is reunited with her older sister Violet. But to her horror, her younger brother Louis is here as well.

Traumatized in seeing Louis, Satellizer shuts herself in her room much to Kazuya's confusion. Later that night, Louis visits Satellizer, revealing the Chevaliers framed the Mably family and their family had suspicious on the E-Pandora project hence why he and his Pandora Holly Rose didn't come. Louis tells Satellizer he can ask his parents help if she becomes his sex slave again. Satellizer tries to resist but Louis hits her and makes her remember the humiliation and abuses he did, mentally breaking her. With her will broken and obedient, Louis is about to have his way with Satellizer until he is put off when his sister says she is his obedient doll. The next morning, Louis has a talk with Kazuya, telling him he should quit being Satellizer's Limiter as he is not worthy as he plans to have his sister quit being a Pandora. But to his anger, Kazuya rejects his threats and bribery as the relationship between him and Satellizer is none of Louis' business. After a talk with Violet, Kazuya heads to a temple where Satellizer is. Louis appears before them, revealing he tricked them to come here as he beats Kazuya and reveals what he did to Satellizer in the past and she is his slave. However, Kazuya is not intimidated, telling Louis that Satellizer is no longer the weak girl he knew but the strong Pandora he loves. Enraged, Louis orders Holly to cut Kazuya's arm.

Emotions run wild as Satellizer and Kazuya square off against Luis and Holly in an epic, decisive battle in Bali.

Furious that the Mark IV experiments are scheduled to resume, the E-Pandora girls plan to escape from the Alaskan base. But the situation only worsens when the regular Pandora learn the truth...

The E-Pandora rebellion tears allegiances apart and pits Pandora comrades against each other in battle. Meanwhile, Amelia continues to transform into a Nova.

The in-fighting between regular Pandora rages on as the E-Pandora rebellion continues. Skills and hidden talents are revealed one after another... as are new secrets.

Seeing Scarlett Oohara and an array of Maria Lancelot clones, Amelia was shocked as Oohara justifies the deaths of her comrades Rattle and Gina and now fully transforms into an unknown type of Nova after her emotions lose control. The clones easily assimilate to Amelia's Nova and destroys the laboratory. Meanwhile, Aoi Gengo removes Spencer from commanding duties and orders all Pandoras and Limiters to mobilize against Amelia's Nova form which is heading to a photon generator. The Pandoras lose their morale as the Stigmata synchronization emits mental disruption, to which Satellizer recalls her saddest memories such as the death of her mother to which she intends to give in to the power of Amelia's Nova. With the help of Kazuya and Rana, Satellizer's mind become stable. As Amelia's Nova gets closer to the generator, Chiffon unleashes her Anti-Nova drive and finally opens her eyes.

Chiffon fights Amelia's Nova in attempt to protect the photon generator and her fellow comrades Satellizer, Rana, Kazuya and her Limiter Eugene. She lands some blows to Amelia but the Nova's armor quickly repairs and protect its core. Chiffon further transforms herself to increase her strength. Amelia's Nova delivers a powerful energy beam but Chiffon manages to nullify its attack. During the fight, Chiffon and Amelia converse each other within their subconscious and Chiffon decides to protect her comrades and suggests to stop the attack while Amelia agrees on Chiffon's suggestion but her emotions completely took over her and the attack is unavoidable. With the assimilation of Type Maria's power to Amelia's Nova, Amelia further transforms her Nova into a powerful self-destructing core and Chiffon decides to sacrifice herself in order to prevent annihilation. After Chiffon's successful absorption of Amelia's attack, her aura spreads throughout the Alaskan laboratory putting Pandoras to tears and realizing it came from Chiffon's love. Even Chiffon's aura reaches to Ticy, which she tells Ticy that she would be the successor of becoming President on their organization. In the aftermath of Amelia's Nova attack, Oohara was hospitalized and Spencer was taken to custody. Kazuya returns to Japan to be with Satellizer and Rana, but afterwards they see a new Ticy Phenyl with hair length same as Chiffon and the ribbon being tied to her right part of the hair walking somewhat grieving due to Chiffon's death.