Wir befinden uns an der „Schule für Maßnahmen gegen Kreaturen aus einer anderen Dimension“. Mit überwältigender Stärke schlägt Satellizer el Bridget eine angreifende Klassenkameradin nach der anderen. Am selben Tag verschlägt es Kazuya Aoi, den jüngeren Bruder der legendären Pandora Kazuha Aoi, auf den Campus von Genetics.

Kazuya Aoi wird in den Kampf zwischen Satellizer und Ganessa verwickelt. Er verwechselt Satellizer mit seiner älteren Schwester, da sie ihr wie aus dem Gesicht geschnitten ist, und entfesselte dabei auch noch ein Freezing. Dadurch verliert Satellizer ihren Titel als Stufenbeste. Kazuya fühlt sich dafür verantwortlich und will sich bei Satellizer entschuldigen.

Der Streit zwischen Satellizer und Ganessa ist mit Satellizers Sieg zu Ende gegangen. Kazuya beginnt sein Schülerleben an der Genetics ohnehin schon mit vielen Fragezeichen, doch obendrein rät ihm am nächsten Tag die Klassensprecherin Hiiragi eindringlich, sich nicht mit Satellizer abzugeben. Kazuya sieht das nicht ein und bittet Satellizer, dass sie ihn zu ihrem Limiter macht.

Satellizer konnte durch Kazuyas Freezing-Fähigkeit den Kampf gegen die Oberstuflerin Miyabi gewinnen. Doch das bedeutet gleichzeitig, dass sie sich nun die gesamte dritte Jahrgangsstufe zum Feind gemacht hat. Tatsächlich taucht auch schon Ingrid Bernstein aus der dritten Stufe vor Satellizer auf und kündigt an, dass sie sie dafür bestrafen werde, dass sie die Ordnung an der Schule stört.

Nach dem Kampf gegen Ingrid hat Satellizer festgestellt, dass es ihr nicht unangenehm ist, von Kazuya berührt zu werden und sie beschließt, ihn unter der Bedingung, ihn nicht taufen zu müssen, als ihren Limiter zu akzeptieren. Kazuya wird sogar auf ihr Zimmer eingeladen.

Von Audrey und ihren Freundinnen brutal in die Mangel genommen, konnten sie nur durch Ranas Hilfe das Ruder noch herumreißen. Doch Kazuya, der mehrere Tage in Folge sein Freezing aktiviert hat, bricht vor Überanstrengung zusammen. Als ihr das mitgeteilt wird, eilt Satellizer sofort zum Rehabilitationszentrum und verbringt viel Zeit am Bett des bewusstlosen Kazuya.

Attia, Arnett und Cleo, drei Schülerinnen aus dem dritten Jahrgang, die den Kampf zwischen Satellizer und Rana mitangesehen haben, sind nun zur Stelle, um Satellizer zu maßregeln. Als die verwundete Satellizer alleine gegen Arnett und Cleo antreten will, bekommt sie von Rana Unterstützung und es entbrennt ein erbitterter Kampf: Satellizer vs. Arnett und Rana vs. Cleo!

Der Kampf gegen die Mädchen aus dem dritten Jahrgang endete damit, dass Satellizer und Rana überraschende Kräfte entfesselten. Da die Oberstuflerinnen gezwungenermaßen anerkennen müssen, welche Kräfte wirklich in Satellizer stecken, beschließen sie, vorerst die Maßregeln einzustellen. Zu diesem Zeitpunkt steht bald die „Prom“ an, ein Schulfest, das jedes Jahr stattfindet.

Kazuya trifft Cathy Lockheart, die Beste der Jahrgangsstufe 3. Sie trägt die Heldenstigmata seiner Schwester. Kazuya erfährt, dass Cathy eines der Mädchen ist, dem Heldenstigmata seiner Schwester Kazuha in den Körper eingesetzt wurden.

Die Nova des Typ S sind nicht mit denen aus der Vergangenheit zu vergleichen. Nachdem sie sich die Pandoras einverleibt haben und daraufhin verschwanden, traten sie in einer Formation wieder zum Vorschein, als würden sie das Gebäude umzingeln wollen. Während all dieser Geschehnisse nimmt Satellizer an, dass Kazuya sie nur mag, weil sie die Heldenstigmata seiner großen Schwester trägt.

Mit überwältigender Stärke erledigen die Novagewordenen Pandoras eine Pandora der West Genetics nach der anderen und kommen dem Ravensbourne Nukeotid immer näher. Sie haben den Heiligen Leib, der in dessen Untergeschoss aufbewahrt wird, ins Auge gefasst! Vor dem Raum, indem er aufbewahrt wird, wurden Satellizer und die anderen aufgestellt.

Im Kampf gegen die Nova-gewordene Cathy Lockheart gelingt es Satellizer – zumindest für einen Augenblick – Cathys Bewusstsein zurückzuholen. Doch als die Nova erneut die Kontrolle über Cathy gewinnt, wird Satellizer durch ihre überwältigende Stärke mit dem Rücken zur Wand gedrängt.

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.