A bordo del modulo 77 della JIOR Sphere 01, Haruto Tokishima perde una gara gastronomica contro Shōko Sashinami per l'uso del cortile della scuola mentre a loro insaputa, cinque agenti Dorssian sotto copertura si infiltrano nella Sakimori High School. Qualche tempo dopo, mentre gli agenti esplorano la scuola in cerca di una destinazione, uno di loro ha un breve alterco con Haruto sulle loro diverse visioni del mondo. Successivamente, gli agenti Dorssian si infiltrano e uccidono gli scienziati in un laboratorio segreto sotto la scuola, anche se uno scienziato ferito espelle il loro obiettivo principale, un gigantesco mecha chiamato Valvrave 01 sulla superficie della scuola.

Kyūma Inuzuka, Aina Sakurai e Saki Rukino arrivano nella posizione di Valvrave per trovare un Haruto e L-elfo privi di sensi. All'arrivo degli altri agenti Dorssian, L-elfo tradisce i suoi compagni e aiuta gli studenti a fuggire. Successivamente, mentre le forze Dorssiane occupano il Modulo 77, Haruto convince i suoi amici di aver in qualche modo posseduto il corpo di L-elfo e in seguito riprende la Valvrave, riuscendo anche a tornare nel proprio corpo con l'aiuto di Saki. Quando la Valvrave si attiva e attacca la vicina nave Dorsiana, si ritrova sbalzata fuori dal Modulo nello spazio. A-drei e Q-vier usano quindi i Dorssia Ideal Mech per attaccare il Valvrave 01 credendo che L-elfo li abbia traditi.

Le forze dell'ARUS catturano L-elfo mentre trasmette una strana stringa di parole ad Haruto. Mentre le forze dell'ARUS insieme al senatore Figaro forniscono sollievo agli studenti dell'Accademia Sakimori, Haruto ei suoi amici cercano di dedurre la natura delle sue nuove abilità senza riuscirci. In seguito, Figaro invia la parola per incontrare Haruto e lo esorta a diventare un simbolo di speranza nella guerra contro Dorssia. Nel frattempo, mentre L-elfo fugge dalla sua prigionia, Cain invia A-drei, X-eins, H-neun e Q-vier in un altro tentativo di riconquistare il Modulo 77.

Il presidente Jeffrey Anderson e il senato ARUS votano per ottenere l'arma JIOR Valvrave per aiutare nella loro campagna contro Dorssia. Nel frattempo, dopo aver rifiutato il contratto di L-elfo, Haruto non riesce a impedire a Figaro di sperimentare con l'Unità 01, provocando la morte di un pilota ARUS. La flotta Dorssian effettua quindi un attacco iniziale contro il Modulo 77 che spinge Figaro a dare la priorità alla sua sicurezza rispetto agli studenti Sakimori in una trasmissione intercettata da Shōko e Akira Renbōkoji. Shōko usa quindi mezzi drastici per informare il Consiglio studentesco del tradimento di Figaro e mentre Takahi Ninomiya distrae i rappresentanti dell'ARUS, Shōko, Kyūma e Yūsuke Otamaya salvano Haruto. Mentre Figaro tenta di andarsene, appare Haruto e rivela le sue vere intenzioni al corpo studentesco incredulo. Avendo perso la pazienza, Figaro inizia a sparare sugli studenti finché Haruto non lo ferma con l'Unità 01.

Con il loro ricatto che tiene a bada le forze ARUS e Dorssiane, gli studenti Sakimori godono di una pace fuori luogo a bordo del Modulo 77, anche se ignari del suo consumo di energia pericolosamente elevato. Altrove, Dorssian Führer Amadeus K. Dorssia raduna le sue forze insieme a una dimostrazione di potere. Durante l'esplorazione delle profondità del Modulo 77, L-elfo fa una scoperta quando la rete elettrica si interrompe a causa del sistema meteorologico sovraccarico. Nonostante sia rinchiuso nell'hangar Valvrave 01, Takumi Kibukawa spiega il problema con Yusuke che è l'unica altra persona da comprendere. Raizō quindi trascina Yūsuke alle altezze del Modulo per ripristinare il sistema, trovando infine l'interruttore quando quest'ultimo cade attraverso il pavimento danneggiato dalla battaglia. Il clima freddo inizia anche a smorzare gli spiriti delle ragazze Sakimori al punto che Takahi e la sua cricca iniziano ad attribuire la colpa a Shōko e Saki.

Nonostante il tentativo di Haruto di fermarla, Saki sale a bordo del Valvrave Four e con sua sorpresa completa con successo la sua procedura di avvio. Osservando segretamente il successo di Saki nel pilotare il Valvrave Four, L-elf deduce che la struttura sotterranea non è stata costruita per caso sotto la Sakimori High poiché gli studenti soddisfano alcuni requisiti per azionare i mech confrontandoli con il tentativo fallito del soldato ARUS. Dopo un po' di gioia, Saki si lamenta del suo passato, facendo abbassare la guardia ad Haruto e lei lo morde, cambiando la loro coscienza. Successivamente Haruto (Saki) usa l'account WIRED di Haruto per aumentare la propria popolarità come idolo. Quando viene confrontata da Haruto, e subito dopo da Shōko, afferma che se non afferma il suo status di idolo, tutti si dimenticheranno di lei.

L'elf hands Shoko papers which include a plan for the military development and territorial expansion of JIOR. A-drei, Q-vier and H-neun interfere and Rukino tries to stop them. Haruto possesses L'elf to use his Valvrave.

Students of Sakimori are mourning for Aina. L-elf is held prisoner by the students, and he recalls the time he first met Lieselotte. Sakimori is attacked by the Dorssians. Haruto and Saki go out to battle against them, trusting L-elf's tactical advices.

L-elf has the students perform military training and establish plans to increase the defenses of Module 77. Meanwhile, Raizo is caught once again trying to hijack one of the Valvraves and is put into prison, while Kyuma dedicates himself to training in order to avenge Aina's death. Soon after, Module 77 is once again under Dorssian attack. Haruto and Saki engage the enemies unaware that they are being drawn away from the base and giving an opening for a second invading force. With Haruto and Saki occupied fighting A-Drei's party, a shortage of power renders the module defenseless until Kyuma takes control of the blue Valvrave and starts a counterattack. However, Kyuma finds himself in a disadvantage until the yellow Valvrave, piloted by Raizo, appears to assist him and they manage to drive away the enemies.

While in the holding bay, Takumi explains to L-elf the circumstances under which Sakimori High School was created, for Project VVV which is virtually a JIOR military initiative. As Module 77 continues to progress towards the moon, Haruto and co. discuss the terms of keeping their possession ability a secret while Shoko continues improving her relationships with their fellow schoolmates. At the same time, Rion announces that Module 77 will hold elections for a new Prime Minister that will handle their public affairs once they get to the moon, with herself along with Raizo and Satomi running as well. L-elf surprises Haruto by volunteering to take care of the election affairs since having an appointed leader would help meet his goals. Later on, the frequency at which the foreign gene within Haruto's system tries to take over increases, as noticed by Saki, and she opts to kill him should he resort to physically harming their fellow students.

Module 77 is headed to the Moon while the students are appointed as cabinet ministers. Akira finally speaks to Shoko and it is revealed that she is Satomi's sister. Module 77 is attacked by the Dorssians and Shoko's father is held hostage by Wartenberg.

In the year 211, Saki is telling the story of the Magius to a boy who looks like L-Elf. Back to the present, Saki calmly rejects Haruto's marriage proposal and proceeds to help the other 2 Valvraves hold off the Dorssian forces. Meanwhile, the drill that was sent into the Module is moving up through the space with the intention of releasing poison gas into the atmosphere of the Module. L-Elf receives a call from Haruto and meets up with him to try to defeat the Dorssians. Satomi calls Shoko and asks her to save his sister, Akira, who is trapped in the school. Akira, who overhears this conversation, tries to stop Shoko but to no avail. Shoko was knocked unconscious by the drill while trying to get to Akira, and this prompted Akira to face her hears of being bullied and come out into the open to save Shoko. Facing a dead end due to the damage by the drill, she almost gave up until a crack in the debris reveals Valvrave unit 6.

The Chancellor of Dorssia is summoned for an audience with the Magius, where he receives unwelcome news. Meanwhile Captain Cain learns more about the Valvraves as he pilots what L-elf though was a broken unit, and Shoko faces new diplomatic challenges...

After breaking through Dorssian forces, the students of New JIOR have made it far enough to begin their decent onto Earth. However an untimely mistake throws the mission into peril, and siblings Akira and Satomi Renbokoji must face their dark past.

After crashing down to Earth, the students find themselves stranded in Dorssian territory, far from their targeted landing in JIOR. In order to infiltrate the enemy forces, L-elf uses his familiarity with his surroundings to devise a plan, however...

As Marie heals from L-elf\u2019s gunshot, it becomes quickly apparent that she has a mysterious history with Valvrave Unit 01. With A-drei leading the Dorssian troops, L-elf finds his plan compromised, and Marie wrestles with losing precious memories.

After Marie pilots Unit 01, the sacrifices and consequences that come with piloting the powerful Valvrave become clear. H-neun begins to act on his suspicions of Captain Cain to protect X-eins, and Haruto must face his nightmares or give up piloting.

The students devise a plan to rescue the JIORans held captive in Dorssiana, and Haruto finds that he will reunite with his somewhat estranged father. As the fateful meeting draws nearer, L-elf receives intel that prompts him to stage a reunion of his own.

L-elf is finally reunited with Lieselotte, however the students find themselves surrounded with Captain Cain having predicted their every move. Saki Rukino also finds herself cornered, and Haruto learns the surprising truth about the Magiuses.

The students arrive at Module 77 to a hero's welcome, complete with in-depth press coverage! Haruto and L-elf each struggle in their own way to come to terms with recent events. Meanwhile, Shoko has been fighting as well on JIOR's political battlefield.

ARUS Golden News is broadcasting the shocking events in Module 77's hangar. Dorssian chancellor declares that the residents of Module 77 are actually monsters that drain human lives. Shoko is devastated to find out that Haruto has been lying to her.

Captain Cain is tasked with the extermination of the Class 7 Special Hazard Organisms. Haruto and L-elf are on a site of a gravity reactor explosion. L-elf tries to convince Haruto that he was abandoned by his friends, but they end up blaming each other.

L-elf tries to infiltrate the enemy position but is caught by A-drei. A-drei wants him to help take out Captain Cain. In the meantime, Haruto comes back, but his memories are fading away as he continues to fight in order to expose the lies of the world.

The explosive season finale of Valvrave the Liberator.