A bordo do Módulo 77 do JIOR Sphere 01, Haruto Tokishima perde um concurso de comida para Shōko Sashinami pelo uso de seus terrenos escolares enquanto, sem o conhecimento deles, cinco agentes Dorssian disfarçados se infiltram na Sakimori High School. Algum tempo depois, como os agentes exploram a escola para um destino, um deles tem uma breve briga com Haruto sobre suas diferentes visões de mundo. Depois, os agentes Dorssian se infiltram e matam os cientistas em um laboratório secreto sob a escola, embora um cientista ferido ejete seu alvo principal, um mecha gigante chamado Valvrave 01 para a superfície da escola.

Kyūma Inuzuka, Aina Sakurai e Saki Rukino chegam ao local da Valvrave para encontrar Haruto e L-elf inconscientes. À medida que os outros agentes Dorssian chegam, L-elf aparentemente trai seus companheiros e ajuda os alunos a fugir. Depois, quando as forças Dorssianas ocupam o Módulo 77, Haruto convence seus amigos de que ele de alguma forma possuía o corpo de L-elfo e depois retoma a Valvrave, enquanto ele também consegue retornar ao seu próprio corpo com a ajuda de Saki. À medida que a Valvrave ativa e ataca a nave Dorssiana próxima, ela é lançada para fora do Módulo no espaço. A-drei e Q-vier então usam Dorssia Ideal Mechs para atacar o Valvrave 01 enquanto acreditam que L-elf os traiu.

As forças ARUS prendem L-elf enquanto ele retransmite uma estranha sequência de palavras para Haruto. Enquanto as forças ARUS junto com o senador Figaro fornecem alívio aos alunos da Academia Sakimori, Haruto e seus amigos tentam e falham em deduzir a natureza de suas novas habilidades. Depois, Figaro manda uma mensagem para conhecer Haruto e o exorta a se tornar um símbolo de esperança na guerra contra Dorssia. Enquanto isso, enquanto L-elf escapa de seu cativeiro, Cain despacha A-drei, X-eins, H-neun e Q-vier em outra tentativa de recapturar o Módulo 77.

O presidente Jeffrey Anderson e o senado da ARUS votam na obtenção da arma JIOR Valvrave para ajudar em sua campanha contra Dorssia. Enquanto isso, depois de rejeitar o contrato de L-elf, Haruto não consegue impedir Figaro de experimentar a Unidade 01 - resultando na morte de um piloto ARUS. A frota Dorssian então faz um ataque inicial contra o Módulo 77 que leva Figaro a priorizar sua segurança sobre os alunos Sakimori em uma transmissão interceptada por Shōko e Akira Renbōkoji. Shōko então usa meios drásticos para informar o Conselho Estudantil da traição de Figaro e enquanto Takahi Ninomiya distrai os representantes da ARUS, Shōko, Kyūma e Yūsuke Otamaya resgatam Haruto. Como Figaro tenta sair, Haruto então aparece e revela suas verdadeiras intenções para o corpo discente descrente. Tendo perdido a paciência, Figaro começa a atirar nos alunos até que Haruto o impede com a Unidade 01.

With their blackmail keeping the ARUS and Dorssian forces at bay, the Sakimori students enjoy an out-of-place peace aboard Module 77 albeit unaware of its dangerously high power consumption. Elsewhere, Dorssian Führer Amadeus K. Dorssia rallies his forces together with a show of power. While exploring the depths of Module 77, L-elf makes a discovery when the electrical grid shuts down due to the overworked weather system. Despite being locked in the Valvrave 01 hangar, Takumi Kibukawa explains the problem with Yūsuke being the only other person to comprehend. Raizō then drags Yūsuke to the heights of the Module to reset the system, eventually finding the switch when the latter falls through the battle-damaged floor. The chilly climate also begins dampening the spirits of the Sakimori girls to the point where Takahi and her clique start assigning blame on Shōko and Saki.

Despite Haruto's attempt to stop her, Saki boards the Valvrave Four and to his surprise she successfully completes its start-up procedure. Secretly observing Saki's success at piloting the Valvrave Four, L-elf deduces that the underground facility was not built under Sakimori High by chance since the students meet some requirement to operating the mechs by comparing them to the failed attempt by the ARUS soldier. After a bit of joyriding, Saki laments on her past, causing Haruto to let his guard down and she bites him, switching their consciousness. Afterwards Haruto (Saki) uses Haruto's WIRED account to help boost her own popularity as an idol. When confronted by Haruto, and soon after by Shōko, she claims that if she doesn't assert her status as an idol, everyone will forget about her.

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.

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.