El día en que Haruto Tokishima se arma de valor para declararse a Shoko Sashinami, su mejor amiga de la infancia. Una explosión se sitúa cercas de ellos. Resulta que Jior, el país en el que viven, está siendo invadido por las fuerzas militares de Dorushia. Shoko muere durante la invasión, lo que vuelve a Haruto histérico y con deseos de venganza.

Después de la invasión de Dorushia, Haruto es herido por L-elf, un agente secreto de las fuerzas especiales de país enemigo. Sus amigos creen que está muerto, pero él está en el cuerpo de L-elf. Mientras tanto, Jior se ha rendido ante Dorssia y Haruto descubre que Shoko está viva.

Haruto ha vuelto a su propio cuerpo, y L-elf al suyo, pero ahora todos piensan que él ha traicionado a su nación. Los agentes de Jior lo apresan y se lo llevan para interrogarlo. No obstante, antes de que lo encierren, L-elf le advierte a Haruto su profecía. Haruto ignora sus palabras, y se presenta ante el senador Figaro de Arus, quien en ese momento ha llegado a para proteger a Jior. Pero las cosas se salen de control y todo lo que L-elf profetizó se hace realidad. Así que, L-elf aprovecha la situación para proponerle a haruto un trato. Ahora la decisión de salvar a sus queridos recaen sobre él.

El presidente Jeffrey Anderson y el Senado de ARUS votan sobre la obtención del arma JIOR Valvrave para ayudar en su campaña contra Dorssia. Mientras tanto, después de rechazar el contrato de L-elf, Haruto no logra evitar que Figaro experimente con la Unidad 01, lo que resulta en la muerte de un piloto de ARUS. Luego, la flota Dorssiana realiza un ataque inicial contra el Módulo 77, lo que lleva a Figaro a priorizar su seguridad sobre los estudiantes de Sakimori en una transmisión interceptada por Shōko y Akira Renbōkoji. Shōko luego usa medios drásticos para informar al Consejo Estudiantil de la traición de Figaro y mientras Takahi Ninomiya distrae a los representantes de ARUS, Shōko, Kyūma y Yūsuke Otamaya rescatan a Haruto. Cuando Figaro intenta irse, Haruto aparece y revela sus verdaderas intenciones al incrédulo cuerpo estudiantil. Habiendo perdido la paciencia, Figaro comienza a disparar contra los estudiantes hasta que Haruto lo detiene con la Unidad 01.

Con su chantaje manteniendo a raya a las fuerzas de ARUS y Dorssian, los estudiantes de Sakimori disfrutan de una paz fuera de lugar a bordo del Módulo 77, aunque sin darse cuenta de su peligrosamente alto consumo de energía. En otra parte, el Dorssian Führer Amadeus K. Dorssia reúne a sus fuerzas con una demostración de poder. Mientras explora las profundidades del Módulo 77, L-elf hace un descubrimiento cuando la red eléctrica se apaga debido al exceso de trabajo del sistema meteorológico. A pesar de estar encerrado en el hangar Valvrave 01, Takumi Kibukawa explica el problema de que Yūsuke es la única otra persona que comprende. Raizō luego arrastra a Yūsuke a las alturas del Módulo para reiniciar el sistema, y finalmente encuentra el interruptor cuando este último cae por el piso dañado por la batalla. El clima frío también comienza a empañar los espíritus de las chicas Sakimori hasta el punto en que Takahi y su camarilla comienzan a culpar a Shōko y Saki.

A pesar del intento de Haruto de detenerla, Saki aborda el Valvrave Four y, para su sorpresa, completa con éxito su procedimiento de puesta en marcha. Al observar en secreto el éxito de Saki al pilotar el Valvrave Four, L-elf deduce que la instalación subterránea no se construyó bajo Sakimori High por casualidad, ya que los estudiantes cumplen con algunos requisitos para operar los mechs comparándolos con el intento fallido del soldado ARUS. Después de un poco de diversión, Saki se lamenta de su pasado, lo que hace que Haruto baje la guardia y ella lo muerde, cambiando su conciencia. Luego, Haruto (Saki) usa la cuenta WIRED de Haruto para ayudar a aumentar su propia popularidad como ídolo. Cuando se enfrenta a Haruto, y poco después a Shōko, ella afirma que si no afirma su condición de ídolo, todos se olvidarán de ella.

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 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.