Aboard Module 77 of the JIOR Sphere 01, Haruto Tokishima loses an eating contest to Shōko Sashinami for use of their school grounds while unbeknownst to them, five undercover Dorssian Agents infiltrate Sakimori High School. Sometime later as the agents scout the school for a destination, one of them has a brief altercation with Haruto over their differing worldviews. Afterwards, the Dorssian Agents infiltrate and kill the scientists in a covert lab under the school although a wounded scientist ejects their primary target, a giant mecha called Valvrave 01 to the school's surface.

Kyūma Inuzuka, Aina Sakurai and Saki Rukino arrive at the Valvrave's location to find an unconscious Haruto and L-elf. As the other Dorssian agents arrive, L-elf seemingly betrays his comrades and helps the students flee. Afterwards, as the Dorssian forces occupy Module 77, Haruto convinces his friends that he had somehow possessed L-elf's body and later retake the Valvrave, while he also managing to return to his own body with help from Saki. As the Valvrave activates and attacks the nearby the Dorssian ship, it finds itself knocked outside of the Module into space. A-drei and Q-vier then use Dorssia Ideal Mechs to attack the Valvrave 01 whilst believing that L-elf betrayed them.

The ARUS forces apprehend L-elf while he relays a strange string of words to Haruto. As the ARUS forces along with Senator Figaro provide relief to the students of Sakimori Academy, Haruto and his friends try and fail to deduce the nature of his new abilities. Afterwards, Figaro sends word to meet Haruto and urges him to become a symbol of hope in the war against Dorssia. Meanwhile, as L-elf escapes his captivity, Cain dispatches A-drei, X-eins, H-neun and Q-vier in another attempt to recapture Module 77.

President Jeffrey Anderson and the ARUS senate vote on obtaining the JIOR Valvrave weapon to aid in their campaign against Dorssia. Meanwhile after rejecting L-elf's contract, Haruto fails to stop Figaro from experimenting with Unit 01—resulting in the death of an ARUS pilot. The Dorssian fleet then makes an initial strike against Module 77 which prompts Figaro to prioritize his safety over the Sakimori students in a transmission intercepted by Shōko and Akira Renbōkoji. Shōko then uses drastic means to inform the Student Council of Figaro's treachery and while Takahi Ninomiya distracts the ARUS representatives, Shōko, Kyūma and Yūsuke Otamaya rescue Haruto. As Figaro attempts to leave, Haruto then appears and reveals his true intentions to the disbelieving student body. Having lost his patience, Figaro begins firing on the students until Haruto stops him with Unit 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.

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.