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.