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’s 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.

Haruto, L-elf and Takumi learn from the Pino AI that the Valvrave 01 began extracting the Runes of Marie's life force when she ran out of memories, killing her in the process. Also showing mild signs of the same phenomenon, this new revelation rattles Haruto to the point of becoming terrified of operating the Valvrave 01.

When the New JIORians learn of the Phantom ship's course to the Moon L-elf decides to use the location of an antique multistage rocket to return to space after rescuing some captive JIORian citizens in the nearby city of Dorssiana—of which Haruto's distant father Soichi Tokishima also resides. The New JIORians later infiltrate the city to secure the rocket while Haruto, L-elf, Kyūma and Takumi rendezvous with Kriemhild's Royalist squad. However, when Kriemhild mentions a person called "Mikhail" L-elf acknowledges it to be his pre-Karlstein name and abandons the operation to search the city for Lieselotte. Moving ahead with the plan, Haruto and co. meet up with the captive JIORians who all turn out to be the scientists behind Project VVV, with Soichi himself at its head, much to Haruto's shock. Soichi explains that the project used JIOR military funding to create new lifeforms with the goal of transcending the human existence—using the genetically modified embryos of the Sakimori students. As Soichi begins to revel in the project's success, Haruto fails to reason with his father about the curse that their ability has become before punching him and adamantly stating his goal to destroy the Valvraves. Meanwhile, as Cain becomes aware of the New JIORians plans, L-elf manages to successfully break into Lieselotte's prison tower and asks to let herself be rescued.

L-elf declares his love for Lieselotte while Q-vier later intercepts their escape attempt. Cain also anticipates L-elf's plan of using the rocket and has his forces surround the hanger and destroy its runway.

Upon arriving in outer space, the Valvrave pilots manage to locate and destroy the threatening Phantom ship and return to Module 77 to a grand reception by their schoolmates.

ARUS News reporter, Barlet broadcasts his discovery of the Phantom ship in Module 77's hangar filled with captive JIORians being drained of their Runes. The Magius then has Amadeus claim that the Dorssian Military were at war against the inhuman Module 77 occupants. Anderson immediately takes action by deeming all the Module's inhabitants an international threat and Youhei Onai's untimely death triggers a massacre of the Sakimori students. Anderson then forms the Dorssio-ARUS Alliance with Amadeus to eliminate Module 77. As the remaining students scramble to escape, the last ship gets damaged by the incoming united armies. Out of fear Iori Kitagawa and the other occupants then trick Haruto into the ship claiming Anderson's offer of safety in exchange for Haruto. However Iori's rages bests her and she shoots Haruto—who resurrects. Feeling betrayed by Haruto's secrets, Shōko agrees to hand over Haruto and L-elf. Anderson then reveals his ploy and orders the ship be destroyed, however the Valvrave 05 protects it. Kyūma then has Akira and Raizo protect the ship while he goes to save Haruto despite Unit 05 sustaining heavy damage. Kyūma then manages to rescue Haruto and L-elf and after finally getting Haruto to admit his love for Shōko, Kyūma throws them to safety before he and the Valvrave 05 destroy the attacking Kirchbaum with a suicide attack.

After having crash landed on a remote part of the moon Haruto mourns Kyūma's death while L-elf tries and gives up on devising a plan. At the same time the Dorssians transport Module 77 to a Dorssian Dyson Sphere. Elsewhere, A-drei interrogates Saki on L-elf's betrayal and realizes that he was acting on their shared goal of revolutionizing the corrupted Dorssia. Meanwhile Haruto and L-elf start blaming each other on everything that had happened which quickly escalates into a physical confrontation. Meanwhile, Shōko decides to pilot the Valvrave 01 and protect the Sakimori students but finds it inoperable until presented with the start up question. The Pino AI then replays the video of Haruto first piloting Unit 01 and she breaks into tears after realizing that everything he did was for her. Back on the moon, Haruto reveals to a disbelieving L-elf that Liselotte was a Magius, with the latter soon connecting the dots. After realizing that they have much yet to accomplish before they die, they put aside their differences and agree to build a unified world where everyone including humans and Magius can live in peace. They then manage to ignite a rescue flare using Haruto's Magius powers which draws a squadron of Dorssian mecha. Much to Haruto and L-elf's surprise however Saki and the Valvrave 04 show up and rescue them. At the same time, X-eins demands answers after A-drei releases Saki.

X-eins listens to the audio recording from H-neun's earring and decides to join L-elf to avenge H-neun and take down Cain. L-elf infiltrates Module 77 by posing as an injured Dorssian soldier and meets up with A-drei, who joins him in his rebellion. While Shoko and some other students are treating the injured, Haruto appears.

The modified Valvrave 02 piloted by Cain destroys the Module 77 communications terminal and proceeds to clash with the Valvrave 01. As Unit 01 becomes overwhelmed by Unit 02's power, X-eins' Kirchbaum intercepts the duel to avenge H-neun. As the Magius also pass off the conference's events as an act to the world, A-drei's Kirchbaum finds himself blocked by a battle crazed Q-vier. When Unit 01 finds itself blasted straight into Module 77, X-eins mounts a failed suicide attack against Unit 02. In the midst of Haruto's Rune deprivation, L-elf shows up and they combine their skills against Cain by way of a possession. At the same time, A-drei kills Q-vier after failing to reason with him. As the Valvrave 01 and 02 head into space once more, Cain blames the Valvrave pilots for disrupting the Magius' attempt at world peace. Amidst the chaos, President Anderson also exposes the Magius to the world, sparking various Dorssian uprisings in favor of the Royalists. As Unit 02 pushes Unit 01 to its limit, Haruto calls upon the fighting spirit of his friends, amplifying Unit 01's power and brutally destroys Unit 02, killing Cain whilst also losing all of his memories in the process. In the aftermath, L-elf awakens in the cockpit and rushes to a weakened amnesiac Haruto. Realizing the steep cost of their victory, L-elf sheds tears for his friend before Haruto passes on. In the epilogue, humanity bands together to hunt down the remaining Magius while peace finally dawns on the new world order. Finally, as Saki and Akira conclude the origin story of the Third Galactic Empire to the Prince, Shōko meets two hostile alien lifeforms in the Memorial Core and offers them friendship—echoing what Haruto would have done.