Shu watches in disbelief as Mana awakens and a stream of pink energy starts to spread across Earth. Realizing they're running out of time, Argo and Ayase decide to hold off Daryl, allowing Haruka to advance. Elsewhere, Tsugumi is having trouble taking control of the building due to someone's interference, and Shibungi correctly guesses the culprit is Kenji.
Awakened, Mana greets Gai before running blithely to Shu and hugging him. Saying that they can finally be together, Mana gloats that she has fully taken over the body of Inori, whom she calls a fake and a monster. Shu angrily shoves Mana away, saying Inori is human and declaring Mana the monster. Enraged at having been rejected a second time, Mana threatens to make Shu pay, only to be stopped by Gai, who states he will kill Shu before drawing Mana's Void: a sword similar to Inori's. The room alters its interior, setting the battlefield for Gai and Shu as Mana begins the Fourth Apocalypse.
Mana's power resonates on a worldwide scale, incasing most of Earth's life in crystal. As he clashes with Shu, Gai cites the apocalypse as the next step for mankind: perfect consciousness forever preserved in crystal. Due to the large genomic resonance, the UN Endlave system is shut off, neutralizing Ayase's Steiner, which Daryl mocks is due to their old technology. While Argo is able to defeat the ghost units, he is unable to hit Daryl, who is protected due to his Void Genome Emulator, which allows him to use his own Void while piloting. Ayase tries to directly connect to her Endlave with a cable, but is stopped by Daryl.
Even with his arsenal of Voids, Shu struggles to keep up with Gai and is quickly overpowered. Shu questions why Gai's objectives have changed from Roppongi, but the former leader of Funeral Parlor simply states Shu would never understand. Elsewhere, Shuichiro Keido revels in his achievement, declaring he has finally outshined Kurosu Ouma. Keido's monologue is interrupted by the arrival of Haruka who holds him at gunpoint.
Standing over his weakened opponent, Gai criticizes Shu for refusing Mana, stating he is no longer worthy of having her or the role of Adam. Just as he begins losing hope, Shu notices the flower that Inori's tear left behind and sees a vision of Inori, encouraging him not to give up and Shu manages to extract Inori's Void from the flower. Fighting for control, Inori disrupts Mana's power and Daryl, who received some of the feedback, is slowed down. Meanwhile, Kenji's computer suddenly stops just as Shibungi, having tracked his location, kills him.
Shu, using Inori's Void, is now able to match and then overpower Gai. Meanwhile Inori's interference allows Ayase to connect to her Steiner and have Tsugumi remote control part of the Steiner to defeat Daryl. Keido then commits suicide by injecting himself with the Apocalypse Virus. As he dies, he tells Haruko that in the end neither he nor Kurosu won.
Dealing him a fatal blow, Shu holds a dying Gai as his former friend tells Shu to never change. Shu then receives a vision of the post-apocolypse world Daath desires as Gai narrates. Gai then takes Shu to the same church where Lost Christmas occurred where he sees a young Mana and Gai still there. Gai reveals the only way for Mana to truly be put to rest is to allow her to fulfill her purpose. Gai, who loved Mana and was afraid of being the second choice to Shu, took it upon himself to save Mana from the Daath who kept reviving her. Gai reveals he wanted Shu to be the one to put himself and Mana to rest.
Declaring his role complete, Gai embraces Mana and both of them crystallize as he tells Shu to save Inori. Finally at peace, Gai and Mana fade away and, as Shu's vision ends, Gai's Power of the King returns to Shu's hand. Back in reality, Shu sees a weak and blind Inori wandering towards him, almost fully crystallized. She mutters her gratitude to Shu, stating that it was thanks to him that she experienced wonderful emotions. Shu embraces Inori, who immediately recognizes him and Shu tearfully states they will move on together. With Gai's power in addition to his own, Shu activates his Void and absorbs every remaining Void and Apocalypse Virus, removing both from the face of the Earth. The resulting feedback of Shu's power destabilizes the GHQ Headquarters and the tower begins collapsing. Elsewhere, Rowan drags Daryl to an elevator and throws him in, much to Daryl's surprise. Believing that deep down he has a good heart, Rowan sends Daryl away, but allows himself to be gunned down by the advancing soldiers.
As Shu completely crystallizes, he has a vision of Inori who once again offers him the 'Guilty Crown' (in the form of Cat's Cradle). This time, Shu accepts it, thus trading fates with her, and screams in anguish as a smiling Inori fades away from his vision. Suddenly, Shu finds himself free of his crystal prison, the crystals, along with Inori, shatter away. The GHQ building collapses and the remaining members of Funeral Parlor evacuate. Ayase hesitates to leave without Shu, but, running out of time, Argo forces the group to evac. The survivors watch in awe as GHQ topples to the ground, their battle finally over, though Ayase can only weep.
A few years later, peace has returned to a revived Japan and a video of Inori singing "Departures" is seen playing on an LCD panel of a building. Inside the building, Ayase, Yahiro (who now has a job), Souta, Tsugumi (who is going to take a teacher's licensure exam) and Kanon are having a get-together, honoring the late Hare's birthday. Shu is the last one to arrive and is seen with a prosthetic right arm replacing his missing one and uses a sight cane, having apparently absorbed Inori's blindness. The others warmly welcome Shu who joins his friends as they begin the celebration together.
Later, Shu is seen resting on a bench facing the river. He puts in an earpiece as he envisions holding Inori.
Tropes in this episode:
- Bittersweet Ending: Mana and Keigo are dead and the GHQ is defeated, the Apocalypse Virus is removed from existence, and Japan is liberated. However, hundreds have perished in the apocalypse; Inori, Gai and Hare are dead; Shu is blinded in the eyes and has a robotic arm, and Funeral Parlor is dissolved.
- Distant Finale: The ending takes place a few years after the Final Battle.
- Where It All Began: The Final Battle takes place in the same location where Inori is escaping in the beginning of the series.