Souichi looks on and can’t believe it’s Ayato. The RahXephon grows wings and sings. Everyone one watches on and guards lie unconscious in Makoto’s cell. At the Federation command center Shirow asks what it is and Johji says it’s his son and calls him Professor Kamina. Elvy crash lands on the Lilia Litvyak and goes to her old fighter jet. Mamoru wonders if it’s Ayato’s true form and destroys some ships. The Lilia Litvyak advances and Elvy says she’ll use the TDD as a weapon. Souichi tells her no suicide runs and she says she’s not that crazy. Elvy takes off and a Mezzoforte attacks the ship. Elvy activates the TDD and fires it into the dolems, but Obbligato escapes before it’s destroyed with the rest of the dolems. Obbligato grabs the RahXephon and pulls out its cockpit. Ayato says he is human and Mamoru is surprised to see the pilot seat empty. The RahXephon grabs onto Obbligato and it’s face turns into Ayato’s. Ayato rips off Obbligato’s arms and sends out a sound blast. Quon says the time of tuning is at hand and starts singing. Ayato looks at himself and Haruka asks why he’s in such pain. Shougo tells her they have to go and Megumi holds back Kim, who calls out for Souichi. A badly injured Souichi says he did his best and Mamoru charges at Ayato. Obbligato hits a barrier and is destroyed. Ayato cries out and sends an energy wave that destroys all the dolems and ships, killing Elvy and Souichi. Kim cries out for Souichi as the shelter door closes. The energy wave continues and destroys the surface of the island. Ayato looks around, wondering if it’s all his doing and Quon tells him it is. He sings and disappears. Quon says that he will continue to live on and Maya says her role as the conductor has ended.
Calm returns and the former TERRA employees help treat wounded soldiers. Shirow thinks about how hard it is to go on but it’s what the survivors must do. Johji tells him they were ordered to retreat but Shirow says he has something left undone. Johji says he can’t let him do it because that’s what he’s there for. Helena, Bahbem and Itsuki sit in an old church while Sayoko wanders around. She hears a gun shot and see Makoto shooting a guard. Haruka and Kim see Ayato through the crowd. Makoto finds the church and kills the guards. He sees his face and asks what it is. Haruka follows Ayato in a forest Haruka says that Elvy and Souichi are gone and Ayato says he’s there. He says he’s inside the RahXephon and the RahXephon is inside him. Ayato says he is the RahXephon and that he’s not alone. Kim points a gun at him and demands her Souichi back. Makoto shoots Bahbem and laughs about his supposed immortality. Bahbem’s aide shoots Makoto and says he’s a D for designer and dolem before Makoto shoots her in the head. Makoto falls over and Itsuki rushes to his side. Makoto says no one calls him a D and dies. Helena adds that D is also for defective. Haruka and Kim fight over the gun and Kim wins. She shoots at Ayato but the bullets have no effect. Kim cries in Haruka’s arms and Megumi and Shougo show up. Ayato apologizes to Kim, but she says she just wants her Souichi back. Ayato says he is himself but no longer human. Ayato says he can’t change what happened and that he just wanted to see them one last time. Haruka says he’s still human but Shougo says he has lost his human heart and gained the heart of God, Yolteotl. Shougo says there is another that compliments him, and asks if he’s found it. Quon says there are two RahXephons that sustain harmony. She starts glowing and Maya tells her to live well with Ayato. Quon merges with her RahXephon and Ayato says he can hear her song. He says there is his world and there is Quon’s world. Haruka begs him not to leave but he says he was glad to be born a human because he had to chance to know Haruka twice. He says goodbye to everyone and disappears. Haruka says she can’t accept it because he was the only person she ever loved. Helena says she’s always been waiting for the conclusion, whatever it may be. Xephon Ayato and Quon face off and human Ayato wakes up in a barren land. He wonders what he is.
Ayato becomes the RahXephon and actually turns pretty grotesque. It’s a shame really because I always though the RahXephon had a really cool design. Ayato becomes god but with his lack of control he causes massive destruction, killing Mamoru, Elvy and Souichi. Makoto manages to kill Bahbem and his aide, but meets his end as well. With the death count up to 8 so far and only one episode left, who knows how much it could rise. Ayato and Quon have both become gods and now we’ll see who has the right to tune the world.