Mulian cities continue to appear over the Earth and Ayato tells Haruka he heard Jin’s voice. Maya appears to Shougo and thanks him before saying farewell. Maya then walks up to Quon. A helicopter arrives and Johji exits, surprising everyone by saying he’s a Federation agent. Johji briefs them on where to unload the civilians and the fleet they will be joining. He says what happened to Jin was unfortunate, but he lives on inside all of them. Johji asks about Makoto and he’s in a cell, writing on the walls, saying he’ll make everyone pay. Itsuki says he needs to talk about his brother with Haruka and wonders if she knew they were. She says she did and that she also knew he came from the foundation. She says she wouldn’t sell out a friend and Itsuki tells her, as a friend, that he and his brother were created by the Foundation. He explains that the Foundation found two mulian girls and kept one asleep, never aging so she could become their genetic provider. He says it’s some one Haruka’s already met and that he wishes she could have remained human. Maya asks how Miwa, who is now wearing a dolem helmet, feels and she says she’s wonderful. Quon addresses Mamoru and says that hatred clouds his timber. She says Bahbem is on the move. Civilians leave the Lilia Litvyak and Kim reports to Souichi. Kim asks to stay, but Souichi assures her he’ll return to her. Dotems, Metronomes and Mezzoforte dolems launch along with Allegretto and Obbligato. Quon says Mamoru has lost his way and is having human sentiments. Johji tells Makoto to get ready for the inquiry, but he says he’s from the Foundation. Johji says the Foundation has never heard of him and that he’s been tossed away. He adds that Bahbem will be there too, so he can ask him himself. Johji says it must be hard on Itsuki, but Itsuki says they both deserve punishment. Ayato sits in front of the RahXephon and Reika appears. Ayato says they aren’t weapons and she says they are the music. Haruka appears and asks if it gave him any answers.
The Federation fleet is attacked by the dolems and the mass produced Schwarzer units are launched. Kim and Megumi head down to a boat but Megumi stops and looks at Ayato and Haruka. Megumi calls out to him and says she used to have a crush on him, but not anymore. She then calls out to her sister and runs down to the boat. Shougo puts a hand on her shoulder and she starts crying. The boat leaves and Ayato turns to Haruka. She comments on how tall he’s gotten and that she’s loved him since they were a couple in middle school. She says he doesn’t remember but he says he loves the current her. He apologizes for making her suffer and kisses her. Haruka is told to go and Ayato says he’ll come back. Elvy, Cathy and Jean launch in their Vermillions as the dolems easily destroy Federation troops. The Schwarzers arrive and take out large amounts of dolems. Ayato prepares to board the RahXephon and Helena appears, saying she finds no fault in him becoming the one. Mezzofortes take out a few Schwarzers and Allegretto tears away Cathy’s armor with it’s song to reveal a dolem underneath. Elvy cries out to her and Cathy’s Vermillion explodes. Helena says the Xephon is still incomplete but that Ayato will make it the true RahXephon and tune the world, since that’s what he was born for. Elvy charges at Allegretto, taking a few hits but firing into it at point blank. Allegretto swells up and explodes, Miwa disappearing as well. Elvy drops her guard and her Vermillion looses an arm and a leg. A Mezzoforte attacks but Jean knocks her out of the way. He takes the hit and tells her to fall back. He ejects but his pod is caught by a Mezzoforte and crushed. Ayato asks if he won’t be human anymore and Helena says bodies are only transient vessels and the will and consciousness go on for eternity. Ayato says he’ll be the one to decide his path. He says he’ll even discard his humanity to protect Haruka, but will remain himself in doing so. Reika says he will stay himself and they become one. Mamoru says Ayato finally threw off the guise of man and destroys a Schwarzer. The pilot’s helmet cracks, revealing Makoto’s face. The RahXephon glows and Itsuki apologizes to Haruka. Helena says no one can stop him, not even himself. Itsuki asks if Helena is even in there. The RahXephon is engulfed in a bright light and begins transforming. Quon says the door to the tuning is finally open and the RahXephon flies up.
The final battle begins in this episode, but first some farewells and other revelations are said as well. Itsuki reveals that he and Ayato are actually clones of Quon, which would explain why he calls her mother. Megumi confesses her feelings, but unfortunately for her, she can’t complete against Haruka. Haruka and Ayato finally have a heart felt moment and kiss. As I stated earlier I don’t like them as a couple, so for me and non romance lovers, the scene was rather bleh. Form an objective stand point however it was a touching moment. Cathy and Jean meet their ends here, but Elvy is finally able to take out Allegretto. With her Vermillion in such bad shape, she might not last much longer herself. Ayato merges with the RahXephon and has become complete. We’ll have to see next episode what kind of form he takes.