Ayato thinks of how they can never go back since they aren’t human, but Quon says that they are. Itsuki and Haruka go to headquarters and Itsuki says they’ll probably send the Vermillion to intercept them. Megumi reaches the command center and Helena tells Jin to send the Vermillion, but Jin doesn’t want to use it against their compatriots. Makoto laughs and says they’re going to charge Ayato with high treason. Makoto orders Elvy to launch and says that if he resists, Ayato’s life is not an issue. Makoto goes on about Ayato having no rights since he’s not human and tells Jin he’s a responsible soldier. Haruka meets Elvy in the hanger and asks a favor. The Vermillion launches. Ayato asks if the RahXephon belongs to Quon, but she says her’s is different. They hear a D1 aria and Quon says it’s welcoming them. The Vermillion closes in and Haruka complains about how cramped it is. Allegretto waits for them and Elvy recognizes it as the one she fought in Tokyo. Elvy targets Ayato and orders him to return. Haruka pleads with him and says it’s not the right time for him to go back. Ayato says he just wants to know the truth and Allegretto attacks Elvy. Elvy asks if it’s Ayato’s friend and fights back. Quon says they should go and that the Vermillion will be fine. They head to Tokyo Jupiter while Elvy continues fighting Allegretto. She notices a quantum corridor opening and Allegretto scores a direct hit. The Vermillion crashes and the RahXephon and Allegretto go through the corridor. The Vermillion recovers and Haruka says they can use it to go after Ayato. Elvy reports it and Makoto says he didn’t authorize it. Jin says the orders were to bring them back no matter what and says it’s ok. Elvy activates the trans dimensional drive and enters Tokyo Jupiter. They see many Metronome Dolems floating in the sky and Haruka says she’s also returned.
Ayato wakes up in the hospital and leaves his room. A nurse tells him not to wander around and he asks where Quon is. She takes him to her room, where she is hooked up to life support machines. Ayato asks how they got there but he’s told to go back to his room. Elvy hides the Vermillion in a forest and they head into town. Elvy asks if Haruka knows where they’re going and she reminds her that it’s her home town. Ayato is questioned by a doctor and asks to see his mother. Reika appears and tells him she’s there and Ayato sees Maya along with Masayoshi Kuki and Shinobu Miwa in Allegretto’s hanger. Kuki reports that Quon hasn’t stabilized and Maya chants in another language. Ayato wonders if it’s really the truth and smashes a mirror with a chair. Quon wakes up and starts chanting. Elvy wonders why the citizens don’t notice the Metronomes and Haruka says the mind control must have strengthened. They take a train and Elvy says she always wanted to visit Japan and she was kind of happy she’d get her chance when Tokyo Jupiter was formed. She asks Haruka what’s between her and Ayato and Haruka just says he’s important. Ayato is about to cut his finger with broken glass when Maya enters and welcomes him back. They visit Quon and she says she’s fine. Her and Maya speak in another language and Maya says she’ll visit again. Maya drives by Hiroko and Mamoru and Ayato tells her to stop. Hiroko says Ayato’s changed but Mamoru says people don’t change much in a month. Hiroko says she was worried because no one seemed bothered he was missing. Mamoru tells her to stop and that Ayato was just away on a family trip. Ayato asks about Reika, but the other two don’t remember her. Hiroko freaks that she’s forgetting something and Mamoru tells her to knock it off. At home, Ayato bites his lip and draws red blood. Ayato asks Maya what she is and she bites her finger. She puts some blue blood on his lip and he freaks out.
Aside from Ayato returning to Tokyo Jupiter, there’s not much going on in this episode. I don’t really get Haruka. She sent him off last episode, but she decides to chase after him anyway. I never really liked her. Hiroko also seems to be getting wise to the fact that things aren’t as they appear. Now that Ayato’s home, hopefully we can get some answers.