Haruka goes through a ride about the history of the Mu war, but she is actually listening to a report on how Quon’s data seems to have been falsified. Haruka picks up a secret file and wonders who Quon really is. Quon wakes up in the examination room and remembers that she’s human. Megumi asks Haruka how her trip was and she says the place hadn’t changed. Haruka puts sugar on her natto, which Megumi finds disgusting. Ayato tries it and says it’s pretty good. Makoto wonders if Quon is complete and Itsuki says she only got inside the RahXephon and didn’t actually pilot it. Makoto says that’s enough reason to try but Itsuki says he’ll make the decision. Makoto says Helena is arriving the next day and will want to see Ayato and Quon. Itsuki says Ayato will be evolving to a new state and that he won’t forgive him if he fails. Ayato says how Haruka is always working and that she doesn’t have a boyfriend. Megumi says she had one once when she was in school and they hadn’t changed their last name yet. TERRA monitors the dolem Arpeggio which is stationary in high orbit. Souichi says they can only watch it since they can only attack if attacked first. They go to class three combat readiness and wait for it to do something. Haruka wonders if the RahXephon could fight in orbit and Elvy says it hasn’t been tried. Sayoko appears and asks if they’re planning a girls’ night out. Elvy says it’s getting stuffy and heads to the hanger. Haruka tries to say something about the other day, but Sayoko says she’s nosey. She asks if Haruka knows about the first human the mu phase was detected in and if it was true it was recorded in 1989. Haruka says that was way too early and that the rest of the samples were taken from Tokyo Jupiter. Sayoko thanks her and leaves. Jin meets with Shougo and says it’s been a while. Shougo asks about Shirow and Jin delivers a gift from him, saying Shirow went to Russia again. Ayato changes after a test and Sayoko tells him Itsuki was pleased. Ayato asks where he went and Sayoko says he took Quon home. Sayoko tells him he should go see Quon later and wishes him luck. Haruka reads Quon’s history and sees she moved the day after the war began. Haruka remembers watching the news report when she was younger and her relatives telling her it was a good thing they left Tokyo before it happened. She reads how Quon looses her parents and moves in with relatives. Haruka remembers in college she met Itsuki and he talks about his studies on the hidden messages in music. She reads how Quon moved to Nirai Kanai and Haruka remembers the day she moved in with Shougo. Haruka remembers asking Jin why Quon was aboard during Operation Overlord and he answers that she’s necessary. Jin asks her the last time she was in Tokyo, and she says it was ten years. Haruka goes to the shrine and Johji finds her there. She says she won’t buy his fiction and he tells her to at least listen to the pitch. He tells her that the Bahbem foundation has had the same CEO since it was founded 1576. Haruka doesn’t believe him but he also offers her the medical charts for the first Mulian specimen. Haruka looks at them and is shocked.
Sayoko and Makoto meet at a bar and she hands him and envelope. Quon plays the violin for Ayato and asks if he wants to play. He says he doesn’t know how but she says he can because he’s an instrumentalist and that Ixtli wants him to play. Haruka asks Itsuki about Quon and that he never mentioned a sister when they were at school. Itsuki says they went through quite a lot and Haruka says he’s dodging the subject. He says she does it a lot as well, like the reason they broke up. Itsuki says she joined TERRA because her clock is stuck in 2012. Itsuki hugs her and says he wanted to get it moving, but he’ll only ever be a substitute. Itsuki says they’ve changed, and kisses her as Ayato enters. Haruka breaks away and sees Ayato and they stand in silence until Quon enters. Ayato and Quon both hear a D1 aria, but the other two can’t. Quon says it’s calling her and Ayato tells her not to go because the sounds are evil. Arpeggio sings as the RahXephon launches. Kim tells him to hold his position, but he goes over to Itsuki’s house. Ayato tells Quon not to listen and she remembers waking up with Bahbem by her side. She remembers back farther to two people saying she’ll understand and even farther to laying in the rain with another girl she identifies as Maya. Maya’s voice tells them to remember and that they must return to where they belong. Ayato screams and the RahXephon forms an energy bow and arrow. Quon says that it’s the path to destruction and Ayato fires, destroying Arpeggio. Makoto meets with Johji in a bar and asks if he recognizes the first Mulian’s medical chart because it had been taken out earlier. Johji has a look and sees a picture of Quon. Itsuki asks Quon if the aria called to her and she said it did. Haruka puts mayonnaise on her rice and Megumi says she should watch it because they have an easily influenced guy, but Ayato doesn’t do anything. Shirow asks Jin how Shougo is doing and Jin says Shougo said that Ayato is a nice young man. Shirow says he should visit him and asks about a package. Jin says it should arrive soon and a ship carrying Helena and the V1 Vermillion arrives.
This episode sheds some light on Quon’s mysteriousness and at the same time adds some more. It appears she has some connection to Maya and they were the two children that were spirited forth. Quon is also the first Mulian specimen, but for some reason hasn’t aged very much, which could only be possible if she was in Tokyo Jupiter. Another similarity to Evangelion in this episode is Arpeggio being rather similar to Ariel, the 15th angel. It even gets destroyed in a similar fashion with RahXephon’s coolest weapon, its energy bow and arrow. Itsuki has also caused a rift between Ayato and Haruka. Helena arrives with a shiny new mech, so it could possibly be time for Ayato’s mid-series upgrade.