Rahxephon consistently walks a line between predictable story structures of super-robot animé and the implied more complex plot in the background; from its opening arc, which laid out both short- and long-term mysteries, it has settled into a clear second act where Ayato has become a part of TERRA and now does his part by fighting Dolems. The Rahxephon is still inscrutable and alien, but it is technology that can be used and its unpredictability is (as shown by the climax of the previous fight) predictable. While it remains unknown how the Rahxephon gets results, nevertheless it does and a sense of complacency – of the expected invincibility of the super-robot (in deference to its roots in very superhero-like stories such as Astro Boy) – emerges. Episode 9 begins with a return to the spiritual from the militaristic, and apparently promises answers; Futagami is exploring the island some more and chasing rumours that an excavated shrine experienced apparent supernatural occurences described as a “god descend[ing].”
From there, the focus returns to TERRA and its attempts at enforcing order and predictability; Ayato is in training and assisting Kisaragi with his experiments. As he fails to repeat even basic combat maneuvers in the test situation, another twist to the viewer’s understanding occurs; the idea that the machine may be sentient resurfaces, and that Ayato is not so much piloting it directly as giving it suggestions to which it reacts appropriately. As with the three-act setup of Episode 8, this is an inference drawn from a metatextual approach; many of Rahxephon’s mysteries focus on trying to establish or subvert parallels between its plot and the “expected” super-robot plot. The idea of an autonomous robot that is often unpredictable was considered as far back as early super-robot series such as Space Runaway Ideon and in other fashions in series such as Blue Comet SPT Layzner and perhaps most recognisably in Evangelion. TERRA and more noticeably the Earth Federation, however, seem oblivious to this possibility and blame Ayato. The background tension between the independent yet hugely-powerful scientific organisation and the apparent unified human government has not been so obviously raised for some episodes, being instead handled more subtly, making this conflict seem more shocking. Kisaragi, apparently the neutral scientist, tries to mediate, but the Federation officers continue to antagonise TERRA. As the scene concludes, however, a new development is revealed – Kisaragi wants to try piloting the Rahxephon and removing Ayato from the picture would make this possible. This lays the seeds, much as his taking the Dolem sample in the previous episode did, for a potential crisis at some point to a genre-aware viewer. Two stock-plot avenues emerge – either Kisaragi will anger the sentient Rahxephon and cause some kind of damage, or he will pilot, prove inept and need Ayato to bail him out.
As Ayato returns home, he encounters Quan; she tells him she knows he is having doubts, and embraces him; her behaviour is still cryptic and apparently ignorant of the discomfort she causes Ayato with her intimacy. Megumi, too, misinterprets her actions and confronts the two of them, revealing something of her own feelings too. Firstly an apparent affection, or at least duty of care to Ayato, and then a definite resentment of Quan, who asks if she may accompany Ayato and Megumi on a trip to the beach. While Ayato responds to her physical impositions with embarrassment and a fear of being misunderstood, Megumi responds to her social impositions with a grudging acceptance. It is clear now, though, that Quan is unpopular around some of TERRA.
The scene that follows is a strange reworking of the one before; Ayato is drawing on the beach (although this time it is Quan not Reika), a woman asks if she can model for him (this time it is Elvy, not Megumi) and Kim is once again the most social and relaxed figure present. Again the happy mood is broken – this time not by the unwelcome arrival of Kisaragi and Sayako but by Elvy getting into an argument with her subordinate and Kim stealing Ayato’s sketchbook. She notices how often he draws Reika, and it is this which ultimately ends the silliness that has begun; once Ayato explains that Reika was an old friend, she becomes more considerate and a more genuine conversation emerges. Kim talks about “The Great Mu War,” evidently the first attacks which sealed off Tokyo, and Ayato reveals he has finally come to terms with the fact his childhood was a lie. As if linked to this, the scene is juxtaposed with one of Sayako trying to find information on Makoto, the Earth Federation officer from the initial scene; her failure, as opposed to Ayato’s new openness, shows in a literal sense the figurative remaining mysteries.
A recurring motif in this episode has been a pop song that Haruka continually listens to; she had it playing in a brief introductory scene of life back at her house which marked the transition from Ayato in the lab to his meeting Quan, and she is listening to it again on this trip. Quan and Ayato both listen to it, and their conversations seem to suggest there is some significance to it beyond the immediate. As Haruka leaves, and at Makoto’s suggestion Kisaragi plans to enter the Rahxephon, the first signs of a plot thread for this episode begin to emerge; Quan and Ayato see Reika standing at a cliff-edge, but she has vanished by the time they reach it. Recurring visions of Reika have driven Ayato to victory in the Rahxephon, and now it emerges Quan sees them too. She leads Ayato into a forest, and in her questions – asking if Reika is “Important to Olen” – causes him to question his own relationship with her, and his understanding of what happened in Tokyo. The scene climaxes with an image that brings together the plot threads of the episode – Ayato and Quan standing in front of a strange temple (as alluded to by Futagami earlier) whose eye-like shape resembles both his birthmark and the shape carved in the ground by an earlier Dolem. Her final question, pitched in front of this portal, is a strange one – “Will you go back?” The concept of returning to Tokyo has not been raised since Ayato’s final contact with his “mother” – when she phoned him just outside of the barrier – and that it now arises at a time when he is beginning to doubt both his capacity to pilot and his understanding of what happened to Reika lays down a potential plot for a third arc.
Back at TERRA, the hinted-at conflict or crisis arc of the episode continues as Kisaragi tries to enter the Rahxephon. While he begins his experiment, Sayako confronts Makoto and reveals that his records only go back a month – while it has previously been hinted that Futagami was the mystery and Makoto was simply an unwelcome observer for the Federation, this has been changed. He threatens Sayako into silence while also trying to seduce her, perhaps continuing a trend of unwelcome intimacy (Quan’s apparent ignorance of acceptable behaviour, Elvy and her comrades’ lewd and raucous behaviour and now Makoto combining apparently sexual advances with blackmail). The two arcs then intersect – as the forest temple opens, Kisaragi is thrown back from the suddenly awakening Rahxephon. Quan says she knows the temple in one scene and then in the very next she does not, and surreal visuals – rapidly rotating trees and repeated pans over the same scene – make understanding the chronology of events in the forest less clear. Even stranger things happen in TERRA as the protective shield around the Rahxephon manifests into a ghostly, naked Reika, while Quan and Ayato enter the temple for it to seal behind them. Makoto again hints at his being more knowledgeable than thought – and thus also not the simple officious Earth Federation agent he claimed to be – by saying “The Goddess” is protecting the Rahxephon. As TERRA’s power fails, a very different kind of setup to the previous episode’s has concluded the first half of the episode. A number of long-term mysteries likely to upset the super-robot cliché complacency have been introduced, and Kisaragi’s interference with the Rahxephon (running parallel to Ayato’s own curiosity) have both separated the pilot from his comrades and also invited some kind of vengeance from the machine itself.
The action skips forward four hours; Ayato and Quan are still missing. Megumi continues to appear inherently distrustful of the unusual girl, more exasperated than concerned. Haruka subsequently finds the temple, but now it is sealed completely by fallen rocks – and then a physical deus ex machina of sorts occurs in the form of Futagami completing his own mission. The temple into which Ayato has vanished was the one he was looking for at the start of the episode, and the complete story reveals itself. Apparently, 38 years ago, two girls were found outside the temple. Futagami talks about how most mysterious disappearances are born from boredom or a desire for adventure, and how many missing persons who are in time found will vanish again eventually. He references Tokyo, calling it in essence a mass disappearance, and thus the purpose of his anecdote becomes clear; as Quan intimated, Ayato may have succumbed to his doubts and believed the temple is a way back to Tokyo. Meanwhile, the rebuffed Kisaragi is faced with tw concerns – what happened in the laboratory, and Quan’s disappearance. A montage of passing time leads into his ultimate decision to call off the search, against Haruka’s will. Meanwhile, all through this, Ayato wanders within the temple; he has been separated from Quan and they each have a series of visions. Ayato’s is of the Tokyo barrier, while Quan sees an egg-cup similar to the egg from which the Rahxephon emerged – and then meets Reika. It turns out she knows Reika, calling her “Ixtli,” and says that “The Olen is looking for you.” Reika’s response is more cryptic – she says the egg Quan found is “the cogwheel that turns time,” and from within it a heartbeat audible. As the conversation continues, Reika talks of “a world suffused with sound,” and some kind of inhuman music which can remake it. This is called “the true power”, wielded by “one who will tune the world,” or an instrumentalist.
Reika calls Quan “Olen” as Quan calls Ayato, and then the egg hatches to reveal a new vision; Futagami’s anecdote of the girls who appeared at the temple. One of them looks remarkably like Quan, creating a new tension; Quan is apparently young, yet Futagami’s story occurred almost 40 years ago. While this vision has circled around, if not directly engaged with, the relationship between Ixtli and the Olens, and the possible importance of the Rahxephon in this, Ayato’s is more direct. He falls towards Tokyo and as he does hears music – Haruka’s singing to herself outside the temple. What this has done is brought him out of the vision, breaking the spell on him.Quan, too, has returned – and her pose mimics that of the pink-haired girl in the flashback. Ayato explains what happened, and how while it was Haruka who brought him back from the vision of “home”, he never wanted to return to Tokyo because he finally feels he fits in at TERRA. Musical allusions have been introduced in an episode featuring the motif of a song, and Ayato begins singing that song as they return home; he claims it makes him feel nostalgic, even if he does not know why. The episode ends on an even more uncertain note; Makoto and Sayako are drinking together, and he gives her some kind of key which will “help him” (although whether this is helping Kisaragi use the Rahxephon remains unknown).