It has taken three episodes but the main plot of Rahxephon is finally revealed; the nature of the conflict against the Mu, and the world of Tokyo Jupiter, is now clear. The episode begins with a recapitulation of what is known to ensure that the viewer enters what follows completely clear about the world depicted, which if anything is a valuable device; while an attentive viewer knows all the information it provides, by laying it out plainly the audience are reminded of any basic developments they may have missed. It also clearly explains the future of the series; Ayato will pilot the Rahxephon and fight against the Mu. This sets it clearly as a mecha series; there are alien invaders, and a machine to fight them.
Yet immediately the viewer is placed on an even keel of setting knowledge, the cycle of building up mysteries begins again; the two figures from Episode 1’s prologue, the quiet girl in purple and the ship’s captain, recur. While their position within the plot is now clearer (they belong to the military organisation TERRA and fight the Mu) their role to play remains unknown. Yet these mysteries remain and the focus returns to Ayato’s acclimatisation in his new, unfamiliar world. Through the scene of him undergoing a medical (to apparently confirm his humanity as the emphasis on a blood sample shows, given the only difference apparently known between human and Mu is the colour of their blood) there is a rush of characterisation for Haruka; even though the viewer has seen her now for three episodes it has been on a military operation in hostile territory, and then stranded with someone alien to her world. Now she is back in familiar territory, what is shown reflects more on her “usual” character – a kind of respect for authority but a will to disobey it.
A whole new setting needs to now be established in a short time; the world outside Tokyo is largely business as usual. TERRA are shown to be a military organisation distinct from the main human forces, or Earth Federation, and disagreements break out over the ownership of Ayato and the Rahxephon. Again, though, the actual furtherance of the mystery takes place away from the protagonists, who continue to carry on with their developing friendship; the viewer, via Ayato’s conversation with Haruka, learns more about the stasis in which Tokyo sits (and how time moves slower there compared to outside). Yet this scene is a short one and at its conclusion the two threads – the official, almost conspiratorial plot and the engaging personal one – are brought together when the other outstanding piece of Episode 1’s puzzle is revealed. The pilot of the red fighter which escorted Haruka into Tokyo, and whose escorts were destroyed by the Dolems, is introduced as Elvy, and immediately another side of Haruka is shown. While Haruka has been shown as easygoing and almost an exemplar of the typical comically rebellious mentor figure frequent in mecha anime (other examples including, perhaps, Misato Katsuragi from Evangelion) her confrontation with Elvy reveals her to be somewhat more scheming and capable; she duped Elvy and her wing into going into Tokyo on what was likely known to be a one-way trip for most of the fighter pilots by getting her drunk and withholding important information. That the likeable, easygoing figure with all the answers so far lies on life-or-death issues such as operation plans thus forces the viewer to reconsider what has gone before in her more personal conversations. Everything she has said has been confirmed either by other characters or the narrator of Episode 4’s recapitulation, but there is now the possibility she is withholding information from Ayato.
The episode continues to provide exposition through personal moments, setting character-based comedy against a more serious and impersonal backdrop. The girl in purple is introduced to Ayato outside a ship’s barber, talking about red and blue stripes on the barber’s pole representing “red and blue blood vessels” yet wondering why blue is so important when human blood is red. She thus appears ignorant of the Mu physiology (as would fit her youth) but at the same time from her previous appearances – examining the Rahxephon and being on the bridge during Haruka’s operation – she is clearly a part of TERRA. The apparent ignorance turns out to be a strange sort of childishness or lack of awareness of how what she says could be construed; she invites Ayato to help her fasten her lifejacket, and talks about how she would rather have her hair cut while naked. Thus while the viewer is disoriented by her apparent distance and naivete compared to how she has been depicted before, this is translated in the plot into simple embarrassment for Ayato. That she calls him the Olen – the name by which he has been called by others previously and which apparently denotes his strategic value – simply completes the confusion the scene builds up. The girl is apparently either naïve or fearless – wandering around on scaffolding, acting without regard to how her actions make Ayato uncomfortable – but similarly knowledgeable in how she knows about the Rahxephon, and the Olen. If Haruka’s conversation with Elvy showed how she is capable of putting up an affable face to dupe others, this mysterious girl seems to be doing something similar.
Yet if, despite a scene introducing her, this girl remains an unknown, the ship’s captain is finally properly introduced. Makoto Ishiki, TERRA’s representative, supervises the impounding of the Rahxephon (called the “O Part” by the Federation) and reminds Ayato he has no rights in this situation. Thus Haruka’s front also collapses; that she has duped Ayato and Elvy is now clear to them both. Now, in order to restore trust, she promises to look after Ayato as the Federation clearly see him as disposable, a tool used to get the Rahxephon into their hands. This proves impossible; Ayato has begun to learn about the world outside, seen how he has been deceived, and also encountered what seems to be the frank truth of the Federation’s aims, the total destruction of Tokyo Jupiter using nuclear weapons if necessary. Set between Haruka’s attempts to reassure him are expository scenes from the Federation defining more clearly the nature of the Mu; while Ayato is probably not one of them, he does have elements of their DNA within his blood. What ultimately seems to bring him closer to Haruka is when she suggests that while others might lie to him for selfish aims, she only meant well. The scene ends with her taking a perversely maternal role, trying to simply talk away the problem with intimacy. It is short-lived, though; TERRA and the Federation are already one step ahead (having discovered his Mu DNA) and his cabin is in fact a high-security holding cell. Haruka is now the one on the back foot; her well-meaning lies have simply strengthened her superiors’ position and she is ultimately the one who was played for a fool. The Federation seek to simply contain and control Ayato, and take the Rahxephon – and TERRA are not planning to challenge this.
The coming of a Dolem in pursuit apparently of Ayato in turn confirms more things – firstly and most importantly that the Mu are capable of leaving their stronghold in Tokyo, if only via their remotely-piloted terror weapons. Conventional weapons prove useless – even the TERRA base’s advanced combat drones – and the Federation, now in possession of the one weapon proved throughout the series to be proof against the Mu, does nothing save use the confusion to cover their withdrawal. The conflict between TERRA and the Federation is now clearly spelled out; each side thinks predominantly of its own interests over those of anyone else. The “battle” against the Dolem, usually the highlight of a mecha anime, is nothing but a massacre; it boards the ship, with Ayato trapped in his cell and believing his imprisonment is just another of Haruka’s deceits, after having bypassed all of TERRA’s island fortress Nerai Kunai’s defenses. Yet at this point the supernatural forces that have defined the conflict so far come into play; Ayato has a vision of Reika on a computer-monitor, and the Rahxephon begins moving autonomously, responding in some way to his (and the girl in purple’s) situation. When the girl in purple has the same vision of Reika as Ayato – a vision which apparently results in Ayato’s teleportation inside the Rahxephon – the link between all three becomes more clearly evident, yet no better explained. The fight which ensues is again physical and decisive, almost a non-event; the Rahxephon punches through the Dolem’s shell and tears it in two without much effort.
TERRA uses their victory to reclaim control over the Rahxephon, and reluctantly reconsider their stance on Ayato – most interestingly, they have apparently been expecting its arrival and have constructed an artificial egg and shrine for it to inhabit. While they are clearly working against the Federation, it is also quite apparent their position is the stronger one. This episode began apparently offering answers to questions, and indeed provided a good deal of exposition about the nature of Rahxephon’s setting – but it did so, much as the early episodes did, by inviting many more and denying simple answers. The repeated shots of the girl in purple (as unnamed and enigmatic as Haruka was previously) and the emphasis placed on her apparently cryptic dialogue make her significance apparent but do not account for the inconsistencies and eccentricities of her character. That deceit and duplicity come to define everyone’s behaviour – Haruka’s for certain, and those of Makoto and his henchmen, and the Federation’s representatives too and even possibly the girl in purple with her conveniently variable extent of knowledge – makes the viewer’s position essentially equivalent to Ayato’s. They know what the series has proved, via out-of-character narration or simple visual evidence. However, they now doubt any speculation about what this will mean based on in-character dialogue.