The first two episodes of Rahxephon built its setting up through continually changing the goalposts of what information the viewer had; each answered question so significantly changed the perception of the setting that it created new ones in turn. Yet finally the viewer has the best possible picture of what they are dealing with; the Rahxephon itself is a superweapon similar in kind to the Mu’s other terror weapons the Dolems. Securing it – and its apparently chosen pilot Ayato, the Olen who the Mu are eager to track down – is the mission of a human strike force sent into Mu-occupied Tokyo.
Now a basic storyline has been established – that an alien civilisation has masterminded an invasion of Earth to some degree, and is capable of shutting entire cities and apparently nations off from outside contact and convincing the people within that all other humans are dead – the questions that remain are what drives the story forward. It is clear there is an organised human resistance with powerful weaponry and an established military which knows significantly more about the Mu than anyone else. It is clear that Ayato is at least partly a Mu himself on his mother’s side – although crucially he did not know this. That the revelation of his mother Maya’s alien physiology was apparently a shock to him as well as the viewer redefines the nature of the Mu’s occupation. It has been shown they can imitate humans – but now it is clear that people cannot tell them apart from non-Mu.
This episode begins with the conclusion of the confrontation between Ayato and his mother; she is trying, by force if necessary, to bring him home. While her affection has always been distant and sinister (as scenes of her monitoring his phone calls in episode 2 show), now she has made her move as everything that is known about the Mu’s modus operandi breaks down. The Dolems are now acting uncontrollably to attack the Rahxephon until Ayato’s mother steps in to assume direct control over one. As the Dolem prepares to attack (and a second breaks into the shrine to back it up), Ayato’s mother meets Reika for the first time – and is apparently shocked to see her. The visual framing of this scene – Maya on the shoulder of her Dolem and Reika on the shoulder of Rahxephon – is obviously framing the pair as enemies and indeed they apparently know each other. Yet this is a fight nobody is ready for – the woman in red, the emissary from the humans who was supposed to extract Ayato from Mu territory, tries to get him to stop piloting the Rahxephon and he has to save her as the shrine collapses. Thus begins the first battle – and with it more revelations. Maya calls Reika “Ixtli”, a name not previously referenced, and Reika herself is now different. She is communicating with the Rahxephon – and by extension Ayato – as if in a trance, ordering it to sing “the song which is forbidden… so that someday all will become one”. The alien prophecy is a stock plot device in science-fiction and especially more supernaturally-themed stories (an immediate precedent in anime of a robotic construct at the centre of a prophecy is Do You Remember Love‘s early scene where the alien archivist Exedol warns his superiors not to “meddle in the affairs of microns [humans]”, or the legends of the “tenth civilisation” in Ideon).
Yet this symbiosis is a short-lived one. The Dolem summarily annihilates Reika with a single shot while the Rahxephon remains unscathed by the near-miss. All this achieves is to anger Ayato – and in the process the machine continues to reveal new functions. The second shot – aimed to kill – is deflected by a force field and with a single punch the Rahxephon completely destroys the Dolem. Previously its invisible beam weapon had severely damaged one, but now it is more fully operational a single blow is enough to disintegrate the enemy. The slow process of the Dolem’s total destruction is mirrored by its controller’s own apparent painful death – it is now ever clearer that the relationship between the Mu and the Dolems is an empathetic one. However, these now capacities Ayato has discovered are not simply combat abilities – apparently on autopilot it enters a wormhole-like event and vanishes. According to the Mu it has “leapt the Barrier” – thus implying how they have maintained their control over the city. But Maya is apparently not concerned by this – or indeed worried Reika/Ixtli is dead. She claims they will both return to Tokyo in time.
The new question – the one which ultimately is the most immediate – is if Ayato has left Mu territory, where is he? The answer appears rather mundane – a deserted town, the horizon dominated by the Mu’s force field with which they keep the citizens of Tokyo trapped. He has never properly had agency in this story – everything acting around him autonomously or supernaturally, or other characters knowing more than him – but now he is more powerless than ever. He is in the woman in red’s homeland, the Earth outside enemy lines and now he is being educated about the truth of the world, and the viewer with him. The Mu force field is called Tokyo Jupiter by the humans. The world was not totally destroyed or depopulated as Mu propaganda claimed, only parts of it affected by their invasion. Yet most confusingly, it seems as though far longer has passed outside the barrier than within it – the part of Japan they have ended up in is a deserted, derelict wasteland. Ayato and his companion trawl through abandoned supermarkets to find food but not everything is as it seems – he still believe it has been only three years since the invasion, but the woman claims otherwise. It is only when they listen to a news report claiming it is 2027 that it begins to become clear. Ayato believes he was born in 1998 and the year is 2015 but the truth is that time has moved quicker outside the barrier than inside it. Now, two and half episodes later, the mystery set up by a passing shot of an unusual watch back in episode 1 is made clear.
Now what matters more to Ayato is whether the others – still inside the barrier, with its different timeline – are all right. That they apparently are reassures him. Yet nevertheless, when the woman awakes, he is gone, run away. His wandering in a deserted country gives a sense of scale to what the Mu have done – the damage that these extra 12 years have caused to Japan. If Tokyo within its bubble is a control population under constant scrutiny and control, Japan outside is in its own kind of stasis, abandoned to its fate. Yet the fact there are radios and telephones that work, and food still in the shops, suggests it may not be completely abandoned. Indeed, the silent cityscape is interrupted by a telephone ringing. Yet the caller is Maya, from within Tokyo. She warns Ayato that the enemy – the humans fighting the Mu – will try to make him “forget” what he knows, and indeed this has been corroborated by the education he has been force-fed previously about the time difference. She reiterates again and again that this unknown woman, who is knowledgeable about the world outside the Mu’s influence, will turn Ayato on her but he is now divided – he knows his mother is one of the Mu, and knows that the Mu are apparently the real enemy, lying to the humans, but at the same time still feels affection for her. As the phone call degrades into gibberish, he finally begins to properly rationalise what he has seen – that his mother is not human – and he runs to the edge of the barrier as if to try and get back in. It is there the human woman finds him again, explaining more about the barrier. Her non-stop exposition interspersed with reassurances of her trustworthiness is suspicious, Ayato’s desire to run away and find out the truth himself understandable, but the ultimate revelation she makes – that even with the Rahxephon’s help, the journey out of the barrier was a one-way trip – sets the scene for the foreseeable future.
The closing image of this conversation, in which Ayato is apparently permanently separated from his mother, is of the barrier reflected in his eyes, evoking of all things the red flare in his – and the Rahxephon’s – eyes when Reika died and it destroyed the Dolem. Again he screams in anger, but this time without his machine, without the supernatural intervention, he cannot achieve what he wants to. Again the camera returns to an image picked up briefly in his wandering through the city, a poster for a science-fiction film called Goodbye Jupiter and a news clipping saying Tokyo Disappears. Now their only concern is survival – returning to the remainder of humanity and making their own life. As they resign themselves to this, almost sympathetically there is a sign of life – a stray cat that has been surviving in the abandoned city. With it accompanying them, the woman burns the boat they have been sheltering in to make a signal-fire, and come the morning the next arc of the plot has begun in earnest with the arrival of the Lilia Lityvak – the human warship from the prologue of episode 1. Finally, after an entire episode of orders and dragging Ayato around, and two episodes of mysterious intervention, the most obvious mystery of all – who is this woman – is resolved. She is Haruka Shitow, a representative of TERRA, mankind’s main fighting force.
It has taken three episodes but now, finally, Rahxephon has begun to resemble a mecha anime in more concrete terms. There is a clearly-defined alien threat in the Mu, a mysterious, prophecy-driven fighting machine in the Rahxephon and a support crew and organised army in TERRA. This long buildup with its mysteries and continued redefining of what the viewer knows makes these revelations if anything more effective; Evangelion, the series which in part inspired Rahxephon has a cold opening that within one episode explains the nature of its own threat (the Angels), the nature of its opposition force (NERV) and the presence of a robot (the Evangelion itself). The introduction is rushed through, creating a different sort of disquieting setting; protagonist Shinji is given no answers, simply orders. He begins as a naif, apparently ignorant of much of his world despite living in it. Ayato on the other hand, through these opening episodes of Rahxephon, is shown to be someone confident in what he thinks he knows who has his quiet life undermined and destroyed. If anything, this presents the Mu as a more insidious threat; they have attacked and controlled part of Earth so effectively that in apparently three years they have normalised the population to their presence and indeed put their children into society. Evangelion’s Angels are initially shown as simply beasts – driven by a purpose (to reach NERV for whatever reason) but not controlled by a higher power, not the vanguard or peacekeepers or tools of oppression of an alien army. It is fundamentally the difference between a war of survival (if the Angels reach NERV, something bad will happen) and a war of liberation (millions of people live in Mu-controlled Tokyo and TERRA aims to save them).