Episode 25 of Rahxephon begins with Ayato having “become” the Rahxephon, its true form being a giant version of him with design elements of the machine itself attached. This is, one could argue, the “mid-season upgrade” of the machine, its point where its true power is unlocked for the final battle – and there is definitely a final battle at hand, with the Mu controlling earth, TERRA in ruins, Narai-Kanai destroyed and the moments of love-confession and resolution passed. Rahxephon has toyed with becoming a super-robot anime at times, but never committed; some combination of events has always subverted or prevented action catharsis. In a way this is the ultimate in the robot representing the pilot – Ayato has never been particularly comfortable in his identity or at home in this unusual world, and TERRA has never really understood what it is doing – and so the “message” being pressed home is that there cannot ever be proper catharsis. When he tries to be decisive, he misunderstands the situation. When he vacillates, people die.
The idea of the super-robot being an embodiment or extension of the pilot is perhaps a science-fiction take on the maxim “人馬一体” (literally “Man, Horse, One Body,” reasonably translated as “The rider and horse are one”); it is certainly something some mecha anime have in mind, with the theme music for Super Robot Wars character Sanger Zonvolt titled “剣魂一敵” (“Sword, Soul, One Blow”). As far back as Mazinger Z the robot is what will allow the protagonist to “become God or Devil”, and the recent remake, Shin Mazinger, reinforced this catchphrase with a visual split between the pilot and the machine as two halves of one body. Super-robot anime combines the idea of piloted weapons of war, the triumph of science and technology over evil, with the super-hero archetype of one person given great power and the inevitable responsibility of its use. It is thus a logical progression that the machine as standin for the human should become something more; while “grandfather’s Mazinger” is a tool to become God or Devil (or surpass both), early series like Steel Jeeg had the protagonist “be” the robot (Hiroshi transforms into the machine’s head) and a common visual play – seen in some scenes in Z and ZZ Gundam and then later in the more super-robot-esque G Gundam – is for the pilot to be superimposed on the machine itself, anthropomorphising it to show a level of synergy and unity beyond simply piloting.
This idea in turn can be considered to develop into the machines themselves becoming conceptual tools, not simply representations of the pilot’s fighting intent but of the whole person for good or ill (God or Devil rearing its head again). Evangelion, among other series, reversed the pilot-into-machine relationship with the pilot feeling the machine’s pain. Ideon had the machine be one living entity, a collective consciousness the pilots accessed to gain power, with its own ideological pursuit of power. Thus one comes to Rahxephon where Ayato has become the Rahxephon. He has accepted his “true face” as, once an Olen, now the new Ixtli. He is unable to explain this to the other humans, and the episode ends with him beginning the “tuning” with the other Mulian Olen, Quan. The episode acts as a takedown, in a way, of the idea of the pilot becoming the machine being true power; Ayato has, certainly, attained massive power thanks to his unification with his machine – Ayato as the figurehead of humanity in a war machine that has his image, fighting the Mulian champion – but he is shown to not simply not be in control (as he kills Souichi and Elvy) but not to represent humanity at all. He represents the Rahxephon now, much as by the end of Ideon the Ideon represents only the civilisation of the Ide. “人馬一体” holds true here, for a very limited definition of “Man” which does not represent anything but Ayato Kamina. As a result, the final battle is between the Rahxephon-Ayato and the Mu, and is completely meaningless. Everything – Souichi’s efforts at humanity and heroism, Elvy’s pointless last stand (which does not give her her foreshadowed death trying to bring down the Mu, she simply misses her shot and is flying home when Ayato kills her with collateral damage), the Earth fleets and the Mu forces alike, simply dies when the Rahxephon looks at it.
The showdown is built up as a clash of ideologies and factions, champions duelling in superhuman form; it reminds me of the later series Tengen Toppa Gurren Lagann, which has a final battle fought on inconceivable, absurd scales; all of humanity’s brightest and best come together in a mechanical combination to form one unimaginably huge body that embodies an entire species, an entire way of life and ultimately an entire planet. They fight a similarly-sized monster in the Anti-Spiral, the selected champion of its own kind given a body to fight hand-to-hand with, and their fighting destroys galaxies as collateral. Yet as these two factions’ champions throw themselves at each other ultimate victory comes when Simon, the hero, rejects this whole reliance on a combined, complex machine; the Gurren Lagann is destroyed piece by piece to smash through the Anti-Spiral’s defences until only its smallest single unit remains, which strikes the winning blow. That moment is the epitome of “人馬一体” in robot anime – an entire ideology and survival instinct put into one blow. The same, perhaps, is implied in Rahxephon as Ayato, having apparently found his will to fight, becomes the ultimate weapon and demolishes in the way that the Rahxephon always has. But the destruction is in his own image now, he has had his moment of glory in the resolution of the love-plots and he is fighting to stop the Mu slaughter of humanity.
In return, all he does is kill everyone that matters to the people he is protecting, and then abandon humanity with reassurances that make no sense. When he tells Haruka “I was glad I was born as a human because it gave me a chance to feel things with my own heart” he is painting himself, almost parodically, as a Christ figure; some entity (the Mu, or the Rahxephon, or someone) sent a son down to Earth to live as a human and “feel things,” informing some ascension and reckoning called the retuning. It is the fitting end to Ayato Kamina’s robot-piloting career, really; his life revolved around Quan Kisaragi and his not fitting in owing to his Mulian blood and his lack of a family to connect with, and so his finally reaching the state of ideological figurehead leads to him accepting his ostracism and beginning the retuning.