In a word, wow!
Although I did spend a lot of these final three volumes happily checking off the expected plot revealations there were enough twists to keep me chortling happily. So I was expecting Bahbem's major revealations that the Xephon project itself was the cause of the Mu's removal from our world. (Or would it be more properly thought of as humanity having been removed from their world?) That the war with the Mu was largely a bit of a sham all designed to give Maya the needed time to prepare Ayato. It even explained nicely that the time differential was simply a side effect of keeping Ayato disjoint from the world which allowed him to grow up unaware of his instrumentalist potential.
I also wasn't at all surprised to see that the Vermillion contained a Dolem within. The signs were pretty clear that these were offshoots of the Xephon itself in general design. The real deal maker was Quon's comment that they warped the Ollin's tone making it quite clear the Vermillion were tied to an Ollins purpose quite closely. Also expected was the revealation that Shirou Watari is indeed Ayato's father.
But what I wasn't expecting was the tricky games played with Itsuki and Quon. Finding that Quon is really Ayato's mother in a sense much stronger than simply figuratively was a surprise. Going back and checking the relevant episodes near volume three the signs were clear that Quon was indeed one of the two spirited forth but what threw me was the age question. I simply hadn't expected that Quon would held in stasis for so many years making her just as much adrift in time as Ayato is. It was a neat touch that preserves the carefully balanced duality/similarity thread that connects both Quon and Ayato throughout the series.
Itsuki's relationship to Ayato is also one that should have been obvious. The end of volume five, where Ayato wears glasses while on the run with Asahina, showed the two were so very similar. For reasons unclear it never occured to me to consider them to be twins even though I had noted that explicit mention was made that Itsuki was the same age as Ayato. Seeing as Haruka was mentioned in the same sentance I think I simply mentally skipped a beat. Again in retrospect with the big deal made during the episode featuring the Foundation Trilogy about the heavy use of cloning by the Foundation it should have been fairly obvious.
The series definitely played fair giving you the clues to work it out. Perhaps the biggest unexpected surprise is precisely just who Futagami is. As expected he was indeed one of the few human leaders present in the series who hasn't been manipulated by either Mu or Bahbem. It was nice to see that his humanity contained a healthy disrespect for godmakers. Bahbem so desperately needed such an ending that as it came I was happily cheering.
While I have enjoyed the English dub greatly there is one issue I do have with it. Towards the end Bahbem talks of waiting tens of thousands of years. Yet the subtitled translation talks of waiting tens of thousands of years, he thinks. That 'he thinks' is important and while I can understand that the temptation to think of it as irrelevant must have been strong from a superficial reading of the script it really should have stayed. Checking the backstories history you can see the explicit linkage to the Mayan Long Count of timekeeping. This only spans five and a bit thousand years so having the indication that Bahbem has lost count of how long it has taken fits with the actual history the series is based on.
Removing it breaks this linkage and is perhaps the biggest mistake I have found in the dub as a whole. Which really means the dub has been splendidly done if this is the biggest complaint I have. It is worth trying the dub out even if you traditionally prefer subtitled viewing simply because the track gives the wonderful musical score room to breathe.
Two very nice touches that lend the series the right feeling of closure is the staging of Ayato's final choice to be occuring in the subway station where he first met Haruka (in terms of the series episode order, not its chronology.). If you notice the first episode introduced this station in the second half of the first episode. It is therefore fitting that it uses it as the set for the first half of the last episode, giving the series the feeling of returning full circle to where it started.
The other nice touch is in both the final after credits scenes that explain exactly where the image Ayato keeps painting comes from but also in the way this image has been used through the series. If you remember Ayato was painting it in the first episode but the sea was overlaid with Mu derived designs and shapes similar to one of their floating cities. Given that we now know that the Mu were trying very hard to erase his memories of the outside world and in particular his memories of Haruka then it is no accident that the image is underlaid with Mu design themes near the start of the series. A very clever visual touch that you only fully appreciate after seeing the series through.
For those who are interested I have placed a timeline of the RahXephon series here. It lists all the major events that occur and a few conjectured ones that had to have occured. The definitive answer to exactly what was going on is contained in the RahXephon bible, something I didn't own at the time of writing these pages but have since acquired. Even that book only covers events up to around episode 19 or so, so does not contain the complete answers for the whole series. It did point out one or two allusions I missed - particularly the 'Operation Downfall' which I was completely unaware was the codename for the planned invasion of Japan.
I have to wonder if the major change that Ayato made when tuning the world was mainly to remove the Xephon System and it's creation from occuring. The Mu empire then simply falls into oblivion for a different reason although still something that destroys the continent.
Anyway what a fun satisfying ride it has been. Not often you get series constructed as tightly and carefully as this one. I think perhaps the one biggest remaining question I have is why the fields and barriers generated all look like Jupiter?
Ah well, some things are best left as a mystery...