Things begin to take further shape with Volume 3 as the hinted at player of the Bahbem Foundation begin to move into sharp relief, coming out from being characters referenced in one scene to now being obviously a major player in the Mu invaded world. The final episode of the three on the disc brings with a confusion of questions. It confirms for us that Quon is akin to Ayato in being an instrumentalist or 'ollin'. This was pretty clear from earlier with Quon both having similar sigils to Ayato on her but also with the Ixtli Reika Mishima talking directly to her and telling her point blank she is an ollin too.
What is a little more disturbing is character of the egg her Dolem is going to emerge from. Jet Black it clearly is an opposite to the RahXephon which does not neccesarily mean that it is evil but rather that it is likely to be a final tussle between RahXephon and whatever emerges from the egg that will decide the final fate of the world. It is too obviously symbolic that you have two ollin who are opposites in many ways. Quon is female, experienced in the events of the world but still quite naieve and very reticent to act. Ayato is male, oblivious to the world at large but definitely not afraid to do something even if he doesn't quite understand enough to make a wise choice in his action. The egg colouring looks to simply reinforce the point that the two have quite different and complementary approaches to life.
We also interestingly have got more reference to the initial events that sparked the standoff between humanity and the Mu. It is especially interesting that commander Kunugi was the person who fired the first shot only to be crucified by his superior officer for following orders. I wonder if we will get to see that officer in the future. It isn't too important as the more important revelation is the guilt that Jin Kunugi feels at both having killed civilians in that action and that it has also cost him his marriage. What isn't clear is if his daughter, who obviously was already upset at the time he has spent working away from the family, was killed as a part of that action or rather whether the public castigation and fallout from the attack cost him any chance of spending time with her. (Actually since writing this, I realise what a silly question that was - Jin was visiting a grave so clearly his daughter was killed as a part of the fighting at Sendai.)
If anything the theme of paradise denied rings through these episodes. Each one deals with a character having to cope with their own personal paradise being denied to them. Jin with his now completely destroyed marriage as his wife is moving on in life. Ayato as he comes to the realisation that he can't go back to Tokyo Jupiter now, not even one designed to cater to his every desire. Quon with her desire to be an ollin who for various unexplained reasons simply isn't ready yet. Haruka is wondering if what she wants is now impossible with Ayato steadily having closed himself off after the psychological attack by Dolem. Finally we get the hints that Lord Bahbem's daughter Helena isn't happy either as we have the confusing images of her being jealous of seemingly a younger version of herself.
Which leads me nicely to the Bahbem Foundation itself. Clearly these people know a lot more than anyone else bar the Mu on Mu technology. So the question has to be how? Have they discovered ruins in South America and been studying them since? Or were these rejects banished from the Mu's dimension for some reason? With the booklet hinting that Lord Bahbem himself having been around for a long time then clearly the next volume is going to have to spend some time bringing us up to speed on the back history of these mysterious people.
Finally we have Isshki. As we watch him ruthlessly use Nanamori to get the information he wants about Dr. Kusuragi we are buidling an image of a not particularly nice human being. He goads Kusuragi into attempting entry into the RahXephon and in the process drops an interesting tidbit. Namely that Kusuragi is as equally qualified as Ayato to pilot the RahXephon. Now call me crazy but they made a specific point in an earlier episode of mentioning that Ayato and Kusuragi are the same age but thanks to Ayato being trapped in the Tokyo Jupiter time bubble he has ended up somewhat younger.
Is Kusuragi a brother of some sort to Ayato? Perhaps a childhood colleague or friend? Clearly there is a link between Ayato and Kusuragi that has yet to be fully stated here. It does answer how TERRA knew to extract Ayato as clearly they knew before the Tokyo barrier was errected that he was important. It doesn't answer why the barrier formed but it begs an interesting question, what if the Mu didn't form the barrier but rather the Bahbem Foundation did as an effort to buy the world more time to prepare for the Mu? This makes more sense but aside from the fact that the Bahbem Foundation obviously has more facility with Mu technology than we knew there is no corroborating evidence.