Canon updating, essay
Thanks to information in the Xenosaga Perfect Guide, the things I'd extrapolated from the ending of Xenosaga III with regards to Wilhelm were confirmed to be true, leaving me able to canon update him. However, this involves changing him a bit! The changes are mostly internal, though there's one major external difference, namely that he's lost his physical body.
I don't intend to have him be disembodied in camp, however! He will still be able to take physical form, and camp can certainly pull him physical against his will. In fact, he will usually be corporealized. I only intend to use his new incorporeal nature for shenanigans. So really, there isn't too much different here. He will also occasionally appear with his right arm missing from just below the elbow, but again, I don't intend that to be the normal state of affairs.
No, the major changes are in his intentions. At the base, he remains the same. All he desires is to protect the physical universe, as is his role, his purpose, his raison d'être. However, his conviction about the means through which this will happen have changed. His prior state was focused solely on bringing about Eternal Recurrence. That was the only way to save the universe that he would acknowledge, because he knew it would work, and to abandon that method for a less certain one went against his strong desire to see the universe continue. After the Key and Zarathustra are destroyed, after Mary becomes KOS-MOS and denies him, he can no longer bring about Eternal Recurrence. It has become impossible.
Instead, he must look for a new way to save the universe. Between the convictions of Yeshua and Mary, he has decided to watch humanity for a time, to see if they can produce that solution. His attitude towards humanity changes with this decision; he ceases to consider them as merely tools towards the end of Eternal Recurrence, but rather as their own potential saviours. He isn't necessarily a very good watcher - immediately after this decision, during the ending of the game, he uses his powers to save Shion and her companions on the Elsa by holding open a hyperspace channel for them, so that they can escape the destruction of Michtam. He's never going to get out of the habit of meddling. But he's not going to meddle in quite the same way anymore, either! Less 'turning people into tools for his own ends' and more 'helping people achieve their ends'.
Another change is that he is no longer the CEO of anything; all that remains of the Dämmerung, Vector's headquarters, is a crippled ship floating in space, limited to what power it gets from backup generators that were never meant to be used. Even if he retained his physical body, he would not return there. He will rarely introduce himself as Vector's CEO, though he will when asked what he does for a living, and he will not deny that that phrase once defined him. Those in camp who are his employees may remain employed or not as they wish.
He will also be more open with information about himself - especially since most of the people here aren't even from his universe. He's not going to play with people's minds quite as much, either. But, again, it's a habit and kind of fun, so he's still going to do it. But where there used to be two classifications of people - useful and useless - there are now more options for how he regards people, and he's open to actual relationships again, instead of closing himself off.
I'm sure there's things I didn't cover, so if you have a question, go ahead and ask!