(I'm gonna use "he" from now on only because a) it's tiresome to reword all the time, b) its technically correct, and c) I don't wanna use "it.")
-Well, the superhero angle is out (no possibility of secret identity unless he learns to cloak/manipulate his 'aura').
-The "Galahad" angle is out (since he has memories, he will not need his history explained to him(us), and there's no need for self-discovery).
-There can be no "mate/love/glory quest" since he has no equal, is an aberration, and there is no real gender nor ego.
-There can be no Unification or Yin/Yang storyline since society has already achieved Harmony (unless it is Unification against an outside influence).
-The memories thing isn't a hive-mind, right? (no real-time updating, only pass memories on conception/ceremony).
-Does personality come with the memories? Will he have two personalities warring for dominance, or will the Universal Harmony extend even to this?
Ooo, wait. I just came up with a possible solution that might reverse your difficult plot points into full-on centerpieces. Rather than having us discover
him, have him be the one who discovers
us. It doesn't even have to be a
First Contact novel, this character could be an ambassador towards the rest of the galaxy (and by extension the reader).
So much would fall into place:
-If he is an aberration, it would make others of his kind uncomfortable. As an ambassador, he is "away" most of the time. Problem solved (social).
-He has the memories and abilities of both lines. This makes him a perfect representative to other races/societies, as he knows everything that has come before and can act in situations requiring the experience or ability of either "caste" without having to drag his "spouse" along all the time. Problem solved (his duality becomes THE reason he is suited best for the role)
-Those he interacts with will not know the story of his people, so he will have to explain it. Problems solved (reader education).
-He will likely not know the story of
our people (or whatever other races he interacts with), keeping him uncertain and cautious. Problem solved (reader empathy).
The analogy I'm about to make will be quite imperfect, but it will hopefully serve to illustrate what I'm going for. Write the character of the Third almost the same way as you'd write a late-series crew member addition to a Star Trek series...such as Seven (of Nine)*. She was a character with a massive amount of acquired knowledge (from an enormous number of individuals in the hive mind) and with no small amount of ability (though it's granted that there was
never any doubt as to her gender), and I can see quite a few parallels as to the mechanisms of how the personality of the Third might develop and might be shown to the reader. I am
not advocating that you write a Borg novel, or a novel about Neelix, Kes, or Data. I bring these characters up only because (at least in the Trek universe) they are pretty much the only member of their respective race that we ever see (that gets serious character treatment, that is). Another example of good singleton treatment might be
Farscape, but as I've never seen the show I can't comment with certainty on it.** Write the story from the Third's POV as he discovers the rest of the
world Universe outside of his relatively eons-of-ordinary experience.
--Patrick
*I almost want to make a 5th/3rd bank reference now.
**Yeah, I know. One series at a time, 'k?