Usually when I come across this kind of situation I end up figuring that most everything had some kind of symbolism that was way over my head and was never meant to be taken as a literal story. The show's Christian imagery and terminology made things all that much more confusing: Is Adam supposed to somehow reference the actual Adam from the Bible? Are the Dead Sea Scrolls supposed to reference the real ones? And what about the Lance of Longinous? What the hell was that thing supposed to be and how does it relate to the Third Impact?
Enter Reichu and her Revelations. Thanks her attempt to fill in the gaps and make certain connections, I've learned that the story isn't just an alagory. It can make perfect sense if you know how to put all the pieces together. For example, among her revelations:
- Adam and Lilith are not "gods" in the literal sense. They are sources of life that were intentionally planted by an advanced extraterrestrial race of humans in order to propigate their species and knowledge.
- Rei has the cloned body of Yui and the soul of Lilith.
- Kaoru has the cloned body of...sombody (possibly Misato's father) and Adam's soul.
- Yui is very very aware of exactly what she is doing, even as she exists as the soul of Eva-01. She is the one who is running the whole show.
- Among other things, the Lance of Longinous is Lilith's substitute for an S2 organ.
Below are the links to the forums where the info is posted, discussed, argued, dissected, and developed. There's a lot of info to absorb so it'll take a good few days of free time to root through it all. But if you are an Eva fan and have been struggling to make sense of it all, this will at the very least give you some good food for thought.
Here's some of the main threads (though there's plenty more in the general Evangelion forums at AnimeNation):
- Reichu Revelations, Part 1: Yui and Kyoko
- Reichu's Revelations: Rei, Kaworu, and Everything in Between (this one that talks about the Lance of Longinous too)
- Reichu's Revelations: The Biology of Souls
- Reichu's Revelations: The First Humans, Angels, and the Dead Sea Scrolls