[AnimePlus]

Originally Posted by ChainLegacy

Was EoE ever officially dubbed an 'alternate ending,' since it seems like the two different endings didn't necessarily clash...

At any rate, I'm kind of confused about the end of EoE...

Spoiler:

Am I right in assuming Shinji and Asuka are the only humans left? If so, why Asuka? What the hell was going on in that final scene? Shinji was trying to strangle her, and they're supposed to represent Adam and Eve? How was Asuka chosen, by Shinji? What happened to Ayanami Rei, the person? Are Shinji and Asuka now expected to begin humanity once again? ?_?

Wow, there are a lot of things you don't understand hehe. EoE is the official ending, episodes 25-26 of the series are an alternate ending. If you think I'm wrong take a few seconds to look it up.
Now I will explain as briefly as I can EoE and such....

Spoiler:

Rei decides to begin the Human Complementality (or Instrumentality) Project after she rejects Gendou. HCP was the ideal of SEELE and what they wanted to do is basically regenerate mankind back to primordial soup (what is seen in the series as LCL). The reason why Rei can begin HCP is because she carries the soul of Lillith. Lillith is the large white body seen in Terminal Dogma (you know that underground lake with the cruiser in it). Mankind, the last angel, also known as Lillum was spawn from Lillith the second angel. The rest of the angels are spawned from Adam the embryo you see inside the case. When Rei (Lillith's soul) combines with Lillith then HCP is automatically begun and basically mankind is taken back into Lillith. (Back to Gendou, briefly, Gendou doesn't want HCP or anything all he wants is Yui, his deceased wife and Shinji's mother, but Rei, as I said, rejects that. She rejects him when he puts his hand inside her in EoE, he is trying to transfer the embryo of Adam into her.) If you watch episodes 25-26 you'll see what HCP is, it's basically a fake world that you make up. Like Shinji meets a talkative Rei and Asuka is his childhood friend and whatnot. This is the difference, episodes 25-26 show where Shinji accepts HCP. EoE is where Rei gives Shinji the choice and Shinji rejects HCP. Ok!
So EoE now. Shinji rejects EoE, he believes that a fake reality, though happy, is running away from reality. If it's fake it's not real happiness. Shinji has the will to live. Asuka too has the will to live, so they are brought together. It's also important to note that both Shinji and Asuka are the only ones protected by AT fields at this point because they are in their Evas (even though Asuka is pretty messed up.) Shinji begins to choke Asuka out of desperation, sadness, etc. a culmination of all his feelings. Remember, Asuka touches Shinji's face and he stops, he is brought back to reality. He knows he is real.
What happened to Rei? She sacrificed herself for Shinji and for mankind. 'She' was merely the vessel for Lillith.
No, Shinji and Asuka are not to "begin humanity over again". Instead it is assumed, though not shown, that the sea of LCL will be reverted back into mankind and everyone will come back since HCP was rejected and the body of Lillith is decaying (falling apart above the atmosphere.)