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I'd thought before writing chapter seven that these two chapters could go together and make something of similar length to chapter six. It seems I was right on that, but the story is much, much better served by having them separate, for they accomplish different purposes. "After Armisael" was all about the futility of living. Here, this is Rei denying what she is over and over until she's forced to accept it.
A bit part of what distances Shinji from Rei is how he says he's afraid of her, that he doesn't want to see her or Misato. What does Shinji do? Run away from painful things. The Rei we have now is colder, and she isn't like the friend he knows. I hoped to take that to the logical extent, and while Shinji would try to run away as much as possible, it stood to reason (at least to me) that at some point he might get cornered, and in doing so, Rei would learn just what it is that makes him avoid her.
Make no mistake: Rei's trying to understand what she is here, why she sees and feels things that shouldn't be. She latches on to the idea of being Yui because that's digestible, palatable compared to the alternative--that she's something much more bizarre and Lovecraftian in origin. What's more frightening--a creature of unthinkable thought and motive with grotesque and disgusting bodily features, or a girl like Rei who is that creature bottled into a human-looking form? For Rei, the fear is that that thing will come out, and she will no longer be herself. I tried to draw as much as I could on "The Case of Ayanami Rei" scene in episode 25, where the image of Rei I taunts the others, saying that they're afraid because of the thing that might not have human form (cue inkblot images). What Rei wants in dying is to no longer be, not to wake up and be something else again, something stripped of what she used to be--or worse, something completely inhuman.
I originally wrote the escalator scene first. The result was a chapter that jumped around a little chronologically. It felt like something more likely to be actually written by a person, but it also seemed rather ineffective at showing, at least to me. I made things more chronological by going to the lockers first (do they even have lockers? the best I've seen are a couple scenes from Rebuild where Misato slaps Shinji in what looks like a bathroom or a set of showers versus Shinji and Rei donning their plug suits in some sort of cargo container).
I spent comparatively more time on Rei's confrontation with Kaworu. I inserted the paragraphs where Rei imagines what Kaworu's saying with more details than he says. This, along with the couple scenes where Rei looks into the mirror and sees something wrong with herself, I felt was necessary. Otherwise, Rei's fear of being something else isn't really catalyzed, and it gives credence to Kaworu's hint that Rei's memories aren't gone, merely suppressed or taken from her, yet something is able to creep back in.
How Kaworu describes the First Ancestral Race is deliberately a bit vague. I didn't want to depict them directly--I vastly preferred to keep their appearance mysterious and secret. Describing their architecture seemed fair, however, and I realized that there had to be some explanation for why they wouldn't have spread to the stars, being as powerful as they were. The calamity that befalls them is no ordinary supernova, but rather a gamma-ray burst, something thought to be an extremely deadly event if one were to hit Earth. I drew heavily from the EvaGeeks wiki to get this background right, but it's very tangled and complex. For instance, a lot of fanwanking has been done just to figure out the possible plot hole in this episode, between Kaworu realizing it's Lilith, not Adam, on the cross and Seele telling him that Gendo has Adam's body already. I put forth my own theory here: that Kaworu, like the other Angels, senses what's in Terminal Dogma and knows it's far stronger than whatever Gendo has. He believes it's Adam because that's what he's been told, and he accepts that that would cause calamity, the Third Impact, because that's also what he's been told, but when he realizes it's Lilith, he understands: there's no extra mechanism here. The only Third Impact there can be is when the Fruits of Life and Knowledge merge, when something of Adam and Lilith come together. They're the same thing, and at last, he understands what Seele's trying to do.
I also consider it likely that what Kaworu says about the hybrid being, of what would happen if he and Lilith were to merge, as being somewhat untrue. I'd think the First Ancestral Race would fear that being's power (as we will see later) as much as they fear it being too prideful to be wise.
I deliberately kept from depicting Kaworu's realization in full until the end of the chapter, to punctuate the use of that name. Giving a name to something you already know of is a powerful thing, so when Shinji looks at her and wonders what she is, she knows the answer, as much as she may try to deny it.