My favorite Eva continuity is actually Campus Apocalypse, although the reason why is likely a reason it's not a proper continuity:
Everything makes sense. The author designed a set of rules for the world and backstories for the characters such that everything makes sense on first read-through if one pays the kind of attention one should in 'Magic A is Magic A' SF, or books like Diana Wynne Jones' where the focus of the story is the characters figuring out what's going on so they can do something about it.
Asuka manages to get a CMOH while still being Asuka. Meaning she does so by giving someone a verbal beatdown and calling them an idiot. Rei is freaking adorable. Kaworu is actually in character, desire to help Shinji combined with complete cluelessness about normal social interaction and all – it's hilarious. (He can be interpreted as having a crush, but for me that's a plus. Go, Rei! For the harem ending!) & Shinji was raised by Kaji.
Sadly, I really can't use anything from it for this fic, since it uses a different premise (alternate dimensions) so have another Rebuild-centered chapter, covering the end of the second movie.
It actually kind of bothers me how much of the End of Evangelion movie makes sense to me. I'm going, "That's an alchemic term, that's your standard medieval flagellant mysticism, that's something Celtic but I'd need to look it up to identify the symbol... Ok, that's completely effing insane." I think that if it all made sense to me, I would seriously have to worry about my sanity.
"This… isn't good," Shinji thought as he wrapped his arms around Rei. "This is… very bad. But I don't know what else I could have done. I don't know what else I can do." He couldn't push her away. Not when she was his little sister. Not when she'd nearly died, he'd nearly lost her before he could even figure out a way to tell her that he considered her family, much less actually help her.
If only Gendo had let him pilot earlier, if only it hadn't taken so long for Misato to get his Eva out of storage: he didn't understand. He'd thought Gendo at least cared about Rei. Had the bastard meant this to happen? Risked Rei's life for some part of his insane scenario?
Well, look at how he'd treated Yui's other legacy.
He'd beaten the angel that beat Rei and started eating the EVA. And now that felt like the easy part.
Rei was curled up against him, her hair pure white and her eyes a clear red, as though he was seeing into her bloodstream, into her heart. And she was so happy.
Their AT fields were melting together. He had to be the one to close her out: Rei didn't know how. But he couldn't. How could he, when she was so happy? How could he reject her and hurt her like that?
"Shinji?" she whispered instead of sending, not even realizing that the two of them were really spirit instead of body right now, that the light she emitted was the light of her soul.
"It's okay, Rei," Shinji said soothingly. Damn, he had to keep his knowledge that they were on the verge of causing Third Impact out of the part of his soul she was melting into. He couldn't worry her or make her think this was her fault.
It wasn't even the crazy la-his mother's fault, either. This was what he'd said, hadn't he? Forget everything else, he was going to save his little sister! If no one else cared for her, not even Gendo, then someone had to! Then he would be the one to rescue her! "It's going to be okay," he told her, even as he tried to calm down instead of either cursing at himself or at Gendo – how dare he make her think she was expendable? How could she be surprised that he'd come to rescue her, and damn the laws of physics? If her body had already been destroyed, there was plenty of LCL here: she could make herself a new one! This universe had been made by and for humanity, the light of the soul was the true power here, the power of the human mind and will. Nothing was impossible: Tabris had taught him that. The only power that could oppose a human was another human. He couldn't have rescued Rei if she hadn't reached back.
His little sister had trusted him, taken his hand, and now her soul was dissolving into his, ending her precious individual life, because he couldn't say no to her. And he was tired, but that wasn't an excuse. Not for failing his little sister when she needed him.
He'd lost his mother but he'd still had Tabris, his friend and teacher. He'd wanted to be that person for her, because it wasn't fair that she didn't have anyone to stand up for her. To tell her that of course she had the power to stand up on her own. To be there when something happened despite all her strength, and she needed someone to help her.
Oh, right. It was disgusting how weak he was sometimes, how much he let Gendo's abandonment affect him. Even though he knew better. "It's really going to be okay," he told her now, and finally believed it.
Rei wasn't the only child abandoned by Gendo that had someone watching their back, Shinji knew, and smiled as the weapon he'd wielded in dreams ran them both through.
Instantly the shock and fear of attack made Rei close herself off, but that was alright. Well, his little sister getting scared wasn't alright, Shinji thought as he looked up with clouded eyes, but they'd mixed around the edges. So she'd take away the important things, the things he wanted her to know. That was, that was good.
"Hey, Tabris. You're late," he managed to joke, even as he sent Tabris his thanks and relief because he didn't have words.
"Sorry, SEELE wouldn't have understood me unilaterally launching unit 06 just to save the two of you. And I knew you'd hold out long enough." The lesser lance Tabris had called on dispersed, freeing their cores now that the fusion had been halted. "She was counting on you, after all."
Shinji blinked, looking down at himself, past the outline of light that was the edge of his skin. "I have a core like that?"
"Of course you do-Ah. A core isn't an S2 engine: we angels can just use the AT field generated by our cores to create and enclose a pocket dimension where the waveform is such that it constantly generates energy." Instead of being bound by the conservation of matter and energy. "Your cores do something very similar, so of course they look the same in a place like this, where the division between mind and body is overruled. She was inside your AT field, but your cores weren't in danger of merging for several more hours. Not when both of you knew that to become one would mean to no longer have the other." Not when Shinji wanted a little sister and now Rei understood what it meant to have a big brother. "I'm sorry you were worried because I didn't manage to explain this well enough." It was a little difficult for him to show Shinji what his own soul actually looked like when it wasn't possible to form anything like a mirror, on top of the difficulty inherent in looking at Shinji's soul from inside Shinji's soul.
"I should have known you'd have my back."
"Shinji…" Of course Tabris wasn't hurt that Shinji hadn't thought of him. "You lost your mother and your father abandoned you. I'm not going to blame you for surviving." When the two people who should have stayed even if everyone else abandoned him were the first to go, of course he had a hard time trusting others. "Could you ask Rei to let me show her how to make a body?" he asked, changing the subject. "NERV has already hailed me, and I'm sure Misato is worried about you."
"Next time Rei puts herself in danger, I want her to know that she'll succeed no matter what, because if she can't do it alone I'll lend her my strength." So she'd never have to feel failure. "And I should have gone out there knowing that I could focus on Rei because I could count on you to take up the slack."
The light that was Rei's soul, the image she had of herself was already reaching towards them, worry for Shinji and the desire to be reunited with her new brother warring with a more protective concern. Who was this person who had taken Shinji away from her?
"It's fine," Shinji told her. "This is my teacher. You know how you tried to tell me I couldn't rescue you just because you didn't have a physical existence anymore?" Shinji thought that was how she'd put it, but he'd been a little distracted at the time. "Come here, and then we can go home." Not that Rei's empty apartment was a proper home, but he was going to do something about that now that he didn't have to worry about Rei telling Gendo about Tabris.
She took his hand, and then the other that reached out to her.
"Alright. You can use the LCL in my entry plug." Kaworu had already primed it, since getting here from the moon without just using hyperspace in front of every eye in the sky humanity had had taken too damn long. "This way," he said, and pulled.
When Shinji opened his eyes again, he was floating in LCL with Rei's foot in his face.
"Shinji, clothing!" Tabris reminded him, then paused, embarrassed. Normally he was the one people yelled at about this. "Well, really, it would be more realistic if you didn't have enough control to impose your clothing as well as your vessels on the LCL, but I thought it might be better this way." He was hoping they would cuddle, since the way Rei's AT field reacted to Shinji in the first place showed that she really needed to feel more connected to other humans.
"No, this is good, thanks for showing Rei how to do that," Shinji said quickly, blushing and hoping that Rei hadn't seen anything.
"Thank you," Rei said quietly.
"You're Shinji's family," Kaworu told her with a welcoming smile. "Is there anything else before I contact NERV?" he asked Shinji, who was more likely to think of these things.
"You look as much like her brother as I do," Shinji pointed out. "But I think we're fine."
Shinji wasn't sure whether his hand found Rei's or hers found his. He hoped the answer was both.
"This is Kaworu Nagisa, the Fifth Child, pilot of EVA 06 assigned to SEELE Moonbase. Sorry for taking so long to respond to your hails, but I had a few things I needed to focus on." First preventing Third Impact, and now the two people leaning over the back of his chair. "I could power down now for debriefing, but could you please direct me to an EVA hanger as soon as possible? I understand that severely damaged units come first, but this was the first combat test of Unit 06 outside simulation." So it would almost certainly need adjustments and SEELE's engineers would want data after such a rough maiden voyage.
Misato stared at the faces on the laptop's screen. Not just because Shinji and Rei were alive, but even though that was the most important thing, this boy… Did he just look familiar because he and Rei had to be related somehow?
She, Ritsuko and the others had come outside to watch the end of the world, Misato in the hope that if she got closer, if she saw for herself there would be something she could do. She hated feeling so powerless. "This is Captain Misato of NERV Japan. Thanks for the assist. Please head towards the main building and drop off our pilots first, while I figure out what we're going to do with your EVA." Misato thought the best idea might be to get it into a hanger first thing, actually. Just for starters, they couldn't move the other three into hangers until they managed to get some cranes and flatbed trucks down here. 06 might be in and out before any of the other EVAs could get to the hanger, especially with all the repair crews on standby.
Eager to look over SEELE's new toy. 02 might be the first production model, but Misato had heard rumors, and not just from Kaji, that SEELE was already working on the second generation of EVAs. The moonbase would be the best place for something like that: the isolation meant it would be hard for certain countries to infiltrate the place and send information back to their militaries.
EVA becoming a weapon of war was inevitable, after the world had seen how nothing could stop an AT field except another AT field. That didn't mean it wasn't worthwhile to try to prevent weapons made to kill angels and protect humanity from being used to attack humans.
It seemed as though the pilot's smile became just for her when he heard that her pilots were her first priority instead of baggage associated with their war machines. "Acknowledged." The Eva started to walk towards them with what Misato knew was unusual control for such a massive, clumsy machine as an Eva.
"Either they've improved the balance systems a lot or he's got a high sync ratio," she said to Ritsuko.
"Hmm," was all Ritsuko said, and Misato looked at her with puzzlement. Ritsuko could talk technobabble in the face of Third Impact, and now was when she clammed up and got thoughtful? It didn't seem as though she was in R&D mode, trying to take Unit 06 apart with her eyes to figure out how it worked either.
"Hmm?" Misato questioned her.
"It might be practice. The moon's gravity combined with an EVA's momentum would require much more precise control," was what Ritsuko said, but the quick glance at the laptop gave her away.
In hindsight, Misato would curse herself for ignoring all the obvious signs that something was up. Years of them. But she'd had her orders, and her mission, and her pilots to look after.