If you don't mind philosophizing: it doesn't produce a streamlined story, but something I like here is that no character is always right. All of them are doing what they think is best, creating and discarding hypotheses, and they're willing to admit when they're wrong. The strength to face reality is sadly rare, especially when the stakes are so high.
A lot of people, when they argue themselves or are argued into doing something with good intentions, who then later are faced with irrefutable evidence that what they did was wrong, was not justified by the circumstances or was absolutely the wrong way to handle those circumstances, cannot admit it to themselves. While they're in denial, they're heroes who did something good. To admit that they were wrong, though? That they hurt their friends, children, world?
Just like Instrumentality as a way to solve all humanity's problems is seductive because who doesn't want all their problems solved, thinking of someone as just an enemy is also seductive. Enemy equals kill them equals no more problem. Often the more steps one takes closer to truth, the further one seems from a solution: this is why people like to believe things are simple, because simple problems would be easy to solve.
That's Shinji's weakness in 3.0: he's so close to fixing everything that when it's revealed that no, something is wrong, it's not that simple after all, he can't face that fact. He goes into denial, refuses to listen to those who say things aren't that simple and triggers another impact.
The equivalent would be Tabris in this fic refusing to face that SEELE was lying to him, insisting that he could fix everything, could bring instrumentality, if only he... tried hard enough, or wanted it enough, or any of the myriad justifications people come up with when the facts refuse to fit what they want to be true.
There's not really much in this fic that should be considered certainly true (other than that Kaworu Nagisa will always love Shinji Ikari), partially because I think of new ideas as I write it, but also because new truths being revealed and people having to adapt to this (Fuyutsuki's exposure of the truth, Shinji finding out Kaworu was Tabris) is such a big theme. If just letting the characters try to get through life didn't provide me with enough plot twists, I'd have to come up with some.
Fortunately, there's no danger of the Eva cast and Eva worldbuilding ceasing to be insane and insanely difficult.
"What we called you to the science department to discuss before everything started happening," Naoko began.
Shinji noticed the 'everything started happening' as opposed to 'my cute little granddaughter swallowed your soul.' Yes, very clear that Naoko didn't want Rei blamed for this.
Ritsuko coughed loudly, as if to say 'speak for yourself.'
"Yes, your past behavior towards my granddaughter and hoping that you'd take the opportunity to take the stick out of your ass was a factor, but that aside, Ritsuko and Kyoko have confessions to make."
Kyoko? It was Ritsuko that Shinji looked at first.
"I managed to get a sample of your boyfriend's DNA the morning after he spent the night in your bedroom for the first time," Ritsuko said, sounding not at all as though she was making a confession. More annoyed that she had to say this at all, rolling her eyes a little.
First time he slept over in Shinji's bedroom specifically, because that was not the first time Kaworu had slept over in the manor: he'd crashed at Shinji's the night before or late night after a performance a few times. Shinji bet the manor security now had a policy of checking the DNA of all visitors. They must be kicking themselves.
What he said aloud was, "Yes?" because he'd assumed they had. If Kaworu had indicated that he cared at all Shinji would have burned the sheets, just to start with. It wasn't as if they didn't already know what Adam's DNA looked like, after making the other Evas. So yes, go on, why was she telling him this?
"We're waiting for Misato to get here for the rest of it," Ritsuko said flatly as Shinji looked over at the projection of Dr. Kyoko Sohryu's avatar.
He had to admire Dr. Sohryu's poker face, but then NERV Germany used to be much more under the thumb of SEELE than GEHIRN, which they'd separated themselves from a little more for the sake of plausible deniability. Not showing her true thoughts was a survival skill.
"I don't see why we couldn't tell Misato first, in private, after we let Kyoko tell Asuka."
"Ritsuko." Naoko's 'mom voice,' could still stop her daughter mid-rant. "What Kyoko had to tell Asuka was a slightly separate matter, and definitely something Asuka had the right to know first, before we told anyone else anything. Yes, telling Shinji at the same time as Misato would be ridiculous, except we're not telling him, we're using him to inform someone with exactly the same right to know Misato has."
"I don't see…" Ritsuko took a deep breath and crossed her arms as the dividing gate opened behind Shinji.
"Someone looks cross." Misato said, surveying the room before she took a step into it. "Is this about why my stepdaughter tried and spectacularly failed to get drunk last night? I thought her tolerance was higher than she thought it was," but psychosomatic drunkenness passed so well for real intoxication that it was hard for even Misato to draw the line with any precision.
"We finished the analysis of Tabris' DNA," Naoko told her. "Get in here and close the door so I can turn all the jamming equipment on." Naoko and Kyoko's signals had to pass through cables, but other than that the room should be secure against anything short of Tabris himself.
Misato complied, looking interested. Not in the DNA analysis itself, but because the three of them wouldn't have called her here unless there was something in this which would interest her.
Naoko disappeared from her screen as she focused on merging with the Magi system to verify that the area was secure.
"Misato, I'm going to warn you now that you might not want to know this," Ritsuko said once her mother was (temporarily) out of earshot.
Well, now Misato was really intrigued, so she just gave Ritsuko a doubtful look because seriously, what effect did her best friend think those words were going to have on her.
Ritsuko just rolled her eyes and reminded Misato that, "As your friend, I'm obligated to warn you."
"It can't be that bad, or you would have staked out 'I told you so,' rights, or advised me to actually leave," instead of just giving her a warning to take into consideration when Misato made the call. She'd trust Ritsuko's judgment if her friend told her to leave. Probably.
"Ritsuko?" Naoko said, nudging Ritsuko to start instead of chastising her at all.
"Shinji informed me that the Lilim DNA used to create Tabris was taken from the preserved body of the prophet of the Dead Sea Scrolls. We'd already decided that Tabris' DNA was too important to be sent outside for analysis" when the UN had cracked down hard on which labs were allowed to even have the computerized DNA of Adam and Lilith, when angels could hack computers and the flesh of a seed was one of the three triggers of Third Impact. When angels could shapeshift, it was theoretically possible – almost certain that they could clone either of the progenitors from a genetic map.
Whatever happened to any human relatives Tabris might have if they were identified and the information leaked wasn't NERV's concern. The half of his DNA that was Adam's leaking was. Possession of Adam or Lilith's DNA outside the NERV facilities was a 'lock you up and throw away the key' level offense, and there weren't many of those left when the effort to hold back the Dead Sea meant that most prisons had been emptied out and their denizens sent to forced labor camps. The people left in actual prisons were there because some government wanted to keep an eye on them and make sure they didn't talk.
"Kyoko was there when I took that call," Ritsuko went on, "and after Armisael was moved into her new body she said that she'd isolate the half of Tabris' DNA that wasn't Adam's and take a look at it for us. She didn't manage to get around to that, or tell me why she'd wanted the project, until yesterday."
"I was on the team that originally extracted and studied the DNA of the prophet. It was my success there," with that contaminated DNA sample, "that made them put me on the EVA project, after Adam was found and samples of her DNA were obtained. The prophet's DNA wasn't the key to immortality some hoped for: no matter how strong the immune system, over the long term the probability of cancer would outweigh the resistance to conventional aging. However, we were able to confirm immunity to all other diseases, and also the presence of a regeneration factor. SEELE loyalists within NERV Germany destroyed all my samples and research when the conspiracy was revealed, but I hoped that I would be able to recreate my earlier work and as much of the original genome as possible. I started by isolating the chromosomes in the sample which did not come from Adam, and then I cross-referenced the remainder with my daughter's DNA."
Misato and Shinji were both visibly startled, but only for a moment. Kyoko's daughter was one of the fated children. One of those who would be sent to fight the angels. If she'd had access to a sample like that, years before the Katsuragi expedition? Even if she hadn't known her daughter was going to be an Eva pilot, she'd known the end of the world might be coming.
Of course she'd given Asuka an advantage that would let her survive.
"So that's…" Misato murmured. "Her level of contamination was almost as high as Shinji's, and we don't know the half of what those two did to make sure he could pilot."
"Shinji's contamination level is purely environmental, not genetic," Naoko reminded Misato sternly: for god's sake she should know Shinji's issues about what his parents did to him. What was she thinking, bringing that up? "Kyoko exercised proper precautions to reduce her daughter's secondhand exposure to Adam. If it weren't for the original DNA contamination level, well, she still would have gotten enough exposure to serve as a beta-type pilot, but no, not that high a contamination level." Not almost as high as Shinji's.
Misato nodded. "Hers is almost exactly the same as mine." And Misato was almost at Ground Zero of the Rapture, and she'd been there with the expedition in proximity to Adam for awhile before that: no one could have gotten as large an environmental exposure as her. Not naturally. "I had assumed Kyoko made sure that she'd be exposed so she could pilot… No?" she asked when Kyoko shook her head.
"I was not told that my daughter would be required to pilot until she was four," and the theoretical optimal windows during which a child could be exposed to high levels of contamination and successfully adapt was past.
It wasn't just brain development: the immune system also learned and grew along with a child, learning about the different possible threats and adapting to handle them. A normal person's body produced an average of one mutated cell a day that would become cancer if the immune system didn't eliminate it. An average person with a high contamination level had more like ten times that, and 'average high' still wasn't enough to qualify as a beta-type pilot like Hikari.
As for Shinji and Misato… Shinji didn't want to know. He wasn't that afraid for his own sake, since he could ask Kaworu if he'd mind checking every so often, but what about Misato?
"I'm not happy that Asuka was told without me present," Misato told Kyoko. "I thought we discussed this." When Misato became Asuka's stepmother.
Shinji could almost picture the battle aura radiating off both of them, Misato shifting her weight to a more threatening posture and the two of them staring into each other's eyes.
Ritsuko was unimpressed. "She compared Asuka's donor DNA with Tabris' in order to see how much of the original genome could be recreated." Asuka would have gotten half the prophet's DNA and Tabris would have gotten half, but those halves would be random. It wasn't likely that combining them would create a complete sample, but Kyoko would have had more than she started with. Asuka'd gotten an X chromosome while Tabris got a Y, just for starters. "There was no match."
"You're saying that they don't have DNA from the same donor," Shinji said slowly, as Misato slowly disengaged from Kyoko, because they would discuss this later. "Since Asuka's egg was made in a lab, Dr. Sohryu would have noticed if the DNA she was looking at wasn't the same DNA she'd been studying for years."
"I did it in secret in the lab where I worked: I picked those chromosomes individually out of the sample myself, to make sure they didn't already have any dangerous mutations." Ones that might harm the baby. Obviously those still-viable cells were cancer cells: Dr. Sohryu would have wanted to make sure she didn't get any of those chromosomes.
Shinji calculated the odds that the sample used to create Tabris could have been replaced accidently, when SEELE was pretending that Tabris' creation was so vitally important to them, important enough to be worth the deaths of billions. "So someone, probably someone on the Katsuragi Expedition, deliberately switched the sample used to make Tabris. Without any of the old men finding out." Or Tabris would have found out when he searched their stolen memories to find the identity of his father.
Thinking aloud, mind racing ahead of his mouth, Shinji was already thinking of who could have done that, who would have had a motive to do that, and…
No.
Oh no.
Someone within SEELE, working to subvert their plans. Someone in the Katsuragi Expedition, who could have switched it in-transit or after verification, if they didn't do the verifying.
If it was verified at all: SEELE hadn't wanted Kaworu to think of himself as any one particular human's child. It made perfect sense that they'd forbidden the researchers who studied him when he was small from looking at his human DNA. Better to think of him as the child of all humanity, a Messiah born of god and man as opposed to a man.
What human would have the arrogance to want a god to be their son? It couldn't be one of the original council of SEELE, or Tabris would have seen that when he searched their memories for the truth of his parentage.
Shinji knew the answer to that question.
What human would name their son True God in order to use them as a tool, no, a sacrifice?
They'd intended to sacrifice him along with all of humanity so she could become a god.
But Yui Ikari didn't have a Y chromosome, and SEELE had wanted Adam's child to be male.
That wouldn't have posed any problem: she had a male co-conspirator. Also on the Katsuragi Expedition. One who would do whatever Yui wished. One who left the day before Second Impact, who could have switched the samples at almost the last minute, when there was too little time for any of the few left there who knew the truth to take the time to check them.
Shinji wished he could tell himself that it couldn't be true, wished that he could go into denial, but it could be true. It really could. His parents were still screwing the whole world over from beyond the grave, and he'd had a special place in their plans.
Had they known that Tabris was prophesized to love Shinji? Had they switched the samples knowing that?
Had they switched the samples so Kaworu would be Shinji's half-brother, one more thing that made it impossible for the two of them to ever be together, knowing that? Was it one more part of their plan to break him, drive him so insane with despair that it would be easy for Yui's mind to push him aside and take over whenever it suited her purposes?
The two of them had never loved him. His father and mother had never loved him. They'd wanted him to know that he would never be loved so he would despair.
Had they done this to poison the only love he would ever receive? If it weren't for his real Father taking him in and giving him a home, then Kaworu would have been the only person to ever love Shinji. Had they done this on purpose to taint that? To make something so wonderful feel twisted and wrong, as though he'd slept with Rei?
"It was… it was him," wasn't it, Shinji said even though he didn't want to know, or perhaps because he knew that when those bastards who spawned him were involved, it could always be worse. Right, he had to… To find out what the damage was.
It wasn't like they could have kids anyway, right? So it wasn't really like it mattered, or that was what he tried to tell himself.
But if Kaworu was his brother, and Shinji slept with him…
Family, family was important. Family love wasn't… To sleep with someone, when they were family like that? It just wasn't right.
To make him choose between the love he had for his family, the concept and sacredness of family love itself, and his love for Kaworu? Either way, something precious to him would be destroyed… No, either way he'd have to destroy something precious to him. Either way he would be the one to either say that his love for Kaworu was perverted and wrong, or his bond with his family was now desecrated, because saying that family relationships didn't matter, even if it was to stay with Kaworu?
His family was what kept him as sane as he was, and to be reminded of how it was poisoned, how he let his hormones overrule their love, every time he thought of them? Either that, or from now on every time he looked at Kaworu he would be thinking of why he couldn't touch him, why he couldn't let Kaworu touch. Struggling with his desire for Kaworu and probably losing pretty often and then feeling evil and wretched and like he'd profaned Kaworu, doing something so dirty with him even now that Shinji knew it was dirty.
"That bastard… Gendo Ikari did it, didn't he." There wasn't a question in that statement. There was a choked-back sob, Shinji's head bowed. He was dimly aware that his fingernails were digging into his forearms, the way Kaworu's had when Shinji raised the topic of shapeshifting. Of Kaworu becoming something less human, something perverted.
"What… No!" Ritsuko said, startled but Shinji could almost hear her thinking that she wouldn't put it past that perverted bastard, when he'd made damn sure that Rei would look like his wife as well as having her genes.
"I wouldn't put it past him," Ritsuko's mother said with dawning horror, "but no, Shinji… Dr. Katsuragi. He's enough of a match for Misato… it was Dr. Katsuragi that replaced the sample. Not Gendo Ikari. I don't know if he tried, but… Shinji, Tabris is not your half-brother." Not Shinji's.
And that would be why it was Misato that was warned and not him, because she was the one about to find out something upsetting. If Shinji was about to have his world shattered, about to find out something just as bad as finding out that Kaworu was Tabris in the first place? Something that would make his love a forbidden one? His family would have warned him. His family would have found some way to make this hurt less, even a little.
He was trained: he should have reacted to someone grabbing him. He would have reacted if he wasn't used to Misato doing it. If he hadn't tried to get used to that so Misato could grab Shinji while he was asleep without Shinji waking up and lying awake there in Misato's bed until he started thinking about his birth parents and everything and crying, when the whole point was to not cry. To make everyone's nightmares go away.
"They would have," he whispered, too overcome with fear and dawning relief to sob. "They wanted to take him away from me: he would have ordered me to kill him for them so that she could do it," Unit 01, "getting rid of an obstacle to her becoming a god. Just an obstacle, even though he loves me." But they'd never cared for their son's happiness, had they? No, their son's happiness would have been just another obstacle. He'd felt her trying to take control in the Eva: his security was what kept her out. What protected him from her. They hadn't wanted him to be happy. They'd wanted him to be desperately unhappy, desperate enough to jump at any offer, even an evil ghost's whispers promising temporary oblivion. How could his heart not have responded to Kaworu's promised love?
Then they would have made Shinji kill him for them. Just another part of their scenario.
His, his precious, perfect… If anything took Kaworu away from him, even whatever power decreed fate, even the universe itself…
"Crying like this…" he heard Misato say as she rocked him a little. "I almost wish he was. I mean, I loved Kaji, but I wasn't… I could go on without him. I'm just really damn annoyed I have to do that."
"You're not dependant on him. On some man," Naoko said bluntly. "Good. I'm going to just say it: back in my day, we were brought up to think that you were supposed to devote yourself to the man you loved, or person you loved, that they were supposed to be everything you needed and this was a good thing instead of calculated to end in divorce court. People have needs: we need certain things from other people and people aren't puzzle pieces. We don't match up perfectly, we're going to have needs that the person we love doesn't fulfill. This is why family and friends. In my entire life, I have only seen one person who loved someone else with all his heart, all his mind and all his soul. At the time, I thought that was a beautiful thing, beautiful enough I wanted it for myself and didn't stop to think that if people really were puzzle pieces, then matching with her meant he and I had to be a horrible match, because I was not just like her. I agree with Kozo: Gendo Ikari never loved anyone but Yui. She was so perfect for him that there was no part of him left over to care about or need anything from anyone else. They were soulmates. I used to think that was romantic." Then she actually thought about it.
"I've read about other people having insane crushes, hormones making them think that they just can't live without someone else. Then there are broken people who think they can't find anyone else because they're not good enough or some rot like that. We like to fantasize that we can just find that one special person and it will be easy to have all our emotional needs fulfilled, instead of having to try to make relationships work with several real people with their own needs." Naoko's labcoated avatar leaned back against the chalkboard this projection used as a background. "This is something else. This was in the prophecies. Gendo Ikari was something out of dreams we should have realized were nightmares – a genius bad boy who cared about only one person, and now here's his son. Tabris falling for him made slightly more sense when we thought that Kaworu was the prophet's son and it was a setup that way, but if the abominations can sense emotions and Tabris was hungry enough for someone to care about him… Shinji inherited his capacity for love, not the love for the people around him," thank goodness, because Gendo might as well have been a sociopath if your name wasn't Yui Ikari, "but for 'that one special person' from that bastard."
'Like father, like son:' Naoko might have claimed that she was going to be blunt about something horrible with that 'I'm just going to say it,' but she didn't quite have it in her to be cruel enough to Shinji to say he was like his birth father right in front of him without dancing around it a little.
Shinji felt Misato tense around him, and the way she cocked her head: she and Ritsuko knew each other well enough to communicate without words when it came to some things.
"King of the Lilim," was what Ritsuko finally said aloud. "Something has to govern souls, if not DNA. Their power level and how 'shiny' or otherwise attractive they are. If someone's soul really does affect their personality, in the same way a brain injury can completely change someone's personality, then that raises some questions. Why would Keel's daughter get surgery to hide her identity and come to Japan to meet one person? If Shinji was specified in the prophecies?" Then what about his father, about his lineage? Had Yui Ikari known that Gendo Rokubungi would be important? They knew that Shinji was born on purpose, to breed herself a pilot, the destined Third Child: was there more to it even than that? "White seeds, black seeds, the elder abominations versus we Lilim: there's so much we don't know about all of this. How the secret reproductive cycle of our own species… No, of our entire biosphere works. Why did Rei do this to Shinji, when nothing like this has ever happened before?"
"He mimicked a mating display in his head without knowing his soul was actually doing it as he thought about it?" Kyoko wondered, since that was the impression she'd gotten.
"For the elder abominations, first come first served." They quested after the seeds, oldest and presumably best at survival first. "For Lilim? There are mobs of us. If Lilith really was supposed to load all our souls up again and go look for another planet, then we need to think about the possible mechanism behind that," Naoko said. "It would be a waste of a good planet if that happened early: we've speculated that the reason so many people were willing to listen to SEELE was that some part of our instincts thinks that's what's supposed to happen. All of us just go crawling back into the womb." No matter how pathetic she found that. "But how is that triggered? If they used the same underlying mechanism, based on human drives, for the 'white tree,' then what about the black?"
"Some unusually powerful souls in among all the others?" Ritsuko wondered. "With the ability to compel Lilith or Armisael to restart the cycle? Possibly to get all the other Lilim loaded up for transport? Hmm, isn't it a little odd that Armisael couldn't call her creations back to her when she was lonely and wanted to do that? Adam is certainly capable of calling its children." That was one reason they needed as much of Adam's flesh as possible in NERV. Shinji could hear her tapping her foot thoughtfully. "I'll have to see if I can calibrate the detection equipment I'm working on to notice smaller differences in power level." Since Lilim had smaller power levels to begin with and NERV's originally was trying to ignore everything that wasn't an angel. "I wonder if it correlates to contamination level? Or at least the ability to survive a high contamination level."
"It's self-serving of me to claim that Gendo Ikari had an unfairly high charisma stat," Naoko admitted. "But." What if he had?
Gendo Ikari had served as one of SEELE's recruiters, in the years when Refuge was first being established. It was widely agreed that the man had a presence, was as compelling as he should have been repulsive. Hell, a certain segment of the population claimed he was Satan.
"So damn much we don't know, just so damn much," Misato said with familiar frustration. "Even though we in theory have all off SEELE's secrets now, it's still not enough." She drew in a breath. "We can ask Tabris if there's something odd about Shinji. If we make him worried about Shinji…" Obvious leverage. "He says that Shinji has a beautiful soul: how beautiful, compared to the average person? Is all of this because Shinji's a looker?"
"You got Armisael to change her mind," Naoko remarked.
"Maybe?" Kyoko replied: so she was the one Naoko was looking at when she said that. "I suppose an Eva does use the AT field: that's why it needs human souls in the first place. It would help if the person involved in the contact experiment was stronger than average. If it was arranged that I would be Asuka's mother…" Damn prophecies. "I thought using that sample was my own idea," but who knew? "She should have been the special one, not me."