[X] Tell Rei that no matter what her secrets or circumstances are, she's already proven her humanity to you. You'll wait for Rei to speak when she wants to.
-[X] Tell Rei and Ritsuko to put down their weapons at the same time. Pledge to do everything in your power to ensure Rei's safety. Reiterate that you're not letting anyone die here.
-[X] Ask Ritsuko what evidence she needs to be convinced of Rei's humanity and right to live.
Rei doesn't react to your words at first. You have to repeat yourself a few times, gently asking her to lower her weapon and reiterating that she's safe. Ritsuko plays the bad cop, pointing out that using your gun wouldn't accomplish any of Rei's stated goals in a meaningful way. Rei seems less receptive to this, but it does have an effect on her. After you ask Rei for a fourth time to give up the gun, she finally relents. She turns the safety on, holds the gun out to you, grip first, and lets you take it from her hands without making eye contact, fixing her gaze on her mutilated foot. You holster the weapon where it belongs. For good measure, you walk over to Ritsuko's gun and pick that up, too.
You keep a watchful gaze on the other two as you do this. They glare at each other. Ritsuko, after a moment of hesitation, presses a few buttons on the PDA to disengage it and stuffs it back into her lab coat's pocket. Ritsuko tells Rei to get back into the wheelchair. Rei doesn't move, reluctant to move any closer to Ritsuko. You take the wheelchair over to Rei's side and she gingerly sits down in it, not taking her eyes off of Ritsuko. At the moment, the crisis has been deescalated from "imminent threat of bodily harm to the people in the room", but the impasse between Rei and Ritsuko remains.
Ritsuko has been ordered to terminate the girl in this wheelchair, and she seems wholly convinced that this is the correct course of action. Rei, on the other hand, obviously prefers not to be terminated, and no matter what, you don't want that either. You gave her your word that you'd keep her safe. But you'll have to find some way to keep her alive without the use of lethal force.
You ask Ritsuko what would convince her that Rei is a person with the same right to life as everyone else. Ritsuko shakes her head. You really don't get it. Rei wouldn't die. She's just being moved. You reiterate that the process would not leave her intact, which is unacceptable. A piece of her is lost every time, and tampering with Rei's memories even further breaks the continuity between the girl with you right now and one of those things floating behind the glass. Besides, there's no guarantee there's even continuity of consciousness between clones anyway.
Ritsuko says she's not going to bother with sophistry about what counts as death for Rei. You've obviously made up your mind. But you will never convince her that Rei is a human being. The evidence refuting her humanity is floating all around you. But fine. You don't know enough. Ritsuko starts to leave the room, gesturing at you to follow. You look at Rei. What little color she had in her face has disappeared. She grips the arms of the wheelchair tightly. You tell her that it will be okay. She's safe with you.
You push Rei forward through the door, back through the hallways you arrived in. Ritsuko stops in front of the pits full of Evangelion remains. The musty stench tickles the inside of your nostrils. Ritsuko says that eleven years ago, there was an accident. Right here. The accident involved Shinji's mother. The Commander's wife. Yui Ikari. Ritsuko told you earlier that Evangelions require souls to function. Dr. Ikari knew this, of course. Ritsuko is a little fuzzy on the specifics, but Evangelion research had hit a dead end. There wasn't, and still isn't, a way to artificially manufacture a soul. The Chamber of Guf is the only place they can be recovered from, and the Chamber was empty.
Dr. Ikari claimed she knew of a way. She proposed another Contact Experiment. Fuyutsuki was against it, at first, anyway. He changed his mind. The Commander of course supported Dr. Ikari. He had absolute faith in her. Dr. Ikari boarded Evangelion Unit-01.
You don't like where this story is going.
There was an accident, Ritsuko says again. Dr. Ikari did not come back. She's still there, in Unit-01.
You feel sick.
Shinji and the Commander saw the whole thing, by the way. Ritsuko thought you ought to know. Shinji probably doesn't remember it.
Now this place is used as a dumping ground for the failed Evangelion prototypes. All those things down there are failed clones of Adam and armor prototypes for Unit-00. Sometimes the regeneration process for Evangelion repairs still goes wrong, so NERV just dumps the refuse here. Ritsuko continues moving.
You're not sure where she's going with this. You look at Rei. She's squeezed her eyes shut.
You return to the unsettling room that resembled Rei's old apartment. Ritsuko says that this is where Rei was born. And where she lived for part of her life. It seems that the memory of this place is strongly embedded in her mind. Rei stabilizes psychologically in environments that mirror this place. It is her natural habitat. Rei stares at the room expressionlessly.
You tell her that treating a child like this is inhumane. Ritsuko says it is. But it worked. Where you two are going next, Rei cannot follow. Loath as she is to leave Rei behind, it's the only way. Ritsuko walks to one of the dusty cabinets and opens one, pulling something out. It looks like a black collar with a red rectangle at its front. Ritsuko walks across the room and puts it around Rei's neck. You start, demanding to know what that is.
Ritsuko says that it is, among other things, a tracking device. So Rei doesn't wander off when you leave her alone. Ritsuko asks Rei if she knows what it is. Rei says yes. There's a hint of anger in her voice. There's obviously something they're not telling you about this thing. Ritsuko fiddles with some sort of remote for a second. The red rectangle over Rei's throat glows faintly with what look like runes of some sort. You don't trust this. You tell Ritsuko to take it off. Ritsuko says it's just a precaution. She'd prefer to restrain Rei more traditionally, but regrettably, Rei was restrained with zip ties she had to cut rather than handcuffs she could have kept on her person. As long as Rei does not leave this room, nothing will happen.
And if she does? you ask.
Ritsuko says that an alarm will be raised. And restraint options will be made available. Ritsuko looks at Rei and tells her to stay put. Rei says nothing. Ritsuko repeats herself and asks Rei if she understands. Rei nods. You say you don't like this. Why can't you just take Rei with you? Ritsuko says you're going to a room Rei categorically should not enter, and for reasons you'll soon find to be sound. It's a safety issue. Going there could legitimately kill Rei. So she has to stay here.
You ask Rei if Ritsuko is telling you the truth. Rei says yes.
Fine. But this better not be a trick. You unholster your weapon to emphasize who's in charge here. Ritsuko eyes the firearm for a moment before motioning that the two of you should continue. Ritsuko again reminds Rei not to leave this room under any circumstances. Rei nods slowly and begins staring off into space.
Reluctantly, the two of you leave her behind. As an apparent gesture of good will, as soon as you're out of Rei's sight, Ritsuko hands you the remote connected to the collar. She knows you do not trust her and figures you're not going to be able to pay attention if you're stressing about whether Ritsuko has an ace up her sleeve. Ritsuko knows you and her aren't exactly seeing eye-to-eye right now, but all of this is for your own good.
You follow Ritsuko down a mazelike series of corridors before you step onto an elevator. There are only two buttons. The current floor you're on, and a button labelled TERMINAL DOGMA. Ritsuko presses it.
At the bottom, you walk down a few more dark hallways before arriving at a familiar sight: the gigantic door that you caught Kaji snooping around. It feels like such a long time ago now. You already know what's behind this door. Ritsuko moves to the keypad and unlocks the door. It groans open, the mechanisms clunking and bumping as the curtain of steel slides away. You can see it again, on the red cross.
Ritsuko beckons you into the room. You look at your gun before following her into the oppressive presence of the giant mounted high above the two of you. It remains unnaturally still, save for the twitching of one of the hundreds of tiny legs emerging from the tumor-like growths where its lower body should be. The only sound in the room is the low wind of its slow breaths.
Ritsuko looks at you. You try and fail to hide your lack of surprise. Ritsuko closes her eyes in annoyance and states that you've clearly been in this room before, haven't you? You don't answer. She had her suspicions when you reacted the way you did to the Eleventh Angel's presence down in Terminal Dogma.
The two of you stand in silence for a moment. Just you, Ritsuko, and Adam. Ritsuko asks if you know what the Angel in the room is. There's no point in playing dumb.
You admit that you're aware that this Angel is Adam, the trigger behind Second Impact. You don't know why it's here and alive. You know that if the Angels make contact with it, humanity will end. You'd like some answers.
Ritsuko shakes her head. The thing up there isn't Adam. It's the Second Angel. Lilith.
What?
Ritsuko says there are many theories about where they came from, but two unusual spherical geological structures were discovered at the end of the twentieth century. The Black Moon, and the White Moon. The second term feels very familiar. Ritsuko says the White Moon was discovered under Antarctica, and it contained Adam. A giant of light. It's what your father was researching. The Black Moon was discovered under Hakone, Japan. Now called Tokyo-3. You're currently standing at the center of it. It contains Lilith.
Adam is most likely the progenitor of the other Angels. And Lilith is the progenitor of all other life on Earth. It is our mother. Mother Night. Humanity is an Angel too, technically. But Angels cannot coexist with each other.
As for why it's here? Ritsuko already told you. It's always been here. NERV and its predecessor organization, GEHIRN, have of course taken precautions to ensure that it doesn't do anything it isn't supposed to do. Which is sit inert at the bottom of this pit forever. Like every Angel, it has the power to annihilate us all.
These revelations are a lot to take in, but they mostly make sense to you. Ritsuko had mentioned months ago that the Angels' microscopic structure resembled the human genome. Still, the idea that this hideous thing somehow created life itself is…unpleasant to consider. What the hell even is it?
More importantly, what does this have to do with Rei?
The accident, Ritsuko says. As you know, Evangelions are clones of Adam. Most of them. But Evangelion Unit-01 is a clone of Lilith. It's special. The methods used to clone Evangelions were crude at the time. You might be wondering what happened to Lilith's lower body. Unit-01 was created via fission. The accident happened when Unit-01 was still attached to Lilith. Dr. Ikari was drawn into Unit-01 while it was fused with Lilith.
You stare at Ritsuko, questions flooding your head. There's still so much you don't understand about NERV. Why make a special Evangelion? Why has its existence been kept secret from you? Are there things about Unit-01 you need to worry about that nobody's told you? What other secrets do the Evangelions hold?
Ritsuko looks out into the distance, a forlorn look in her eyes. It was Fuyutsuki's idea, at first, but the Commander unhesitatingly signed off on it. Gendo Ikari loved his wife. More than anything else. He would do anything to get her back. There was a procedure, Fuyutsuki conjectured, that could retrieve Yui Ikari from the body of Unit-01. They worked to salvage her soul and put it into a new body. There were some remains in the Entry Plug. Not much. The salvage process was supposed to make the constituent parts of Yui Ikari dissolved in the Plug's LCL back into a person again.
The process failed. Yui Ikari didn't come back. She's still there. But there was another soul salvaged from the wreck. Another body formed, from what was left of Yui Ikari, but also the biomatter of Unit-01 and Lilith. It wears Dr. Ikari's face and walks around in a warped version of her flesh that needs constant medication and monitoring to stay alive. The contradictions within its form threaten to tear it apart. Its mind and spirit belong to the terrible being in front of you. You already know its identity.
Rei Ayanami.
They did not get Dr. Ikari back. They got a thing that is not Yui Ikari. They accidentally trapped the soul of the Creator in a coffin of rotting flesh. And it wants to escape. But Rei has her uses. An infinite supply of loyal pilots to sync with Unit-00 or Unit-01. A living guarantee that Lilith will remain harmless so long as she remains physically separated from it. A sentimental object for NERV to remember Dr. Ikari by. A container for the Infinite for everyone's protection.
But these purposes are only served so long as Rei is stable. Rei is aware of her nature, on some level. Up until recently, Ritsuko assumed Onze lacked the imagination to understand what that means. But recent events have shown that time and time again, Ritsuko has underestimated her. She is a container for the Endless. She contains unimaginable destructive energies within her. That containment is failing. If something is not done to correct the psychological and spiritual damage from her time as pilot, and the rapid destabilization of her personality, the consequences would be apocalyptic. She is a reactor on the verge of meltdown. She is a dam about to break. She is dry grass in a lightning storm. She is a tumor about to metastasize. The disease must be cut out.
Lilith needs to be transferred to a safer body.
What will you do, Major?
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Looking forwards to that revelation.