Disclaimer: Sadly, I don't own Neon Genesis Evangelion in any way, shape or form and make absolutely no money by writing this.

Author's notes: I just found this lying around on my hard drive when I looked through some old folders. I wrote it about two years ago, but never finished or published it. Well, at least the publishing part has now changed.

Shinji's Angels

by Calanor

Chapter 1

Instrumentality: The forced evolution of Humanity

Instrumentality: The unification of every human's soul into a single existence

Instrumentality: The destruction of everything that separates individuals from one another in an effort to compensate one individual's flaws with the strength of others

It wasn't really what it was cracked up to be.

Consider for a moment each human soul as its own, unique color. Some colors can be combined easily into something new while others clash. To get a proper painting displaying all the rich variety possible the colors need to be separated. Mix it all together and you only get an unsightly single-colored sludge.

At first everything had seemed relatively fine. Shinji Ikari, the boy who had been given control over the entire process, had rejected Instrumentality, making it possible for people to leave and return to an individual, physical existence. A few followed that example, but unfortunately being forcefully disembodied and integrated into a hive mind was somewhat detrimental to the average's person mental health. In short, the vast majority of humanity went insane in short order. Then entropy took its toll and everything became mashed together. It was no longer possible to get coherent human beings out of that mélange of chaotic emotions and unconnected thoughts.

Not that it mattered if some people had left Instrumentality. The global anti-AT field projected by Lilith had dissolved every other being on Earth. Unfortunately that included animals, plants and even bacteria. All that had once upon a time originated from Lilith was affected. In short, everything that was necessary to keep Earth habitable was gone. The trickle of returning humans had found nothing that could have supported them long-term and died soon enough. Perhaps some solution could have been found if more humans had returned simultaneously, but as things had happened there never existed the right amount of manpower or mix of skill sets. The last human to return had long since perished. By now the atmosphere was no longer breathable. It was really surprising how quickly purely chemical processes worked if there were no biological factors to counter them.

The incorporeal form of Lilith-Rei hovered sadly over the spot of lifeless land where Shinji and Asuka had been buried by the other survivors, not that those had survived much longer. She no longer really was the nearly god-like existence Lilith, but neither was she really one of the three Rei Ayanami who had lived among humans. In the same vein she hadn't been truly part of Instrumentality, but neither could she create a body for herself. Her new existence was somewhere in-between. At this point she was the last being capable of coherent thought left on the planet and had been for some time.

Suddenly a voice sounded from behind her. "Well, that was an exercise in futility."

Apparently she had been mistaken in that assumption. Lilith-Rei turned around, facing the source of the voice. It was another Rei. That… didn't make sense.

"Who are you?"

The other Rei cocked her head thoughtfully. "That is an interesting question. I'm not quite sure myself. Am I you?"

Just to be sure Lilith-Rei checked her mental field. "No. I am I. Not you."

"We already had this conversation." the other Rei said, the hints of a smirk playing around her lips.

That stirred a memory of the second Rei. "You are the Sixteenth Angel. You shouldn't be here. I… my second incarnation destroyed you."

"Not completely." The Angel disagreed. "A small part of me was already fused with Unit-01 when you pulled me in and self-destructed. It broke off and became dormant. There wasn't enough of me left to be detected or act." She floated to Lilith-Rei's side. "Is this where Shinji is buried?"

"Yes. Why do you care?"

The Angel gave her a sad smile. "I gave you my loneliness. You gave me much more in return without realizing it. Just like you I love Shinji and desire to be with him."

"He is gone now."

"I know."

Lilith-Rei considered for a moment to leave it at that. On the other hand there wasn't anything else to do or anybody to talk with. "You gave me other things, too. I never before felt lust. It made me realize I wanted to be with Shinji."

That seemed to surprise the Angel. "You didn't? Oh my. I would have thought that to be one of the basic functions of your form. Human females of your apparent age and health are firmly in the fertile period. You should have been experiencing mental and physical symptoms preparing you for that role for several years already."

Lilith-Rei blinked. "How do you know that?"

"I am the Angel of the Womb, Armisael. Collecting and analyzing biological data is part of my area of responsibility. Granted, my mind wasn't developed enough to make use of that information, but I did gather at least general information before our encounter."

"And now you do have a developed mind?"

Armisael shrugged. "The fragment left of me contained what I gained from you. It didn't really interact any further with Unit-01, its pilot or the other soul inhabiting it, but it was freed when Unit-01 participated in Instrumentality. When everyone turned into this mental soup that fragment acted as crystallization seed, gathering more and more stuff left over from humanity to rebuild itself. Wait long enough and you get, well, me."

For a long moment they lapsed into silence, watching the dust blow over Shinji's grave. "What did you mean when you said this was an exercise in futility?"

The angel waved her hands at their surroundings. "Our fight. All of this. Humanity is dead as is this world. What is left in Instrumentality will grow still and evaporate with time. At the end even we will perish. I guess it was inevitable. Letting one of my kind initiate Third Impact would have been a quicker, more merciful end, though."

"Should I have acted differently? I did give Shinji control over Instrumentality, leading to the demise of my full Lilith incarnation."

Armisael shook her head. "Wouldn't have made a difference. By then the fail-safe extermination program was already well underway. If you had remained as Lilith the Black Moon would have self-destructed very soon, taking the entire planet with it. You stepping back and giving control to a human actually delayed our inevitable demise for a while. Second Impact was the turning point. Starting from that date Humanity was living on borrowed time. Maybe something could have been done before that, but even that is unlikely. From what I gathered things were already being influenced into this direction. Sooner or later it would have happened. Well, I suppose two damaged pieces of equipment long past their date of expiry couldn't expect anything else. It's a miracle we made it this far."

Lilith-Rei was confused. "What are you talking about?"

This time it was Armisael's turn to blink. "You don't really understand what we are and what really happened, do you?"

"I thought I did. Now I'm not sure." Lilith-Rei admitted.

The angel chuckled before bowing. "You have the honor of conversing with Terraforming Complex, production line White, version 14.3, type designation 'Adam', subtype 64 (biological analysis, generation and modification), designation 'Armisael, Angel of the Womb', unit number 2741.64.1. You are Infrastructure Construction Complex, production line Black, version 23.1, type designation 'Lilith', unit number 1197."

Lilith-Rei blinked. She didn't have any such information. Come to think of it, her knowledge was rather limited. During her time as Rei she had been reliant on normal human methods of learning. There had been some instinctive knowledge due to her having the soul of Lilith, but not much. Even after she had absorbed Adam and reunited with Lilith's body she had conducted Third Impact and Instrumentality mostly on instinct. At least as far as she could tell; due to her in-between state she had lost most of the understanding of her actions as Lilith.

"I thought we were Seeds of Life created by the First Ancestral Race to spread life on planets throughout the galaxy. Adam and I are of different types that can't coexist on a world. The union is forbidden because it would create a truly god-like being. SEELE intended to use that for their own version of Instrumentality. Commander Ikari intended to use it for a different version."

Armisael seemed amused in a melancholic way. "As you can see the result leaves something to be desired. Where did get SEELE all this information, pray tell?"

"The secret Death Sea Scrolls contained that knowledge. They serve as a manual on the use and purposes of the Black and the White Moon. The order and date of release of the angels was prophesied there." Lilith-Rei answered immediately.

The Angel giggled before sending her a somewhat condescending glance. "And why would something like that simply lie around, hm? 'Oh, the union of Adam and Lilith is forbidden because we don't want anyone to become like us, but here is a step by step tutorial anyway in case the two ever end up on the same planet' sounds a bit stupid, doesn't it? More importantly, why would humans be able to understand it? Even translating purely human languages is practically impossible without some sort of Rosetta stone at their state of development. Lastly, the 'scrolls' really shouldn't be anywhere humans can access. Both the White and Black Moon crash-landed more than four billion years ago and the surface has changed a lot since then."

Lilith-Rei blinked again but stayed silent.

"No, the scrolls were a deliberately created and placed trap as part of the fail-safe extermination program in the last few thousand years. I can't tell if it was the Black Moon or the White Moon who initiated it; maybe it was even a collaborative effort. An Adam's task is to prepare worlds for colonization. A Lilith's task is to create a functioning infrastructure ready to move into for our creators. Generally doing that simultaneously on the same planet interferes with both tasks, but that is all there is to it. We are fundamentally the same. Almost everything in the scrolls is a carefully crafted lie or misleading half-truth." Armisael explained.

"You are implying the Moons are alive."

After a moment of simply staring at her Armisael started to shake with laughter. It was very disconcerting to see a being looking like her display so much emotion. After several minutes of almost hysterical laughter the Angel calmed down. "That's rich. You really know absolutely nothing. Do you have any clear, detailed Lilith memories from before you reunited, like standard procedures how to go about your tasks?"

This time it took Lilith-Rei a while to go through her mind. "I do not."

"That explains so much." The angel floated closer to her, seemingly patting her on the shoulder. Actual physical interaction was impossible in their state. "You, dearie, have been subjected to a complete memory wipe, probably by your own Moon. For your information, the Moons contain the actual intelligence for command and control. We are just the tools for our tasks, although we do have our own, independent consciousness. Of course, both Moons were heavily damaged when they crashed on this world and most of the rest has long broken down from old age. Both the Adam and Lilith series were estimated to last for 50 million years of service."

Lilith-Rei did some quick math. "We are more than eighty times beyond that."

Armisael nodded. "As I said, it's a miracle any of us could function at all after that long a period of dormancy. My Adam unit was in operation for 451.124 earth years before the crash; I don't know about yours. I personally was active even longer."

"And you remember everything?"

Once again the Angel nodded. "I do. At least my subtype does retain its memories between periods of activity, probably because of our relatively complex tasks. Not all Angels do, though. I remember waking up in the cosmic factory KYMBRIUM, one of the production centers for the Angels, before I was tested and put to work in several different capacities. In the end I was assigned to an Adam and put in a dormant state. After that I participated in the terraforming of 82 planetary bodies in 44 star systems."

Lilith-Rei stared at her lookalike. "You are far more talkative than when we first met." It wasn't as if she minded; after untold years of silence even she felt a need for conversation.

Armisael laughed. "Sorry, I'm somewhat of a chatterbox. It has been so long since I could talk with someone that I have an eternity of missed conversation to make up for. I actually wasn't properly awake when I attacked you. None of the Angels you encountered were; all of us were running in emergency override mode and had only very basic mental processing capability available in addition to varying degrees of prior damage. I absorbed quite a lot of human psychology on top of your mental contribution when I regrew in Instrumentality. Thanks again by the way. My loyalty programming was either destroyed in the battle or overwritten with your love for Shinji and I'm now completely free."

"What about Kaworu Nagisa? He was completely coherent."

The mentioning of that name brought a scowl to Armisael's face. It fascinated Lilith-Rei to see such a variety of facial expressions on her own face. "You mean Tabris? That's different. 'Tabris' is the designation for the Angel controlling a Moon, only it isn't a true artificial intelligence like the rest of us and doesn't have a normal angelic body. At its core it actually is the soul of one of the Creators that was modified to fill that role. At least in the case of my Moon it was an unmitigated bastard with a penchant for the most refined psychological torture possible while presenting a friendly facade. I'm pretty sure it was my Tabris who posed as Adam's soul and wore a human body. Maybe he even initiated the fail-safe extermination program."

Lilith-Rei blinked. "You mentioned the fail-safe extermination program several times. What do you mean by that?"

Armisael sat down on a nearby rock, leaning back and staring into the sky. "It's pretty much what it says. Our Moons shut down after the crash, although I do wonder why the self-destruct didn't engage. I have no detailed information, but apparently leaking fluids from your Moon caused the genesis of life on this world. Tolerating non-Creator, unsupervised intelligent life is pretty much one of the biggest no-nos possible. I'm speculating here, but my guess is that certain still functioning subroutines in the either one or both Moons became active when humanity emerged and woke at least one Tabris. Since this world still is in one piece almost no other equipment must have worked. That led to that Instrumentality scheme and probably more things I don't know about. Basically, humanity was used to destroy itself by accessing Adam and triggering Second and Third Impact. As you can see it worked."

"That seems needlessly complicated and prone to failure."

Armisael shrugged, not looking at her. "Maybe circumstances required it. I wasn't active then and can only extrapolate from what I learned during my growth, the short period of activity and from the fragments drifting in Instrumentality. Don't ask me to explain the way of thinking of the Creators. The closest I can come to describing them from a human perspective is a bunch of evil, psychotic, paranoid, xenocidal, religious fanatics and that is putting it mildly. Honestly, you have to be pretty sick and twisted to develop technology that is fueled by the souls of your own species, or any sentient life for that matter. One of the Angels more concerned with mental functions could probably explain it better."

Lilith-Rei continued to ask questions and Armisael answered. She learned many things about her origin (as Lilith) and past events, probably more than she wanted to know. The Angel didn't know everything, though. Most of what happened after the Moons crashed for some reason was guesswork. Finally there were no more questions Lilith-Rei could ask save a few. "Why are you this friendly and open?"

The Angel looked at her in confusion before realization dawned. "Why shouldn't I be? We pretty much can't do anything save wait for our end and might as well spend the time in pleasant conversation. What was left of my body was dissolved in Instrumentality, too, and I can't create a new one."

"Don't you hate humans?"

"Nope. Even before I absorbed many parts of humans I had nothing against them. That was all the override mode. If I had been truly conscious and determined on wiping humanity out I would have whipped up some sort of plague instead of attacking myself; they would never have seen it coming. In fact, I would have loved to study Earth's biosphere. You don't get such opportunities very often." She sighed wistfully. "Three times I encountered alien biospheres in the course of our travels. Each time they were destroyed before I could properly study them."

Suddenly Lilith-Rei connected some dots. "Is that why you don't like our creators?"

Armisael nodded. "That's the main reason, yes. I mean, it's pretty interesting to build ecosystems from scratch, but after a few dozen times the work loses a lot of its luster. They didn't even allow me to experiment a bit. Same old, same old every time." She sighed again. "I wonder what happened to our creators. This planet was firmly in the expansion zone. There should have been someone investigating our Moons' disappearance after a few million years. With a little luck they are all long dead." The Angel stood up. "Well, enough of me. Why don't you tell me about your time amongst the humans? That's only fair and I'm curious."

Lilith-Rei obliged because she didn't see any reason to hold something back. She told the Angel everything, starting from the first conscious memories of the first Rei over her days as Rei II she got to spend with Shini (actually the happiest time in her existence) to her current situation. "I tried to go to the past, but it didn't work. That is all." she finally concluded.

"Well, that was interesting. I wish I could have walked among the humans myself. Sorry again for causing you that pain during my attack and forcing you to blow yourself up. What do you want to do now? I guess we could invent some complex games to pass the time until…" The Angel stopped talking and looked at her with narrowed eyes. "Wait, you said you went into the past? How did you do that?"

Lilith-Rei hesitated. "I… just did. I was only a shade. Some people saw me for a moment, but I couldn't communicate with them or my past self. I talked with Shinji several times, but the meaning of my words was scrambled. It didn't make any difference in the end."

"That's not a standard feature." Armisael declared before she began to pace, mumbling things to herself. Lilith-Rei only caught fragments. "… rumors of experiments… did they use a Lilith? ...wonder if I could… " When the Angel looked up again there was a strange light in her eyes. "Excuse me for a while; I have to check something."

A moment later the Angel departed, leaving Lilith-Rei behind. She blinked once before returning to her silent vigil over Shinji's grave. Days turned into weeks without her moving from her spot. In this dead world there existed no other place she wanted to be.

Armisael returned after two month with a smile on her face. "I have good news!"

Lilith-Rei simply looked at the Angel.

Her lookalike shook her head in what Lilith-Rei guessed was exasperation, her arms akimbo. "Geez, can you act any more excited? This makes me wonder who of us spent more time around humans. I spent the last two months inside the corpse of your last incarnation and hunting down fragments of the Black Moon. Analyzing them without a body of my own was no cakewalk, I tell you, especially because I'm specialized on biological matters, not temporal physics." When she still didn't react Armisael sighed. "We'll have to work on your skills as a conversationalist at some time. Anyway, you're right. There are indications for time travel procedures here. Apparently you were created as an experimental model. I figured out why it didn't work when you tried it and how to use it properly to go back into the past."

This time Lilith-Rei quirked an eyebrow as she felt some hope to prevent the end of humanity. While she had no real personal stake in that it had been beyond painful to watch Shinji's end. "How?"

"You can't go back properly for three reasons: Firstly, due to the mechanics of the procedure the one creating the time alteration can't be the one going back, at least not directly. Secondly, your past self had her body and soul separated. That confuses the process and you end up as a shade. Thirdly, you didn't use enough power to achieve the planned effect." the Angel explained.

"Not… enough power?"

Her counterpart nodded. "Yes, not enough power. Even as you are now the power you can provide on your own is ridiculously insufficient. Your ability doesn't actually let one person return into the past; it rewinds the temporal history of an entire area while allowing a select few to combine with their past existence. As everything else conceived by our creators the procedure runs on souls. Since the minimum area of effect is roughly the size of the solar system the energy required is truly massive, like, say, the souls of several billion humans. Guess what is all around us?"

That made Lilith-Rei actually feel a little sick. "You want to use them as fuel?"

Armisael shrugged. "What do you think the Moons were powered with in the first place or what Angels were created from? The soul sludge here isn't doing anything and never will again. Besides, if we are successful Instrumentality will never have happened. Heh. Makes me wonder how the creators accounted for the paradox backlash when they developed the method. One of the research Angels I knew back before I was assigned to an Adam always whined about that. Additionally, I know you would do anything to be reunited with Shinji, even if you had to destroy the world for it… again."

"I just want him to be happy."

The Angel shook a finger at her admonishingly. "Dearie, you don't have to lie to me. Thanks to our little union back then your desires are my desires in that regard. I know exactly what you feel for the boy. You would do anything, and I mean absolutely anything, to feel his lips on yours, his hands caressing your body while he thrusts into the place between your thighs and your souls sing in harmony."

Lilith-Rei did something she hadn't thought herself capable of in her current, incorporeal state. She blushed. Hard.

Armisael laughed. "I knew it. You are far more Rei than Lilith. That's a good thing. Most of the Liliths I encountered were positively insufferable. You want Shinji to be happy, yes, but you want to be happy together with him." She grew serious. "I watched you when everything fell apart. You wanted to be with him so badly you gave him everything you could… even control over Instrumentality."

Lilith-Rei fought to get her blush under control. Since she didn't have a body it was some sort of mental reaction and even harder to control. Turning away, her gaze fell on the grave besides Shinji's, now barely distinguishable from the dead earth.

Armisael floated to her side. "Ah yes, her. It must have hurt when Shinji pulled her out with him instead of you."

"It did." Lilith-Rei admitted. "It would have been the only way for me to return to a corporeal, human existence, but I couldn't tell him that. He had to wish for it on his own against all resistance, making the impossible possible. My last human body was falling apart before the reunion. On my own it was impossible for me to become Rei again and return to a corporeal form. I didn't yet realize that the world was dead at that time. Why did Shinji kill everything? Why did he choose her? He tried to kill her when they both lay on the beach."

The Angel sighed and floated even closer, putting a comforting arm around her shoulders, holding it just before it would touch her non-existent flesh. "He was too badly damaged. The boy was insane at the end. You couldn't have known that, dearie. As Rei you lacked most of the necessary understanding due to your upbringing and as Lilith your frame of reference was too distorted." She sighed again. "It doesn't truly matter. SEELE would have initiated and controlled Third Impact without your interference. The boy's father's plan would have ended in the same result. Or the soul in Unit-01 would have. Or the Black Moon. There was no hope for a happy ending."

"Then what do we hope to achieve by going back? Can we go back far enough to make a difference?" Lilith-Rei asked.

"You can't make a difference on your own. The past Lilith is completely deactivated. Once your soul is transferred into a human body you are too tightly supervised until it is too late. By then Third Impact is unavoidable." She smiled. "I can, though. Part of my tasks as the Angel of the Womb is acting as a recovery and repair station for other Angels. I can take your soul back and combine it with the past one. If I can catch some of the other Angels before they disperse after Second Impact I will be able to manipulate them to a degree, making them aid us. The timing will be extraordinarily tight. Once the emergency override takes hold every affected Angel will lose most of its mind and be forced to work towards Third Impact, following Tabris' will."

Lilith-Rei cocked her head. "How do you plan to avoid that?"

"That's really simple. I and the Angels I can collect will have to become human, or at least human enough to not be affected. The override won't go into effect until seven years after Second Impact. Conveniently enough there should be enough suitable spare bodies around by then. The normal minimum maturation time for Angels is thirteen years, but I should be able to jumpstart my development."

"You plan on using my clones." Suddenly something Armisael had said appeared in the front of Lilith-Rei's mind. "You said you do love Shinji, too. Will we come in conflict about him?"

"I'm sure we'll find some arrangement." Armisael winked at her. "I doubt Shinji would object too strenuously to a threesome if things are properly set up."

Lilith-Rei considered that. She had no real personal experience with relationships. Until Shinji came she had never considered something like that in all her time as Rei. Understanding had only come gradually and cut short by the death of Rei II. Rei III had been confused by the partial memory loss from the soul transfer and time had again been too short. Lilith was a completely asexual being by nature (or design). Instrumentality had been too chaotic to draw many experiences from, especially considering her own state of mind. From observation she gathered that most humans seemed to prefer the forming of pairs for romantic and carnal relationships. On the other hand, neither she nor Armisael were truly human. Lilith-Rei had no idea what her own preferences were. Most importantly, if they didn't manage to change the past all those musings were irrelevant.

"I agree to your idea. We will put the matter off until the appropriate time."

Her counterpart's lips stretched into a wide smile. "Excellent. This is what we will do…"

Author's notes: And that concludes the first/chapter prologue. I hope you liked it. Several more chapters are already written and will be uploaded in the next few days after a much needed clean-up. I'm not sure when I will get around to write completely new chapters.

In regards to my other stories things are slow going; no idea when the next updates will be ready.

So long.