Author's PSA: just because I'm not actively asking for it at the beginning of each chapter like many other authors doesn't mean feedback wouldn't be welcome. As things are right now, I'm not 100% convinced whether this story is worth continuing, especially in light of my fairly recent other story having already gotten more feedback than this one did over the past ten years I've been writing this in one form or another. And no, this is not April's Fool BS.


Geofront, AEL Headquarters
January 9, 2042
1452 hours

"I read your report about this latest engagement, doctor. I am... disappointed."

"I know there is no excuse for a slip-up of this magnitude, but this latest Angel was far beyond our expectations." – Yui replied in a tone that made it clear she wasn't going to apologize for something that, in her own eyes, wasn't her fault. – "We simply don't have the means to fight anything like it at this time. I don't even have a rough estimate of when that will change."

"First things first, doctor." – Keel's hologram shushed her with a raised hand. – "What is your current state of readiness?"

The scientist released a strained sigh. She spent just about the entire day up until that point trying to assess exactly that. – "As of right now, only Unit-02 is ready for immediate combat deployment. We will try to expedite repairs on Unit-00 as much as we can, but our options concerning Unit-01 are extremely limited."

"I see. I may be able to arrange for something in that regard."

That was about the last thing Yui expected to hear. Not that it was unwelcome. – "Indeed?"

"I understand the development of your non-cybernetic hardware has been outsourced to Gehirn, yes? I believe they may be able to devise a way to perform emergency repairs on Unit-01 in a timely manner, provided your company shares the necessary physiological data."

Yui looked aside uncertainly for a moment before steeling her features. - "I'm concerned about sharing too much information pertaining to the Evangelions." – she admitted. – "Gehirn has access to superior industrial resources and could easily drive us out of business once they have the means to produce their own Evangelions."

And considering just who she was forced to deal with in order to even get this far, Yui didn't feel her concern was unwarranted whatsoever. As much as she prided herself on having went from project leader to chairwoman in only ten years without anyone propping her up with connections or money, that accomplishment was eclipsed by her ex-husband's meteoric rise in the corporate world following their divorce. Founding an industrial company out of scratch and turning them into the Confederacy's primary defense contractor took a special kind of businessman and Gendo Ikari's cold and calculating ruthlessness was only matched by his paradigm-breaking approach to business by insisting on product quality over immediate profit in order to ensure repeat payments.

Under his name, Gehirn Industries wasn't just a name, but a name with prestige, akin to the likes of IBM and General Electric before Second Impact. Under his name, Gehirn Industries wrote its name into the history books by taking the concept of a mechanized combat walker, much maligned and ridiculed in professional engineering circles prior to Second Impact, and revolutionizing it to the point of pretty much singlehandedly convincing the Confederate military to invest into battleframes instead of conventional armored vehicles.

Under his name, Gehirn Industries had more than enough brainpower and industrial assets at their disposal to reverse-engineer an Evangelion. And as much as Yui was aware of her own failings, she also knew from experience that Gendo Ikari was even more unscrupulous in seizing opportunities when it came to projects he saw promise in.

It was the very reason why she divorced him, after all.

"A pragmatic view, doctor." – Keel mused. – "However, in light of your current failure, we are not in a position to choose. I have already sent Gehirn an executive order to provide technical assistance."

Now that was the kind of arrangement she was definitely not agreeing to. – "Mister president, I did not-!"

"13,587."

His abrupt declaration cut right off what would've been a furious tirade on her part at him going above her head. – "Beg your pardon?"

"The official tally of military personnel casualties against the Angels so far." – Keel continued, his words chilling her to the core. – "This is not public information and civilian casualties are not included; however, if the outcome of your latest engagement is of any indication, this is only a prelude to what is to come. You will contact Gehirn to finalize the details."

"But-"

"Doctor." – he cut her off again, leaning forward to all but glare at her through his visor. – "This is non-negotiable." – Then he looked aside and cut the video call without a further word.

But Yui was not the kind of woman to give up when something unfortunate came her way.


Ten minutes later

"You wanted to speak to me?"

"Yes. Come with me."

When the PA system of the facility explicitly called him by name to head on up to Yui's office, Shephard expected her to continue chewing him out for yesterday. Not that he was going to apologize; those kids needed some slack, damn it. The first unexpected factor was her immediately leading him back out of the office with a flashlight in hand and down the facility's corridors, which is where the second unexpected factor greeted him in the form of an elevator he had seen a few times before but never dared approach.

It was quite impossible to miss the large number of warning signs over and around it, after all.

SECTOR T MEGA-DEPTH
RESEARCH FACILITY
PERSONNEL ENTRANCE

WARNING: NO UNAUTHORIZED ENTRY

TRESPASSING IS GROUNDS FOR
IMMEDIATE TERMINATION AND
CRIMINAL PROSECUTION TO THE
FULLEST EXTENT OF THE LAW

"What a welcoming place." – he quipped.

Yui didn't reply, instead marching straight to the instrumentation next to the elevator door.

"State identification." – came a synthetic female voice from hidden speakers, identical to the one from the PA system which Shephard remembered was the voice of the facility's mainframe. He heard it all the time since his arrival but it wasn't until he got acquainted with that technician guy in the command center – Hyuga, he recalled – that he found out the MAGI was actually a weak AI, not just a simple loudspeaker system. Aside from managing the facility's automated infrastructure, it apparently also assisted in the actual research, though he naturally wasn't in the know about the details.

Before him, the scientist looked into the retinal scanner mounted onto the wall while simultaneously placing her palm on the handprint scanner at waist level. – "Recognize Dr. Yui Ikari, authorization code 2359253628735. Authenticate." – she spoke into the microphone underneath the retinal scanner.

"Authentication confirmed. Identity established."

"Add temporary access, single-use only."

"Request logged. Awaiting identity."

Yui stepped away from the instrumentation and motioned at Shephard to take her place. – "Name, rank and occupation will be enough. It's for the record."

The man nodded and took her place, doing as he saw earlier. – "Adrian Shephard. Lieutenant colonel, Confederate Armed Forces."

"Identity logged. One-time access authorized."

He genuinely lost track of how many minutes went by after the elevator doors closed behind them before finally asking – "How far down does this thing go?"

Yui didn't reply immediately. When she did, her tone was uncharacteristically somber. – "The part of the facility you are about to enter has been decommissioned and shut down several years ago. It is where we carried out the initial development of some of our more... sensitive projects like the Evangelions, while the topside facilities were under construction. Whatever you see down here will not go beyond this elevator, do you understand me?"

"I saw the signs, doc."

"I'm not bringing you down here for a frivolous reason, Shephard. I understand your reasoning for why you broke protocol yesterday, but you must understand just how serious the situation is. You are not the sole person here whose daughter is in harm's way."

A valid point, he had to admit. Truth be told, he had almost forgotten the relation between her and Rei due to how little he saw them actually talk to each other. He had a nagging suspicion there was something not quite right there, but decided it was better to leave it be than to try butting into someone else's personal life.

Though he had a feeling Asuka would do otherwise.

"I'm not trying to make you adhere to the rules just for the sake of adhering to them." – Yui continued. – "I need you to trust me. You will see why shortly."

After a while more, the elevator doors finally opened to reveal a pitch-black corridor beyond, illuminated only by the flashlight Yui turned on.

Dark, cramped interior with only a flashlight, bare concrete walls with none of the sterile white plastic covering seen everywhere in the facility above. Looking closer to a pre-Impact bunker than what he was seeing until they entered the elevator, which itself was visibly old. Shephard had to suppress a wistful smile at how familiar the scenery was to him, even as it brought back a legion of unpleasant memories. He wasn't afraid of the dark... but when you know for a fact that there are monsters in there that want to do more than just scare you, you quickly learn not to ridicule others for being afraid. That was a lesson he'd rather have not learned at all.

And it wasn't just the dark. The air itself felt heavy, almost oppressive. And then there was the complete silence. In the facility, he could at least hear people in the other rooms and corridors, the PA system in the distance, even the ventilation. Here, there was nothing. It was so quiet he could actually hear Yui's breathing between their footsteps, even from where he stood.

"This place is giving me the willies." – he muttered.

"We are nearly two kilometers beneath the Geofront's ground level." – Yui replied without stopping. – "No external sounds except for seismic events can penetrate down here. The ventilation system has been offline ever since we closed down this wing, but the depth means the air pressure here is higher than normal. Enough to be felt by humans."


About a minute after leaving the elevator, the two of them walked into what Shephard recognized was a utility room. Yui spent a while trying to decipher the faded labels inside a fusebox under the flashlight's glare, visibly trying to remember something before cycling a handful of fuses and heading back out of the room.

Another few corridors later, the two stood on a raised platform looking down upon a yawning darkness. Yui flipped a few switches on the wall, faintly illuminating a massive chamber with giant, tarp-covered masses lined up on the floor in a grid pattern. Each one had a four-digit number and the word FAILED stamped on it in red.

"What are those?" – Shephard asked, slightly leaning over the rail to get a better look.

"Have you ever wondered why Unit-00's serial number is #0023?"

He slowly looked at her... then back at the objects below, his brain finally making the connection of what the tarp reminded him of.

Bodybags. And based on the shapes he saw, at least several of them contained something whose bodily proportions weren't quite... right.

"...I have a hunch there are exactly 22 of those things down there." – he guessed.

"21." – Yui clarified in a clinical tone. – "Unit-00 is not the first one we created. It's the first one that worked."

"And the missing unit?"

"Prototype #0022 was the closest one that got to completion." – the scientist said, leaning against the rail with one hand while gesturing with the other as she continued explaining. – "It's still alive on life support, but the limbs never developed the muscle mass necessary for it to even be able to remain standing, let alone be independently mobile under its own power. It's been in cryogenic storage for several years now. We occasionally thaw it out to monitor the level of cellular deterioration caused by long-term cryofreeze and to test out some more sensitive changes to the operating system before rolling them out to the active units."

"And these?" – Shephard pointed at the bodies below them.

"Failures. #0021, #0020 and #0019 were harvested for their cores to serve as the MAGI's central wetware, then terminated. The rest didn't even reach Quickening." – Yui paused for a moment before continuing. – "I told you once that the reason why Evangelions are humanoids is to streamline the nerve signal translation between the pilot's brain and the Evangelion's body. Without it, body parts that have no corresponding equivalent on the pilot would remain unusable at best and interfere with synchronization at worst. This goal was set in stone right from the beginning and our greatest challenge was to make it happen via manipulation at the genetic level. Each prototype's development was monitored constantly and when deviations were detected, we traced them back to the DNA to find out where did we go wrong and why. Introducing human genetic sequences from sections of DNA common across multiple terrestrial species helped, but actually making those sequences express in the final result was a whole another thing."

For once, Shephard actually understood what she was talking about.

"To say that we rewrote the book on genetics... is less of an exaggeration than you'd believe." – Yui continued, her tone sounding almost... tired. – "We went through... I don't know the exact number of failed tries. We only started numbering them once we had roughly human anatomical proportions and even then, there were some traits that were exceedingly difficult to eliminate. The oversized cranium and ventral forelimb were the hardest ones."

He gave her a sharp look. – "You didn't cook these things up from vorts, did you?"

"No." – she replied bluntly. – "The numbered prototypes are the only ones we kept after termination. We initially wanted to recycle the rest for their biomass to cut down on expenses but after we had several unexpected mutations due to junk sequences left over from previous subjects, they all went to the incinerator. Now they only exist as digitized DNA sequences in the MAGI's archives."

"I don't suppose you could reuse any of these."

"Impossible. They are little more than mummified skeletons now and all cybernetic components that we could reuse had been stripped years ago." – Finally she pushed herself away from the railing, walking back to the door. – "Come."


"These are high-security storage areas." – Yui declared as they walked down a larger, almost cavernous corridor with massive octagonal doors on each side, pointing at one to her left without slowing down in her step. – "The spear-like object we used against the second Angel is in that one."

"What about this one?" – Shephard asked as they stopped at the lone door at the end of the corridor.

"You are about to see."

Instead of going through the large door, however, Yui took him to a normal-sized door to the right, which lead the two up a flight of stairs to a glass cubicle looking out over a massive, dark cavern.

"Observation area?" – Shephard guessed, looking out into the darkness but not seeing anything, not even the door.

"Remember when I asked you to trust me?" – Yui asked back, locking eyes with him as soon as he looked away from the window. – "What you are about to see is not just the company's most closely guarded secret, but is also one of the highest-level state secrets of the Confederacy. I am not authorized to reveal it to you and I'm already skirting high treason just by telling you that it exists."

Which, for Shephard, was about par for the course by this point. Not that he said it out loud, of course; he could tell from her look that she was being completely serious with her warning. Which, in turn, reminded him of something he once heard someone else to say just before things went to hell.

'Babysitting job, my ass.'

Just like old times.

"And if the brass finds out I saw it..." – he slowly pressed the one million credit question.

"'Ten years of corrective labor without the right of correspondence.'" – Yui quoted.

"...right."

"You can still turn around and walk away." – she pointed out. – "I will not blame you and no one will know why I brought you down here. The official records will state that we merely inspected the Spear in case it somehow reacted to recent events like it did a few months ago. Nothing more."

Shephard gazed out into the darkness below for a minute in silence. It was the same deal all over again – except this time he apparently had the choice of just walking away from trouble. That is, unless she planned on blackmailing him or something... in which case he decided he would rather take his chances with the commissars. Frankly he has had enough of the fear and uncertainty, even as words he'd rather have forgotten echoed in his memories.

'While I believe a civil servant like yourself understands the importance of... discretion... my employers are not quite so trusting and... rather than continnnually subjecting you to the irresistible human temptation of telling all, we have decided to... convey you in a way where you can do no possible harm. And where no harm can come to you. I'm sure you can imagine there are worse... alternatives...'

To hell with it. Just rubbing it into the face of that creepy fucker would be worth it, consequences be damned.

"I've seen a lot of shady shit during the years." – he said finally. And for her credit, Yui didn't interrupt him for his language either. – "Sometimes I got told it was none of my business, most of the time I was left to wonder what the hell was going on and what else I didn't know. For years I've listened to nothing but lies, secrets, good men who were just as much in the dark getting portrayed as violent thugs in propaganda for just doing what they were told. I know I'm about to sound like a hypocrite due to having secrets I only ever told my wife about, but right here, right now?" – He sighed. – "The fact that you are even offering me the truth means you trust me. And if I'm going to sleep at night knowing that I entrusted my daughter's life to you, I guess I'll have to trust you too."

"Remember, Shephard. Once I show you the truth, I cannot undo it." – she warned.

"I know. I choose the truth."

Nodding, Yui walked to an old console off to the side. – "In that case, I present to you..."

She flipped a switch and powerful floodlights came on in the chamber, two of them immediately burning out with a flash.

"The Source."

Up until that moment, Shephard thought he had seen the ugliest that extraterrestrial life can offer in the form of that tentacled... thing he had last seen before the world went to hell. Now, he knew for a fact he was wrong... but had no idea whether that was supposed to be a good thing or a bad thing. What laid beyond the window was a misshapen... thing that could only be called humanoid in a very roundabout way. Its skin was an unnatural shade of gray, more akin to ash than skin, and while it had a mouth, it was closer to triangular than slit and honestly reminded him of a certain bit of anatomy not discussed in polite company.

He couldn't even see any legs, only partially-disassembled machinery on its bottom. He could, however, see the spindly arms, as long as the entire creature was tall, along with a small third arm emerging from the center of the chest, hung up above the body by cables, all three appendages ending in three long fingers that didn't even look like they could bend. The entire body was full of cables, pipes and scars, with the sole exception of the disproportionately large head with looked as if the entire top half of the skull above the eyeline was seared off, the flesh charred and blackened. He could even see some of it having flaked off to rest on the massive, cross-shaped metal slab the creature was lying on like a surgical table.

"...that does not look like any alien or synth I've seen before." – he murmured. The three arms reminded him of vortigaunts, even though the rest of the creature looked nothing like the friendly aliens kilometers above them.

"It's not of Combine origin." – Yui remarked, walking up next to him to look down at the entity. – "We analyzed the cybernetic components, there is no material or construction commonality. The lifeform itself is carbon-based, but... something about its composition is off. All the chemical elements and isotopes match, all the chemical bonds are the same, but there are extremely subtle differences in the way it interacts with other matter on a quantum level. It should've rotted away years ago, yet no known bacteria native to Earth is capable of digesting it and we just don't know why."

Shephard looked at her. – "So if it's not Combine... then what is it?"

"It's an extremely difficult answer. It's not from Earth, but its cellular structure is an identical match to terrestrial life. Not only does it have DNA, but a sizable portion of it is a direct match with multiple lifeforms native to Earth." – That bit of information made the man's eyebrows rise all the way to his hairline. – "However, there are signs of mutation, genetic damage and large chains of sequences identical to those in vortigaunts."

"How is that possible?"

Yui shrugged with a perplexed look. – "Artificial splicing. Has to be. Vortigaunt biochemistry may be compatible enough with ours for nutritional purposes, but their DNA isn't even made up of the same amino acids as ours."

"So someone cooked this thing up in a lab." – he guessed.

"That's our idea too, but the genetic engineering capabilities required are beyond ours. Beyond humanity's, I mean. We've seen limited examples of Combine bioengineering but again, the cybernetic components are not of their origin and their own applications of the technology tend to gravitate towards cybernetic replacement, not genetic modification." – She looked down at the creature again, a sigh of frustration escaping her lips. – "A creature like this simply cannot come into existence via natural evolution. Not this type of anatomy and at this scale. We don't even know how it sustained itself nutritionally."

Shephard tilted his head to the side. – "Why, what do you guys feed the Evangelions with?"

"Concentrated nutrient mixture introduced intravenously. Even if we knew exactly what kind of food their digestive tract is capable of processing, it's the only option that doesn't involve bankrupting the company by feeding them every two hours every day just to keep them from starving."

"Well, there you go. Maybe that's what they used for this thing too."

Yui shook her head. – "There's physical evidence of extensive surgery all over the body, but nothing that looks like an injection port. In fact, it doesn't even have a brain."

"What?"

The scientist gave the surprised officer a look that pretty much screamed 'I swear I'm not making this up'. It was a look she was inevitably going to give him at one point, he knew. – "We could hardly believe it ourselves when we first examined it, but the brain has been replaced by a device of unknown purpose, plugged directly into the nervous system. The entity's demise destroyed most of the instrumentation so we didn't have much to examine, but based on eyewitness reports..." – She hesitated. – "As difficult to fathom the idea is, there's a high likelihood that the device controlling this entity was a displacement field generator."

Now the surprise made its way to sheer, undiluted incredulity. – "Are you telling me somebody scooped out this thing's brain and plugged a portal into its place?!" – Shephard demanded.

"Seems that way. The best guess we have is that it was remotely controlled from somewhere else. Like a drone, but organic."

He stared at the creature again. Now he knew where the burn marks on the head came from, but the idea still sounded completely bananas.

And yet, the part of his brain that kept him alive all those years ago looked carefully at her words, the name she used for the entity... and found a connection.

Slowly, Shephard looked back at Yui and found himself speaking words that sounded insane – and yet the more he thought about it, the more he felt it wasn't.

"...or like an Evangelion."

When Yui's reply came, it was underlaid with uncertainty. Guilt. – "Yes, only except the operator isn't within the body."

"...there's more to that, isn't there?" – he pressed, straightening up to his full height as he fully turned to face her. – "It's artificial, just like the Evangelions. It's cybernetic, just like the Evangelions. It's controlled by someone else, just like the Evangelions. And it's inside the same facility where the Evangelions were created. Are you going to tell me that's coincidental?"

Yui looked aside. – "...no. It's not." – Her words were almost inaudible.

"So what's the deal, then? I don't suppose you just tripped over it one day."

He saw her visibly swallow. This kind of behavior was so wholly unlike her, so far removed from what he had come to expect from her, that he was almost dreading her answer. Especially in light of her earlier words about how much the Confederacy didn't want anyone to know about the creature.

"The... the government retried this creature from Xen about... nine years ago." – she began. – "It was a secret operation as everyone involved was fully aware of what kind of public reaction its relocation to Earth would cause. Our company was entrusted with safekeeping and studying it, but only a very small number of us had any knowledge of it. Even some of those who worked on tissue analysis weren't told where the samples came from-"

"Doc." – he interrupted her, being just plain done with her delaying. – "What. Is. This. Thing?"

Unlike her earlier offer of the truth, the scientist really didn't look like she wanted to answer.

When she did, she was even quieter than before.

"This entity... was at the center of Second Impact."

"How?"

"It's all in the history books. Black Mesa. Why the vortigaunts came to Earth. Why they stayed here. This... is the Nihilanth, as the vortigaunts call it."

He just stared at her for... he didn't know how long. And when words finally came to him, they came straight from his heart.

"...oh, what the fuck."

He whirled around to stare at the giant carcass below, his stomach threatening to nosedive straight through the window despite knowing the source of that emotion (no pun intended) was well and truly dead thanks to the handiwork of one certain war hero. And yet, that knowledge was anything but enough to calm him down.

"Are you seriously telling me that this thing-"

"Is what kept the dimensional rift open long enough for the Combine to invade."

"And you guys... made the Evangelions from this?!"

"This entity is what the Evangelions were conceptually and genetically based on, yes." – Yui retorted, finding her composure once more. – "But our incomplete knowledge of it, coupled with the level of genetic damage and anatomical differences, meant that we had to improvise for the most part. The power of the Evangelions is not even a tiny fraction of what this being was capable of and despite our best efforts, we couldn't figure out the missing link. It could be the cybernetics, it could be something innate to the creature itself, we just don't know."

Shephard promptly planted his forehead against the cool glass with enough force to make an audible thump. – "Jesus Christ... and you are the one lecturing me about meddling with the unknown?" – he seethed.

"I'm well aware of my own failings, Shephard." – she shot back, indecision fully gone. – "We all have skeletons in our closets. I may have more in mine than you do in yours, but in the end, I am aware of what I did and why it was wrong. If there is any retroactive justification here, it's that if I hadn't taken that leap of faith, there would be no Evangelions for us to hold back the Angels with. There is no way humanity could've created them in this timeframe entirely from scratch."

"Doc, this thing is why everything went to hell 43 years ago!"

"And it might very well be our only hope for survival this time around." – the scientist retorted with heat.

That sentence stopped Shephard's next words short. – "What do you mean?"

"After the first Angel attack, I had a personal meeting with the president." – Yui revealed, folding her arms. – "The Evangelions are the only option humanity has against the Angels and he has reason to believe that if we fail to hold the line, there will be a Third Impact and it will dwarf everything we had ever seen before. Even if he's wrong, he still believes in it. We have no choice at this point."

"But-"

"Colonel." – she cut him off. – "You know how things are. If the president wants us to act, we act or we are replaced. Would you rather have your daughter serve under me, who just told you something that could get me locked away for the rest of my life, or the very people who stonewalled you from finding your wife's murderer?"

Shephard narrowed his eyes. –"That's a cheap shot, doc. And rich, coming from you after having pulled me into this."

"I don't want an accomplice, Shephard." – she replied. – "I have enough of those. I want an ally. Do you seriously think I would've showed you this" – She pointed at the Nihilanth. – "if I didn't trust you not to immediately alert your superiors? I need you to show that same trust to me. I don't know what's coming, but you and I cannot afford to be at each other's throats. Because if we do, our children will pay the price."

And the worst part was that he found himself agreeing with her.


Chapter finished on 20/04/01. Not 100% satisfied, but it will do. Parallel to writing this chapter, I also updated chapter 2 to be more consistent with Kaworu's characterization in later chapters.

Corrective labor without correspondence was a frequent sentence during the purges in the Soviet Union. As pronounced during the trial, the relatives of the convict were told that the convict was in the gulag, banned from sending or receiving any letters for the duration of their sentence while in truth, the convict was sent to the firing squad right away and the bureaucracy now had years to manufacture evidence of an "unfortunate accident".

Also, a notice for all readers (but especially new ones) since this question was already asked of me once. This is a plot-focused fic (AKA gen fic), NOT a shipping-focused one. All planned relationships are already set in stone, but they are NOT going to happen for a VERY long time and they are NEVER going to be the story's primary focus. Just a heads-up in case you read fanfics solely for the shipping and don't want to waste your time with anything that doesn't satisfy that.