Next chapter. No action here either, only exposition. Hard to believe but I actually wrote this in one go – a far cry from my usual snail-pace of one paragraph then several days of laziness.
Geofront, AEL Headquarters
February 24, 2042
0012 hours"You're here. Good." – Yui remarked as Shephard entered her office. It was the time they agreed on three days before.
"Of course I'm here, doc." – the man retorted. – "Are we going or what?"
She merely nodded and left the office with Shephard in tow. They navigated a long maze of corridors before they finally arrived to an elevator door with a pair of cameras watching it, various identification measures piled up on the wall next to it and a large sign above it.
SECTOR T MEGADEPTH RESEARCH FACILITY – RESTRICTED ACCESS
Yui paused abruptly and turned to Shephard. – "There are two things you should be aware of, colonel. First, what you may see down there will change your entire outlook of the situation we have here. I advise you to consider very carefully whether you truly want to know what we're hiding from the public because once you say yes, there is no turning back."
"Doc... if I wasn't sure, would I even be here?" – the man quipped dryly.
"...point taken. Second, you must keep to yourself everything you see down there. Not even your superiors must know about it or they will march in here guns blazing 'for our own good'." – she added the last part with air quotes. – "Unless you agree to this, you will not go beyond this point."
He groaned. – "Ah, for cryin' out loud... doc, do you even want me to know or not? Decide already."
"That's it, then. Just don't claim I didn't warn you." – she said finally as she turned to the elevator and tapped a long sequence on the keyboard, her finger lingering on the final key to let the machine scan her fingerprint. Next she looked into the iris scanner until the machine beeped affirmative and extended a breath analyzer she blew into. Finally, she spoke to the console. – "And they became pregnant, and they bare great giants, whose height was three thousand ells; who consumed all the acquisitions of men. And when men could no longer sustain them, the giants turned against them and devoured mankind."
The console beeped thrice in rapid succession and the door opened, revealing an elevator.
"Spooky... what was that?" – he asked, referring to the passphrase she said.
"Jewish apocrypha. The Book of Enoch, chapter 7 verse 2." – she said curtly as looked into the camera near the ceiling before entering the same sequence into the keypad inside the elevator. The doors closed and the elevator started descending with such a speed Shephard staggered and winced as his sense of balance completely disappeared.
Yui didn't seem affected by it as she merely leaned against the wall with arms crossed in front of her. – "We're about to enter the oldest part of the facility. What you've seen so far was constructed fairly recently but this shaft predates Second Impact."
Shephard's head perked up at that. – "What do you mean? I thought you built this place!"
"The Geofront was originally discovered mere weeks before Second Impact. They didn't have much time to study it before the Seven Hour War destroyed all records. It was rediscovered when the Confederacy expanded into Japan. As far as we could tell, the Geofront is a near-perfect sphere with a diameter of approximately 13.75 kilometers; the bottom is only a few kilometers away from the local Mohorovičić discontinuity, even deeper than the Kola superdeep borehole dug a decade before Second Impact. It has an extensive natural cave system but that's not the most interesting part."
"Then what? Get to the point, doc."
"The sphere has a hard outer shell made of a material unlike anything we have ever seen. It simultaneously shows physical properties of metal, plastic and glass. Metallurgically, it shows distant similarities to the Lance of Longinus."
"Which you have no idea what it's made of either." – he added with a sigh.
"That's not my point. This material is completely alien to us; it's not found anywhere else on Earth or the colonies. Not even the Combine's dark matter alloys show the same properties. And that cave system... what few seismic tests were done show it extends beyond the Geofront. All indications point at the Geofront being artificial in origin – and it wasn't built by us OR the Combine." – she pointed out.
"Are you saying we have another bunch of wannabe alien overlords out there?"
"Perhaps. Perhaps not. But that is not why we came for." – She sighed as she continued. – "Project E started back in 2026 when I and my then-husband were jointly heading this company. We received an open-ended contract from the military to study and replicate Combine synth technology. This presented a unique opportunity for us since... something was entrusted to us for safekeeping only the year before."
Shephard nodded. – "The Lance of Longinus."
"Not quite. True, we received the Lance too but it was only secondary to what you would call a 'motherload': a unique specimen of an alien species never encountered before. Unfortunately it was already deceased but for some unknown reason, its carcass does not decay at all – most likely inedible to terrestrial bacteria. It took us several years but we managed to extract enough genetic material to get a preliminary study."
"Quad-helix DNA instead of the double-helix of terrestrial organisms but it was badly damaged; we were outright surprised the entity was still capable of protein synthesis before it died. Heavy mutation was present across all chromosomes – at least we presume they were chromosomes. There is no way to tell for sure what was natural and what wasn't. It had some internal cybernetics but nothing on the level of Combine technology."
"Most surprising, it had strands of vortigaunt DNA in it. The rest wasn't even similar so we presume it was artificially spliced in using gene therapy decades, if not centuries, more advanced than what we currently have. For entirely valid reasons, we didn't want to experiment on the creature itself so we started experimenting on its DNA instead. First off, we wanted to see what would happen if we were to replace those vortigaunt strands with human ones, what morphological differences would we see?" – She smiled fondly. – "Tell me, did you know Unit-00's full production number is PrE-0025?"
Shephard shrugged, finally regaining his balance as he felt the elevator slow down. – "I do now." – he managed to get out just before the elevator shaft was replaced with a glass tube descending through a vaguely tubular chamber with what looked like huge black body bags hanging from the wall. Each one had a four-digit number – 0001 through 0023 – stamped on it in red, followed by the word REJECTED. It didn't take him much to guess the content of those bags.
Corpses. Evangelion corpses.
Yui continued as if nothing unusual was going on. – "Genetic engineering is a slow and laborious process with lots of dead-ends and backtracking. The first prototypes were nothing but a bloated mass of flesh with no clearly recognizable anatomy other than the occasional malformed leg; those we euthanized and cremated as they were useless to us. We only started numbering them once we achieved a roughly tetrapodal body shape, although many had missing or malformed limbs. 0021 was the first anatomically complete humanoid model. That one." – she said as she pointed to a body bag with near the bottom. Shephard noticed the top was much larger than the bottom as if a giant fetus was inside. – "It still couldn't survive without external life support, nor the next two." – She pointed at the final two. – "Still, they're on minimal life support. 0024 was the breakthrough we've been waiting for." – she said with a victorious smirk.
"Which one is it?" – the man asked as he looked around but didn't see a bag with that number.
"You won't find it here. It's morphologically identical to Unit-00 but has underdeveloped extremities. It can't even support its own weight without external assistance. It served as the test bed of Unit-00's cybernetics but was never finished." – The elevator went dark again as they reached the bottom of the chamber and reentered the shaft.
"Is that one alive too?"
"In a sense, yes. We put it in cryogenic storage but periodically wake it up to monitor the effects of prolonged cryopreservation on Evangelions."
"And what about the three failed ones?" – Shephard asked as the elevator finally stopped and they disembarked.
"This way." – Yui motioned and marched off to a long corridor with doors on both sides. All were closed so Shephard could only guess they hid laboratories. – "We wanted to turn them into obedient war machines but all prototypes ended up vegetative and completely non-responsive to outside stimuli. It was most frustrating for the development team when all our efforts seemed to be in vain. That was the case with 0024 as well when it became operational in 2029. The entire project was on the verge of falling apart when the works of your late wife came to our attention."
The man instantly stopped. – "What? How the hell does she come into this?" – he demanded.
Yui turned around. – "Her work unexpectedly ended up helping us. The paper she published about metaphysical biology turned out to be the final piece of the puzzle. It showed us what we've been missing the whole time!"
"And that was...?"
"An Evangelion's core contains a unique neuron lattice with performance on par with a human brain, if not above it. Problem is, biology isn't magic. Merely cloning a human doesn't mean the clone would be mentally functional. That was the case with the Evangelions as well: they were grown artificially and lacked all lifetime development usually experienced by humans. What we needed wasn't a modification in the gene sequence defining their nervous system; what we needed was a consciousness, a soul, if you will."
"A soul." – he stated deadpan, clearly skeptical.
"Yes. I know it sounds unlikely to you but to us, it was a revelation on par with a divine vision at the time." – She turned around, silent for a few moments. – "Some say the ability to create a soul is reserved to God; others say the same souls are being reincarnated over and over again. We're not gods, nor do we have the ability to control souls. Our only options were: harvest an existing one from a human or create one ourselves. The first was obviously out of the question as no self-respecting scientist should resort to human sacrifice. The second one was equally difficult at first glance but then we realized: we already had the technology to create what we were searching for. It took us two long years but we finally managed to upload a specially crafted AI into 0025's core. And thus, Lilith was born."
"So that's how you created the Evangelions."
"Indeed." – She shrugged dismissively. – "0024 served as the prototype for the process. I doubt you heard about Naoko Akagi but she had a theory to use Evangelion cores as wetware before her untimely death. Her research resulted in the MAGI system running this base by giving 0021, 0022 and 0023 simpler AIs then wiring their cores into a computer system, creating the MAGI. The rest is not quite interesting as Evangelion development slowed down afterwards and I had personal problems, the foremost of which was my divorce back in 2031. My husband left the company around the same time." – She suddenly resumed walking, forcing Shephard to hurry after her. – "We're here." – she said minutes later when they were standing in front of a heavy door with the same security measures she used to enter the elevator. – "All security measures you saw so far are in place to protect this." – she said as she went through the checks. – "If unauthorized people try to access the elevator, the MAGI triggers a base-wide security alarm. The elevator shaft itself is lined up with shaped charges which automatically collapse the shaft if the elevator is compromised."
"You're serious about keeping out intruders, aren't you?" – he asked dryly.
Yui smirked. – "That's not all. When the facility was built, President Keel was gracious enough to provide us with enough fissile material to implement a final safety measure in the form of an advanced radiation weapon. When activated, the warhead releases a high-energy burst of neutron radiation and instantly kills every lifeform down to and including bacteria. The isolation tube and the newer facilities aren't affected."
"Jeez... don't you think that's extreme?" – Shephard asked with a sweatdrop as the door opened and they entered a large observation room with glass floor, although the area below was pitch black.
"Like I said, it was all implemented to protect this." – she said as large floodlights below them switched on and illuminated the dark area. – "The entity in the middle of it all: the Source."
A minute-long silence followed, broken by Shephard's indignant yell. – "ARE YOU PEOPLE COMPLETELY INSANE?"
Yui raised an eyebrow. – "Did I not tell you we have a valid reason not to experiment on the Source itself?"
"Whatever! What the hell is the NIHILANTH of all things doing down here? I thought this fucker was supposed to have died on Xen!" – he yelled as he pointed at the gray creature sprawled out under them.
"Language, colonel." – she warned. – "And don't worry; it truly is dead, thanks to the handiwork of Gordon Freeman. From his account of the Source when it was still alive, I don't think we would've wanted to go anywhere near it, much less get samples to experiment on." – She looked at the entity below them. – "Although I was never told how exactly did they bring it to Earth. My field is biotechnology, not teleportation; not even the Lambda Reactor back in Black Mesa would be powerful enough to teleport that much mass."
"Maybe they rigged something up at Focal Point Station but still, this thing caused Second Impact singlehandedly! How could anyone think bringing it to Earth was a good idea?" – he insisted.
"As far as we know, the Combine is unaware of the Geofront's existence. The Confederate leadership probably wants to keep the Nihilanth out of the Combine's hands. If their Advisors were to have even a fraction of the Nihilanth's power..." – she shook her head seriously.
"There wouldn't be much of an Earth left behind the next invasion." – he finished grimly. – "Shiiit... first the Nihilanth, then the Combine, now these Angels. Freeman would have a field day here! What's going on, did the entire universe decided to pick on us?"
"That's not quite the case." – At his questioning glance, Yui finally dropped the bombshell. – "We cross-referenced the Nihilanth's DNA with those of the Angels; if the vortigaunt sequences are disregarded, it's an almost identical match."
Shephard looked like he's going to be sick. – "So... what? The Nihilanth was another Angel?"
Yui shook her head. – "No. The difference is more subtle... an evolutionary ancestor or offshoot, maybe? Again, that isn't my field so I don't know. What we do know is that the Angels somehow know it's down here."
"So you're saying-"
She nodded. – "Exactly. It's highly possible the Nihilanth is what's attracting the Angels like flypaper."