Matters of Faith

by jclong

Gendo is out to do some good, in the only way that he can; by being the most magnificent, manipulative bastard that he can be. Rei is out to help us all, by doing SCIENCE!

29. Chapter 28

Gendo pulled his turtleneck back on as Misato watched from her chair, her expression a mix of horror and interest. Tucking the shirt back into his slacks, he sat down, forgoing the uniform jacket and gloves.

"I was born the bastard child of an American soldier and a Japanese whore," he began, hands folded in front of his face, eyes trained on his newest Sub-Commander. "I grew up in the streets, whoreson and half-breed, never knowing the face or name of my father. My earliest education was not in any school, but on those streets, I learned to fight and, even more importantly, to win. I also learned that one person cannot challenge the system from the outside. I learned this lesson the hard way, Sub-Commander. My time on the streets ended, and I was given a choice."

"I was told that I could die or I could leave. I had run afoul of both the law and the local Yakuza." Gendo smiled into his hands as he thought back to his uncouth youth. "I was never very good at showing respect to people who considered themselves my superiors. If I stayed on the streets, I would have been hunted down and killed. If I allowed myself to be arrested, I would have been killed on the inside. My only real option was to leave, and so I did. I joined the Merchant Marines, lying about my age and my background. I was always big for my age, something I must have inherited from my father, along with my blue eyes. Life at sea was hard, but no more so than life as a street thug. I made good money, and having nothing else to spend it on, I bought books. Books at each stop, all of them going to the ship's library when I was done. I learned more in those years on the ships than in my entire life, and I soon discovered I wanted to learn more.

Eventually, I had no choice but to go to school to gain what I desired. The next time we returned home to Japan, I jumped ship. The first thing I needed to do was obtain a diploma equivalent for high school, which proved to be easy enough. Competing for entrance to the university and the scholarships to pay for it was more difficult."

Gendo paused in his story, watching the woman, who was sitting perfectly still, transfixed. Nobody had ever heard the man say so much at once in a long time, she thought to herself. That he was talking about his past was even more shocking, but it put Sub-Commander Fuyutsuki's comments about him in context. His humble beginnings were indeed at odds with the amount of power he now commanded.

"I overcame those obstacles as I would eventually overcome all others. School life was ridiculously easy after the demands of life at sea and on the streets. All that was expected of us was to do our assigned work and turn it in on time. Essentially, I was being rewarded for reading books on mathematics and science. I learned that not everyone saw it the same way: people who had never worked for themselves and never wanted anything in their lives.

I don't begrudge them their opportunities or the privileged situations they were born into," he said as he leaned back in his chair. "A man cannot control the circumstances of his birth, or we would all be born princes. What does cause rancor is that they squander and waste their opportunities; they do not see that we are all equal, be it in function and in death, and they believe those of more unfortunate birth are below them. A poor man can think and reason as well as a rich one, and the richest of princes will die just as surely as the poorest of paupers, but they believe themselves to be a special breed, superior to the peasantry. They believe we are different from them and that we cannot begin to grasp their ideas and thoughts. They refuse to accept that the blood flowing through our veins is of the same source. That is one source of my discontent with those who would rule mankind as KADMON, the gestalt cosmic over-soul."

Gendo smiled, leaning back in his chair, his eyes shut. "I had a hard time learning to keep my mouth shut and my thoughts to myself. Fighting was something I had grown up with, and physical altercations were second nature to me. None in that school could hope to beat me, but I was still beaten. Not all power is physical. Political capital can be even stronger as the mightiest of muscles. I was placed on academic probation and almost expelled from the university several times. It was only because of a few people, some of them students, some of them professors, that I remained.

Yui Ikari was a brilliant and beautiful woman in several of my classes. We had a few mutual friends and were part of a regular group that studied and drank together. She asked her father to pull some strings to keep me in school."

Gendo sighed regretfully, closing his eyes. "She never lorded it over me, never held it over my head. She had done it out of genuine interest and friendship. That was the first time SEELE heard about me, although it would still be some time before I met her father. Before he granted his daughter's wish, he looked into my past and my present.

She might not have lorded it over me, but he was planning to use me in the future. A hard-working, intelligent young man who owed his education to him? Too good a deal to pass up. But he and the rest of SEELE underestimated me. I might have been an argumentative, abrasive, and arrogant student, but I was also brilliant, audacious, and possessed an indomitable will. The very things that endeared me to that group also were what would set me against them in the future."

"So your wife was involved with SEELE since the beginning. The family business, so to speak." Misato said, having found her voice again after the initial shock. "But what does this have to do with anything other than you deciding to fight SEELE?"

"All in good time, Sub-Commander. All in good time." Gendo shook his head slowly as he watched the younger woman. "Our perceptions shape our realities. How we think is just as important as what we think. To understand someone and truly know their thoughts and motives, you must know as much about them as possible.

But it is impossible to completely know other people, no matter how much you might know about them. As we grow, our realities and world views are molded by our experiences and perceptions. Our memories of events are in constant flux, recreated each time we think of them, colored more by our current attitudes than by the actual event the memory is of. To completely know someone requires more than knowing their history and opinions; you must understand how they think. A careful student of humanity can build models and predict how people might react to certain things, but in the end, it will still be an imperfect model. We are all self-contained universes, alone and inviolate, but we can reach out to others, expand our worlds, and expand ourselves through our relationships with them. That is the truth of this universe; that we are alone. It is not a sad truth or a reason to be bitter and hateful. It is simply just the bare truth. It is not to be lamented but rather celebrated; because we are alone, we are unique. The eventual aim of SEELE is to join all of humanity into the cosmic gestalt KADMON, where each of us is layered into one another, merging and mixing us into a single, omnipotent, and omnipresent soul, over which they will be the ruling consciousness. They will place themselves in the position of Keter, of the crown, of ruling, during the ceremony that drives Third Impact. Their philosophy is flawed because they do not understand the truth. They seek to end, not celebrate, our loneliness. To this end, they wish to harness the war between ADAM and Lilith, seeking to usurp the power of the ancient gods."

Gendo paused momentarily before speaking again, his tone sharp and cold. "I will not, I cannot allow this to happen. We are the children of Lilith as the Angels are the children of ADAM, and their paths are not ours. She made us this way for a reason and gifted us the fruit of the Tree of Knowledge. Do not mistake the power of the Angels; we are the ultimate in this universe, for we have created a force more than the match for those things. They cannot create. Their only purpose is to destroy. For all that they bleed and scream, they are not alive. They do not live. What will they do after they destroy Lilith? Their father is dead and gone, passed from this world in the Second Impact. An empty and hollow existence awaits them, which is what SEELE would do to us all.

The ultimate form of slavery, and they will not even do anything with the power that it will afford them. Their arrogance is disgusting in the extreme, and for this, I will do everything in my power to stop them. They have no right to try to control the divine; they do not even understand what it is that makes us so.

When I learned what was happening, I didn't believe it at first. I could not believe it. How could such a thing be true? But for all the nonsense surrounding the story of the Illuminati, they exist and have driven the world's history to this one point, this one goal. The promise of immortality, of power unimaginable, of godhood. The more I learned, the more I researched, and the more I knew that I could not deny the truth. This was a plan centuries in the making, and there seemed to be nothing that could stop it.

SEELE is far too entrenched to be stopped merely through assassination, Sub-Commander. The terrible truth is that Third Impact cannot be stopped. It is inevitable. You may have thought my planned treason was to stop Impact before their noses, to halt their machinations with my own."

Misato watched him as he watched her, the man's eyes cold and hard over the hands that hid his face. He lowered them slightly so that while they still were held before him, they did not mask him. It made little difference, for all the emotion his stony face held, he might as well not have bothered to reveal his face.

"That is, of course, a lie."

Misato stared at him in silence, swallowing slightly before speaking. "What do you plan on doing?" she whispered, gripping the arms of her chair tightly, her knuckles going white.

"I will initiate Third Impact ahead of them, take control of Instrumentality, and change everything." Gendo smiled a tight, savage grin, his eyes glittering with dark amusement. "You asked me what Purgatory was, the room of orbs. They are Evangelion cores, each one waiting for a pilot. You know the Evangelions must synchronize with their pilots, that the pilots must, in essence, become the Evangelions to give motive to them. The higher the synchronization, the more control the pilot has, and the stronger the AT-Field they can generate. It's all explained with quantum physics, neuroscience, and psychology, documented with a thousand nigh incomprehensible proofs that all remain highly proprietary and hidden in numerous patents.

It's also another lie. You know my wife died in a failed contact experiment, the first of our synchronization attempts. The truth is that her contact experiment was a success. She was consumed in the core of the Evangelion. She resides now in one of those red orbs, as does half the soul of Kyoko Sohryu, as do over a million different women, all mothers."

"What?"

"The power of the Evangelions comes from the merging of souls, from attaining on a small scale what is achieved through Instrumentality. However, on a small scale, it works best if there is a strong emotional bond between the two souls, depending on our individuality instead of brute force to attain this microcosm of Instrumentality. You see, we can form bonds with others because we are unique individuals. Simply put, two friends are stronger together than one person alone. I have turned friendship into a weapon, although we have found out that the bond that drives synchronization the best is that of maternal love. To this end, SEELE orchestrated the absorption of the souls of a million mothers into the cores, disguised as a new medical procedure to safeguard their health. Across the entirety of this poor, broken world, shattered by Second Impact and war, they used the guise of the United Nations Maternity Protection Act to take the system developed by GEHIRN to take the souls of these women, to afford themselves a plentiful pool of pilots in the future.

The original plan was to keep the selection pool limited. We knew the costs of the Evangelions would be astronomical, and we would only need a few pilots simply because there were limits to how many Evangelions we could make. Thus, the damage would be contained in a small group of volunteers, but SEELE wanted insurance against possible treason, pilot death or injury."

Gendo glowered at Misato, his brow furrowed in anger, his eyes like glaciers. The eyes on his hand also glared, a faint reddish glow emanating from them. Misato's grip on her chair's arms tightened even more, her hands white.

"So they took the mothers of an entire generation. Took them, and then entrusted them to me for safekeeping. They saw it as a yoke to keep me chained to them after they realized part of my intent."

"There's over a million cores in there…" Misato whispered, her voice sick.

"Did you ever wonder why so many children in Shinji's class had no mothers? Did it ever strike you as strange, that bizarre epidemic that spread itself like wildfire amongst women between twenty-three and thirty all across the world? That they all had families, that they all had children?"

"But Asuka's mother… she went insane and killed herself. And you said that your wife was entirely taken into the core."

"Yes. My wife was taken, body and soul, into the Evangelion core. This was her intent – this was how she would help control Third Impact. She would be the key by which the process was controlled, and inside the Evangelion, she could remain separate and apart from KADMON."

"But why?"

"She and Unit-01 would be an eternal monument to man's existence. Like the pyramids or acropolis, or a gravestone." Gendo sighed deeply, a resigned wretchedness in his voice. "She always saw man as a temporary thing. On the geological timeline, we've only been around for about five minutes. We are a bright flash of light in the dark, and she believed we would pass from the cosmos. All our history, all of our monuments and creations, everything would be reduced to nothing, eventually erased from existence when our sun dies. She saw Unit-01 as a way to ensure something of man would exist forever. So the contact experiment she designed and executed took her in her entirety. Kyoko wasn't in on the plan, though. She thought something had gone wrong. The original goal – as she knew it – was that we were trying to create a new consciousness based on one of our own, much like the GLaDOS systems. She thought she had fixed it, that she had found and corrected the error."

"And she was wrong," Misato said, her eyes wet with tears, a glistening sheen of moisture laid over them, threatening to break free and pour down her face. "What happened?"

"Her soul was broken, and half was taken into the core of Unit-02. She did not go insane as everyone else thought. She just was literally not all there. A broken mind and soul were left behind in her body, and she lingered in this world that way, not even a ghost of who she was until she killed herself.

SEELE took the systems we had created and finished the work we started. They did not want it to be too obvious they were responsible for the madness and deaths that would follow the new medical checkups, after all. Instead, the women selected for 'recruitment' would linger and waste away, dying by inches, their souls sealed away in those damnable cores."

"Leaving their children available as pilots if the need ever arose."

"Indeed. And no one was ever the wiser for it; no one suspected a thing. It was just another tragedy of this poor, broken world. The UN had already warned the people about plagues and new illnesses. After all, wasn't that the point of the new medical checkups, the new medicines being distributed? Some were just luckier than others."

"So all of the pilot's mothers are in the Evangelions?" Misato said, trying to change the subject before she threw up. She could already taste the bile in the back of her throat. "Was Rei's mother a team member in the original development crew?"

"No, Rei's mother is down in the Chamber of Guf," Gendo replied, picking up a phone and sending a text message. "I am sending for some refreshments, Sub-Commander. You look like you could use a drink."

"The Chamber of Guf?" Misato asked, ignoring his comment. "But… Her mother is Lilith?"

"Yes. Rei, you see, is not a normal human. She is… special. She is another part of the equation, another piece of the puzzle in the solution of how to control Third Impact. She is a Human/Angel clone, a hybrid made to help bridge the gap between us and our mother, Lilith."

"She's a… a… she's a clone?"

"Yes. Below us is a floor reachable only through a sealed and restricted elevator. On this floor is a collection of rooms, and these rooms house the laboratory where Kozo Fuyutuski and I created her, the imaging machine by which we can make copies and back up her mind and soul, the aquarium that holds her spare clones, and the rooms in which she lived the first years of her life."

Misato found herself capable of only making a few strangled sounds, unable to form coherent words. She wasn't sure what to think or feel at the moment or how to take the Commander's matter-of-fact tone or the content of his message. Part of her mind screamed at her that none of this could be true, and another part screamed at her to kill the madman who sat in front of her.

"It took us some time, and we had many setbacks, but we eventually succeeded. There was nothing we could do about her pigmentation issues, but we were happy with having an otherwise healthy young girl. I suppose it is expected, as she is half Angel." He watched the younger woman squirm in her seat, her face as white as a sheet. "It's making sense now, isn't it?" He asked, his voice soft, almost an amused whisper. "Her background and past, a mystery sealed in secrecy. Her unusual health issues keeping her from interacting with the general populace until a few years ago. Her being my ward when I sent my son away. I created her, Sub-Commander, just as surely as I created NERV. I created her, and I raised her. Her entire existence has been guided by me."

"But…" Misato trailed off as soon as she spoke, aghast at the entirety of the man's statement.

"You are thinking of her social ineptness, of how sheltered she is. Think of her as a captive bird, Sub-Commander. I have clipped her wings so she might not fly away. I have molded her mind and temperament as much as her body. My signature is written in her thoughts, and my fingerprints are on her organs."

"You're a monster! You're sick!" Misato screamed at him, her eyes wild, spittle flying from her mouth as she convulsed suddenly, vomiting on the floor before his desk. She heaved again, emptying the contents of her stomach.

"It's all necessary, Sub-Commander," Gendo replied, seemingly unperturbed by her reaction. "It needed to be done if I was to succeed and stop SEELE. But to answer your original question, it is Rei who sits in Unit-00. The first Rei, if you will. Unit-00 was only supposed to be a test bed for armor and control systems and never intended to have a pilot. Rei's part in Impact is outside an Evangelion, not in one. However, the Senior Doctor Akagi changed things."

Gendo looked up as the door unlocked and opened to admit Kozo, who was pushing a cart laden with food and drink. "Ah, Kozo. I was just telling Sub-Commander Katsuragi about Rei."

"All of it?" the older man asked hesitantly, his tired eyes moving between the woman and the man, resting briefly on the pool of vomit in front of the man's desk. "Is that wise?"

"She asked for the truth, Kozo. She's done some snooping and wants to know what is going on."

"And you're telling her," Kozo said with a sigh. "Did you warn her that she might not want the burdens that knowing the truth will bring?"

"She was rather adamant about it. She insisted on the truth, and I'm obliging her. I was just about to tell her how Rei ended up in Unit-00." He turned his attention back to the distressed woman. "Naoko, for whatever reason, killed Rei. She didn't know the girl was a clone; she thought she was a prospective pilot, much as Asuka was over in Germany. She strangled Rei and then stuffed her into the Evangelion and conducted a contact experiment. We're not sure why she killed Rei, but she tried to run a salvage experiment on her. You see, it's theoretically possible for us to take out what was once put in the Evangelions. To bring back those souls and for them to form new, whole bodies from LCL.

It's never been successful, though. After the failed attempt at salvaging Rei, she threw herself off the observation deck in Central Dogma."

Gendo shook his head as Kozo handed Misato a glass of water. "We decanted a new clone and brought in Ritsuko."

"She knows?" Misato asked, spilling ice water over herself but ignoring it in her outrage. "SHE KNOWS?"

"Yes. I wasn't about to have a repeat of whatever had just gone down. She would have to step into her mother's shoes and help Kozo and me spearhead the development of the Evangelions. We knew we had some time left, but it was a race against the calendar. So yes, she knows everything I do, as soon will you." He paused, frowning slightly. "Don't blame her for this. Her deception was a matter of life and death. As you will find out shortly, it will not matter if you take this story to anyone. Enough inertia has built up to the point where we cannot be stopped. You know the value and weight of secrets and know what we are fighting against."

Kozo sighed, carefully lowering himself into a chair. "It is monstrous, yes, what we must do to save this world. But we must. To stand by and let it happen without objection or resistance is even more monstrous."

"This is not a perfect world, Sub-Commander. I know this more than most. You know this more than most. But it is our world; for now, it is the only one we have. Any place can be Heaven if we're willing to work for it. My wife used to think that, or at least she used to say that she did. She said it a lot after our son was born, and I thought I would be able to use him to enlist her help." Gendo looked sorrowful, suddenly looking much older than he was. "Instead, she chose to use him in the murder of the world."

Vier, Drei, Zwei, Eins!

Husband and wife watched the technicians working on the final preparations for the contact experiment, busy completing the last checks on the grotesque puppet of meat and metal. The grinning skull was covered with as many cables and wires as it was muscle, the bare sections awaiting metal armor implants that would be attached after the experiment.

"It's not too late to back out, Yui," Gendo said, watching his wife's reflection in the glass. "We can change the plan."

"Oh honey," Yui said softly, "it's far too late. Besides, what you want to do is dangerous. Promise me you won't try anything rash after I'm gone." She rubbed his arm, already wearing the prototype neural interface suit, all hard rubber and silicone. Boxy metal sections housed circuitry and amplifiers sat at regular intervals across her body, making her outline look less like an attractive woman and more like a robot. "Our time here was short, and it's quickly running out. This is all for the best, trust me. You're still new to the whole idea. We all had the same thoughts when we were first brought in."

"At least leave our son out of it." Gendo pleaded, turning to Yui and taking her hands in his, caressing her fingers through the black silicone. "He doesn't need to see this. No one should have to watch their mother die, especially like this."

"It will be good for him, dear. It seems harsh, but it will make everything easier in the long run. We are building eternity."

Gendo opened his mouth to argue but stopped himself as the elevator opened, and their son came running out, leaving Doctor Akagi in his wake. The boy was grinning and plowed into his mother, hugging her. Naoko had a slight grin, obviously having enjoyed playing babysitter to the boy.

"Are you ready to watch history in the making, Shinji?" Yui asked her son, smiling benevolently down at him. "Are you ready to see the future?"

The exuberant boy grinned and nodded, giggling at the texture of the suit his mother wore. Gendo forced himself to smile, although a ball of ice was slowly growing in the pit of his stomach.

"Well, go ahead and watch the window, watch the Evangelion." She carefully extracted herself from the boy, who rushed to the window, eagerly watching the nightmarish construction below. Yui leaned in and kissed her husband for the last time, her dark eyes locking onto his. "Don't try anything rash," she whispered. "It'll all work out in the end."

Swallowing, Gendo could only nod, his words catching in his throat. He kept his eyes on her until the elevator doors closed, only then turning to join Naoko and his son at the window, his face a frozen mask.

Shinji waved back to the helmeted form of his mother as she walked towards the waiting plug. She mimed, blowing them a kiss before she slid into the entryway, the gaping hole that reminded Gendo of an open tomb. The metal plate swung into place, and the entry plug spiraled down, locking clamps engaging with a muffled thud, still audible through the armored glass.

It was all over in five minutes, his wife gone into the gleaming red orb, leaving behind a husband and a son, having forsaken them to the hideous machinations of SEELE in the pursuit of eternal KADMON.

Later that night, long after Shinji had finally gone to sleep, exhausted with grief, Gendo sat in the darkness of his son's room, head in his hands, planning.

It would not be until the early hours of the following day that he would leave his son's side, and it killed him to do so, but there was work to be done.

Eins, Zwei, Drei, Vier!

Misato stared at her Commander, her lower lip trembling slightly. "So she sits in the core of Unit-01? She's what causes the berserker behavior of the Evangelion? She's keeping him safe during battle?"

"No," Gendo answered. "Her orb is not the core that sits in Unit-01. I do not; I cannot trust her. My plans run counter to hers, and while rash, I am winning. This would not be possible with her in control of Unit-01. She could simply not synchronize with Shinji; she could ignore the commands given by him or us. She remains loyal to her father and SEELE. She is a wildcard I could not allow to remain in play.

But it should be apparent to you that someone else provides the soul of Unit-01, Sub-Commander. Think now, and see if you can puzzle this out. Why would Yui care about Rei when she was taken by Gaghiel into the bay? Why would she expend such effort to see her safe again when she abandoned her husband and son? No, it is not Yui who is responsible for my son's vicious and bloodthirsty behavior on the battlefield. It is not Yui who is responsible for his victories or triumphs."

"Who is it?" Misato asked, eyes flicking back and forth between Gendo and Fuyutuski. "Who is the soul of Unit-01?"

"My sins are great and varied, Sub-Commander. They are both large in nature and number, and I have sinned against the natural order and against man. I plan on becoming a god, Sub-Commander, and I have created new life. I have created plans that pit man against man and have placed my son and his friends into a war against supernatural beings of unknowable powers and thoughts. There is much more to this tale you have yet to hear, and while it may sicken you, the truth of who it is that sits in Unit-01 is my worst sin. Even worse than what I have done to my daughter, for all the social and mental conditioning, for all of the carefully calculated abuses that have left her completely, dogmatically loyal to me."

He paused as he watched her, his face a stony mask, not betraying anything he felt, his voice smooth and emotionless.

"You know that Yui went completely into the core. You know that Kyoko went only partially and left behind an insane husk, a broken shell of what she once was. You know that SEELE took our work and continued it, making it so the women selected for recruitment would waste away and die after a few years, leaving no trace of their work.

I took all of it and perfected it. You may recall an earlier conversation where I said that I had made the children into titans and colossi. This is truer of Rei than Asuka, as a small fragment of my daughter sits in Unit-00. It is entirely true of Shinji."

Gendo leaned forward over his desk, his eyes like dark pits threatening to swallow Misato. "I split Shinji's soul in half, cleanly and evenly cut in two. All of his tameness, all the psychological issues, these are not the result of abandonment and abuse. He is this way because half of his soul has resided in Unit-01 since before he was eight. This is the secret to his unnatural abilities with the Evangelion, Misato. He can do these things because he is not just 'becoming' the Evangelion. He already is the Evangelion. He is Unit-01. Unit-01 is him. When he synchronizes with Unit-01, he becomes complete. His soul is rejoined, and the berserkergang that comes upon him is the exultation of his soul. The power he wields in that barely conscious state is the power lying within the unconquerable spirit of every man, woman, and child. I have given him the means to harness and use that power. In your earliest reports on him, you noted you were unsure if we could retain his voluntary services as a pilot, but I tell you he will never choose not to pilot the Evangelion. He desires completeness; he wishes to be whole. The only thing we ever worried about was getting him into the Entry Plug the first time."

Gendo leaned back in his chair, watching the woman try to absorb the information. Kozo reached over to gently pat her on the back, but she jerked away from him.

"That was why you brought out Rei that day! To goad him into the Entry Plug, to reel him in." She stared at Gendo before turning to glare at Kozo. "You helped, didn't you?" She asked, her tone accusatory and sharp. "You helped him create Rei. You had to have helped him with this."

"I helped him," Kozo confirmed. "I only had a small part in splitting Shinji's soul, but I did play a larger part in creating Rei."

"And Rei!" Misato said, whirling back to stare at Gendo. "You said she was a clone and called her your daughter. Who is she a clone of? Your wife? She looks a little like Shinji. Family resemblance?" Misato coughed slightly before swallowing. It was apparent to the two men that she was trying not to throw up again.

"No, she's not a clone of my wife," Gendo said irritatedly, as if there was something obvious she was missing. "It's not like I had a surplus of genetic material from her to do this. Rei is much younger than she appears. I didn't create her until several years after Shinji had been sent away for safekeeping and NERV was created. We didn't know we would need a Human/Angel clone to properly control Impact until then. Our current Rei is only about nine years old from a purely temporal point of view. She's a clone of Shinji, mixed with material from Lilith."

Eins, Zwei, Drei, Vier!

Ritsuko glared at Gendo as she inserted the IV into Misato's arm, eyes moving back and forth between the unflappable asshole and her friend's vein. "And you're completely positive that there wasn't an easier way to deal with this?" she asked, ignoring the other Sub-Commander as he shook his head.

"She wanted to know the truth, Ritsuko," Gendo said, neither protesting nor explaining. He was simply stating a fact. "It is past time I think she was told the truth anyway. She's already gotten most of the shocks out of the way now, and when she comes back around, it should be smooth sailing. Only some minor details about the path to Instrumentality and our plans for what lies past it remain to be told, and possibly some clarification on the larger pieces of the Scenario. You should be able to answer most of the questions she might have. There are still parts of my true plan we have not yet gotten to, but if she wants to hear about them from me rather than from you, send her back up. I'm going to go back to work, as the custodial staff should be done cleaning the office by now."

He nodded to her and left, Kozo slipping out behind him into the hall, chuckling. Ritsuko glared at them until the door slid shut, and she looked back down at her friend with a sigh. After checking the IV drip, she went to the counter and poured herself a cup of coffee. After settling into her chair, she read the latest reports concerning Asuka.

It was about five minutes before Misato stirred, coughing. She sat up straight in the chair, glaring at Ritsuko. "You!"

"Me indeed," Ritsuko answered, lowering the tablet. "How are you feeling?"

"Are all of you fucking insane?" Misato screamed. "How do you think I'm feeling?"

"I imagine you are feeling stressed and physically ill. You're taking this rather badly, I think. I took it better, and I got the whole thing all at once, on top of having just lost my mother. You've been eased into things."

Misato stared at her friend, her mouth agape in anger and horror. "I'm taking this badly?" she screeched, falling back against the chair. "Ritsuko, we're working for a megalomaniac that's cloned his son, cut his soul in half, and shoved it into a fifty thousand-ton war machine! He doesn't intend to stop Third Impact at all but is instead planning on replacing SEELE with himself!"

Ritsuko sighed as she set her computer back down and rubbed the bridge of her nose. "You passed out before he could tell you what he would do with that power."

"Of course I passed out! I just discovered I've been playing matchmaker between a boy and his gender-swapped Angel-mixed clone, on top of everything else!" As she pointed at the doctor, a look of newly realized horror dawned on her face. "That's why you were against them hooking up in the beginning! It had nothing to do with them being Evangelion pilots at all! It's because they'd be dancing the horizontal mambo to the tune of the incestuous flipper-baby band!"

"Well, not exactly," Ritsuko said with a sad half-smile. "It's not technically incest. It's more a sort of masturbation, for all that incest in and of itself is a social phenomenon. Still, it doesn't count because the genetic drift is more than enough for any potential offspring to be perfectly healthy. It's a little counter-intuitive because Rei isn't human apart from being Shinji's clone. She's more a half-sister to humanity, thanks to the genetic contribution from Lilith. Homo Sapiens Angelus, if you will. Since she's closer to the ancestral matriarch than anyone else, any coupling would result in another hybrid but would, in theory, be fertile, unlike a mule. Of course,"

"Ritsuko, please stop." Misato groaned and clapped a hand over her eyes. "If you're trying to make me feel better, it's not working."

"You knew what you were getting into when you agreed to become a Sub-Commander, Misato." The doctor said, utterly unsympathetic. "You knew he was a world-class bastard. You knew we were doing terrible things here. You knew that even before then. What sort of organization makes use of child soldiers, especially in war machines that inflict harm, both physical and mental, on their pilots?"

"The kind of organization that is fighting against the impossible, that has no other choice, that stands alone between the world and destruction," Misato grudgingly replied after a short silence. It was a sort of unofficial motto of the men and women involved in the various parts of Project E, a kind of catechism to help them sleep at night or reconcile with them the harsh truth of what they were doing.

"What does he plan to do with Instrumentality?"

"He will, theoretically, have ultimate power. He will adjust the laws of causality, release the trapped souls, end Instrumentality, and exile himself into Unit-01 along with Yui Ikari. The souls of mankind will reincarnate and be returned to the world. NERV will be in place to provide leadership and order across the planet, and Kozo will be in place to command NERV. We will be able to make new Evangelions, taking core samples from Unit-01, which will give us an army able to handle anything. Using the AT-Field, we will be able to reshape the world, protect it, help explore space, and help us colonize it. Anyone who wishes to protect mankind and see it prosper and grow will be able to synchronize with an Evangelion core grown from a sample of Unit-01's."

"A literal army of guardian angels?"

"More or less." Ritsuko smiled, but her eyes looked sorrowful. "A few details are missing here and there, but that's the general gist of the plan. It's all he's worked to achieve ever since Second Impact. He has always looked to the future to ensure that never again such a thing could happen. Third Impact cannot be stopped, Misato. It will happen, one way or another. SEELE's plans have been in place for far too long for it to be otherwise. We can only try to conduct damage control, limit how bad things will be, and ensure it can't ever happen again."

"How much does Rei know?"

Ritsuko waved dismissively. "She knows most of it. She was created for this reason, to grant control to the Commander during Impact. She has lived her entire life waiting for the day of Third Impact, waiting for the day on which she may die and be released."

Misato's face was one of horrified shock. "She knows that she's going to die, and she's gone along with it this entire time?"

"Yes, she knows. For the longest time, it was all she longed for and looked forward to. She'd often ask if this was the day on which she would die." Ritsuko shook her head. "It was the most depressing thing you could ever hear. A little girl of seven, in all reality only two years, asking you in that emotionless voice of hers every single day if this was the day she was going to be allowed to die?"

Misato swallowed, trying to imagine it and finding that she could picture it. It was a terrifying image. "You said she had done that. Did she only recently stop asking?" In her mind, there was only one reason why the girl might have ceased asking such a question.

Ritsuko shook her head again. "No, she stopped asking a few years ago, right about when she burned down the building she lived in. Whatever happened, for whatever reason that she burned it down, she stopped asking. But she was still set on it, you could tell. She had nothing else to live for. Gendo needed her to trust him unequivocally, to have her give him total and complete control of not only her soul but all the souls of mankind and the process of Instrumentality. She worships him. She has followed every singular command he gave her with her entire being. Then it came time for her to be introduced to Shinji, and the Commander told her that she should get to know him, to be close to him."

"And she did. But why? Why does she need to be close to him? What part of that plays into the Commander's plans?"

"Because she must know what it means to love another. As the key to Instrumentality, she needs to know what choosing means. If she did not know how to love, if her existence was completely empty and devoid, why would it matter to her if the Commander's plan or SEELE's came to fruition?"

"How will it happen? What's the thing that's inside the Commander's arm?" Misato leaned back in the chair, rubbing at her forehead.

"That was a nascent embryonic clone of ADAM. It is part of the equation to achieve Impact. ADAM's power will counter Lilith's, and Rei will act as the intermediary and pass control of Instrumentality to the Commander instead of a new, joint consciousness being born inside of KADMON. Unit-01 will replace Lilith as the new source of future Evangelions, and the Lance of Longinus, the only weapon that could stop us, is safely locked away."

"So what happens to the kids? What happens to Rei, to Shinji, to Asuka? Will Kyoto return? What about Rei I?"

"Rei I isn't a separate entity; she was just the first of the cloned bodies to be used as host by Rei's soul. Only a small piece of her soul was taken into Unit-00, which is why she has such low synchronization scores. Kyoko only has part of her soul in Unit-02. She'll pass from this world, I guess, unless the rest of her soul was absorbed into Unit-02 after her physical body died. We're not sure what will happen with her. Shinji, well, Shinji's part of the burnt offering." Ritsuko swallowed. "He's going to die during Instrumentality, Misato. Unit-01's the final part of the puzzle, you see. Without it, Instrumentality cannot happen. His death, and Rei's, gives mankind a future. There is no other way but..."

"But what?"

"Gendo thinks there is a very small chance they might live through it. I don't think that it'll happen, though. Rei will choose to die, to be released from her bonds here, and Shinji will follow her. He won't choose another life of loneliness and despair. He will choose death."

Misato had nothing to say. She could only stare in horrified accusation at the other woman, who, in a complete inversion of how she normally was, had twin lines of tears running down her face.

"Don't look at me like that, Misato! Don't! I've helped raise Rei! Don't you think I wanted a family, once? Don't you think that they're as close to children as I'll ever have? They practically are my children!" Ritsuko snapped her mouth shut and swallowed several times, wiping away her tears. Breathing hard through her nose, she stood up after regaining her composure. "Follow me," she said, motioning to Misato to get up. "I'll show you where we keep the spares."

Eins, Zwei, Drei, Vier!

Kaji smiled as the door slid open, the troublesome lock finally giving way to his skilled ministrations. Tucking his tools back into his bag, he hurried into the room, pushing the black satchel to the side as he took stock of the room's contents.

Kaji Ryoji was by any reasonable definition a jaded individual, not much given to shock or surprise. He had long ago burned out the last bits of his innocence or naivety, leaving behind a cynical man who liked to collect secrets. Much like a priest in the confessional, he would often remark to his friends in the industry that he had seen it all, especially now after his time at NERV.

He was entirely unprepared to see a huge aquarium tank running the entire length of the room filled with LCL and naked clones of Rei Ayanami. A shiver ran down his spine, and he moved closer, slack-jawed with shock. There appeared to be hundreds of them, and that was just counting the ones he could see in the clouded depths of the viscous liquid. Although powerful lights lit the aquarium from below, bathing the room in an amber glow, he could only see about a meter into the tank. The clones swam and floated about like fish, a disturbing emptiness in their eyes matched by empty smiles. Over the hum of machinery, a faint, inane, girlish giggling could be heard through the thick glass.

Clones they might be of the serious young woman, he thought to himself, but they could not be more different from her. She always had an icy coolness about herself, although she did have her sporadic flashes of warmth, sometimes disturbingly warm, but her eyes were not empty and devoid of thought. Neither did she smile so, for her expressions were faint and as carefully measured out as rice during a famine. She was a girl of subtle emotion, and he doubted she even knew how to giggle.

Stepping up to the glass, he reached and placed his hand against the transparent barrier. The clone closest to him smiled dumbly and mimicked the movement; her delicate alabaster hand stained a pale orange inside the tank. Others swam closer, acting like a school of fish but lacking any trace of curiosity on their faces. The identical swarm retained their slack-jawed smiles, acting more like a mirror to him than any sort of actual person.

What was this all about? What was Rei? This raised so many new questions that Kaji wasn't sure he would have time to answer.

He was so engrossed in puzzling out the riddle presented by the tank of cloned girls that he almost didn't hear the door unlock and open behind him. He turned around slowly, casually, and leaned against the glass with a grin that slid off his face as he saw who had entered the room.

"You... you're not supposed to be here. You're locked up in solitary!" he exclaimed, staring at Rei, who had paused just inside the door. She stared at him silently for a heartbeat before moving again, walking off to one of the counters and putting down the box of parts she had been carrying.

"You are not supposed to be in here," she said, throwing the spy's words back at him. "This is my laboratory. I am allowed to be in here if I wish."

"But you're locked up! I just saw you before I came down here!" Kaji protested, watching the girl as she emptied the pockets of her lab coat, setting the juice box and half-eaten sandwich on the counter next to the box.

"I am locked up inside a cell. I am also standing in front of you, inside this room where you are not supposed to be. I am in almost all of the places that I should be. You are out of place." She watched him, her face betraying nothing, as unreadable as the face of an Evangelion. "Why are you here?"

"Well, I'm on an errand for the Commander. You see,-"

"That is a lie, Agent Kaji." She interrupted him. "The Commander would not send you in here. This room is not used in any part of his Scenario. If you had business with the clones, you would be in the room on the other side of the tank."

Smiling weakly, he waved at the tank behind him. "Okay. Okay, so I'm here on my own. Nobody knows about this room other than you and me. I came in here to find out what you were doing in a room that's secured against a top-level security access code."

Now it was Rei's turn to look shocked, and while the look was fleeting, Kaji saw it. She had not expected to hear she had been under observation, that much was clear. The only question was what he could do with this information and how to keep her off balance.

"You should not have come here," she said. "The Commander had warned you about going to places you should not go. You should have listened to him."

"You're not going to tell Ikari I was here." Kaji scoffed. "Then you would have to explain what you're doing out of confinement and what you're doing in this room."

"You are correct, Agent Kaji. I am not going to tell Commander Ikari you were in here. I cannot, however, allow you to continue to work against his Scenario, and I cannot let you work against mine."

Kaji grinned at the girl. "You surely don't think you can do anything to stop me, do you?" he asked as he leveled his pistol at her. "I think I'm going to leave and do some more investigating. Threats don't work against me, Rei."

She did not answer but picked up a strange-looking device that was vaguely gun-shaped from the counter. "Your nine millimeter has a maximum of sixteen shots before you must reload. My infrared laser cutting torch is effectively limitless in ammunition against a soft-skinned target."

"Rei, don't think for a second that I won't kill you," he warned her, eying the device in her hand. "You don't live very long in this job if you get hung up on dealing with threats to your life."

She did not answer but brought the torch up and aimed at his chest. "You will sit down and allow yourself to be restrained until I can determine the best course of action. I will not tell you this again, as past data suggests you habitually ignore warnings."

"Last chance, Rei. Drop it."

Her finger closed around the trigger when the pistol barked as Kaji shot first. The round took her through the throat, and she collapsed against the counter, bouncing off of it, emitting a horrible gurgling sound as she drowned in her own blood as she tried to breathe through a ruined windpipe.

Kaji shook his head sadly as he walked up to her shuddering form, picking up the torch and putting it on the counter as he squatted down next to her.

"I told you, you stupid little girl." He sighed as she stared wordlessly up at him, pink froth bubbling out of the wound above her sternal notch, where her neck met her shoulders. "Whatever you are, you're not bulletproof." He frowned as a grin spread across her face, her eyes empty. "Now that's just creepy," he muttered to himself as the girl started to giggle through her drowning gasps.

"I am not creepy, Agent Kaji."

Kaji whirled around, the pistol coming up as he drew a bead on the source of the statement, his eyes going wide with shock as Rei stood behind him, naked and dripping. His eyes darted back to the dying girl next to him and then back up to the one that was very much alive. Fear spread across his face as he saw the tank behind her, seeing a hatch that he hadn't noticed before standing open. "What-"

"I am not bound to a single body, Agent Kaji," she stated, cutting off his question before he had finished asking it. "Nor am I bound to a single body at a time."

Behind her, two blank-faced clones climbed out of the tank and stepped towards them, with more following behind. Kaji's finger curled around the trigger as he shot the speaking clone in the head, which crumpled to the floor amidst a spray of blood and brain matter. One of the other clones stood up straighter and stopped advancing. He turned and shot her as she opened her mouth to speak, dropping her, and then he hit the one next to her as he stood and ran to the door.

The door was locked and refused to open. He spun around, eyes wild with fear. His pistol spoke twelve more times, and twelve more bodies hit the floor, twitching as they died, but there were far more than twelve clones at Rei's disposal.

Agent Kaji, she noted, took much less subduing than her brother.

Eins, Zwei, Drei, Vier!

"How many are there?" Misato asked, her voice low and dead as if she could not be shocked anymore. "What are they doing?"

"Right now? They're just swimming around. They're kind of like fish. Mindless, soulless fish that look like Rei. If you walk up to the tank, they'll swim over to you and mimic your actions. They are receptacles for souls and mirror your own if you're near enough to them. We have a few thousand of them."

"A few thousand? What was he planning on doing with Rei that he would need so many?"

"At first? I don't know." Ritsuko said with an indifferent shrug. "You know that he likes to be prepared for anything. You've seen the fail-safes, the emergency protocols, all of the drills. Half of what he does is think of how the Scenario could be threatened and devise countermeasures. However, the plethora of available clones offers us some other options besides Rei's replacement should she die in battle or accident. These things are the core of the new autopilot that we've been working on."

"I thought that one of the issues with using the Evangelions was the temperamental synchronization process, which makes more sense when you know how it works, by the way," Misato commented with a dark look at her friend. "How did you get an autopilot device to work?"

"I told you they mimic souls, didn't I?" Ritsuko replied, somewhat irritated her friend hadn't put it together. "We load a scan of the pilot's mental patterns and run it against the dummy plug insert," she explained with a wave at the tank, where two clones waved back, "and the clone mimics the pilot's soul and then synchronizes with the Evangelion. We're still working on some issues, and it's still in beta mode for all intents and purposes, but it's a stopgap measure as it stands."

"How close do you think you are to completing it? We might not even need the pilots at all, except for brain scans." Misato paused before continuing, thinking for a moment. "Wait, how well does the autopilot reason? What would its fighting capabilities be?"

"It has no reasoning capabilities. With the autopilot engaged, we have to control the Evangelion from Central Dogma. It's less an autopilot than a subsystem that lets the Evangelion be run remotely like a UAV drone."

"Well, that's better than nothing, I suppose." Misato made a disgusted face. "So we still need the pilots."

"We still need them," Ritsuko confirmed. "C'mon, let's go. I don't like spending more time down here than I need to. They kind of creep me out."

"They creep you out? What about those of us who aren't mad scientists? Wait... You said you practically raised Rei and considered the kids your kids. What gives?"

Ritsuko felt an eye twitch. She sighed dejectedly. "What did the Commander say about us?"

"About us? What do you mean?" Misato stared at Ritsuko, uncertainty sliding into understanding and then something less than horror and more than revulsion. "Rits, ewww! He's so old! He's what, fifteen, eighteen years older than you?"

"I wanted a family, Misato! I wanted a family and had no time for anything else but work! He was here, and he's brilliant, and he's driven, and he's not bad looking." Ritsuko said, her eyes glistening with moisture.

"He's also planning on reuniting with his wife."

"I know!" Ritsuko snapped, her tone bitter as the first tears began to run out of the corners of her eyes. "He's going to leave, and my ersatz children will be dead, and all I'll have is the knowledge that I helped save the world."

"You have a weird way of playing house," Misato said as she hugged her friend, trying to cheer her up. "A husband who's married to the interred soul of a war machine, a son with half a soul in a war machine, and a daughter who's a hybrid clone of your son. Not to mention that the boy lives with me, and the girl lives with a friend from school."

Ritsuko sniggered into Misato's shoulder. "You're terrible at comforting people, you know that?" She sniffed. "It's not fair. Growing up, I never thought it would end up this way. Even in college, with you and Kaji-"

"I thought we had agreed to never talk about that," Misato said flatly, but she grinned at the doctor. "But yeah, I understand. You're all still crazy, but I suppose I understand."

Ritsuko pulled away, rubbing her face. "Let's go. There's still some more to tell you, mostly about what we know that SEELE is doing. They know that we plan betrayal, so they've taken some measures of their own."

"Great." Misato groaned. "More plots? Where do they end? Do the plots and counter-plots ever end around this place?"

"No."

"How much of this is true, and how much of it is just another set of lies? Is there another deeper plot within a plot, another secret conspiracy hidden out of sight?"

Ritsuko laughed, a short, somewhat bitter titter of amusement. "There's to be no more secrets between us. If anything else remains hidden, it's not anything I know. If there is a deeper plot, then Gendo's playing it by himself."

"But, it's so horribly, complicatedly simple! How could any of it be true?"

"How else do you explain it, Misato? How else could you explain it? I'm glad I don't have to lie to you anymore."

"And what about Maya? Asuka? What about all the other technicians?"

"Why do you think I take so much of the work with the Evangelions and Pilots on myself, handing out only the simplest tasks to the others? It would be insane in a normal organization. It would be insane if what you are learning now wasn't the truth."

Both women waited in the elevator in silence. When the doors opened and Ritsuko stepped out, Misato stayed where she was, prompting the doctor to look back.

"Misato?"

"Are we friends, Ritsuko? I mean, really, are we friends?" Misato asked, looking at the woman she had known since college. "Are you telling me everything, or is it just another lie?"

Stepping back into the elevator, Ritsuko carefully wrapped her arms around the Sub-Commander, drawing her into a hug. "It's the truth. No more secrets, no more lies. Just the plain, stark, terrifying truth."

"Okay."