Under New Management

by 049 Faithless Observer

Teamwork is important, whats the worst that could happen? . . . Oh.

3. A time to die, a time to live

Chapter 2: Time to Die . . . Time to Live

"Poor thing, she's back in there again?" One of the nurses asked.
"Yes, they say that damn thing she has to pilot went berserk again."
"Unbelievable, what they do to these children."
"And that's not all. The mental stress they're under."
"That doesn't surprise me, I tried to talk to her once, she just starred at me with those eyes, didn't say a word."
"Maybe things will be better with the new Commander."
"Perhaps, I wonder who he will be, have they announced it yet."
"No, but the sub commander is a shoe in, strong and dependable, he's my kind of man!"
"He's also three times your age."
The nurses laughed at their colleagues expense before getting back to work.
Why am I here? Rei wondered in the space between sleep and reality.
I want to be here. She decided.
But why? Why do I wish to be here? Memory came back slowly, not flooding, not because the memories didn't return quickly, but because there were so painfully few.
I have been given a reason to live . . . a reason . . . beyond my duty?
Is that . . . why I have destroyed my core . . . so that I may live as a human?
Rei's eyes opened slowly as she took in a deep breath, she felt weak, and very tired, and there was a burning sensation where her core had been. The burning had gone down from what it had been however. She struggled to sit up and looked at the clock frowning, she had never required more than four hours of sleep before, now it didn't seem like enough. Perhaps this was the price of what she had done to herself.
She slid her feet out from under the blanket and carefully placed them on the floor, she felt like she was walking on pins and needles as the blood rushed back. Using the bed, and then the wall for balance she staggered towards the restroom to relieve herself.
It stung a bit to urinate due to dehydration, Doctor Akagi said she would need to drink lots of water as her S2 core had been more akin to a very dense concentration of minerals rather then organic cells, all of that spare matter slowly entering her blood stream was going to reduce the amount of available water in her body if she wasn't careful.
I must stay well now, so Ikari and I can find what I am missing. She thought firmly, it was the first time, somebody had promised to help her, not to complete a task, but to find happiness to make her whole. It caused a strange sensation to run through her when she thought about it, not bad, just . . . different.
She staggered back towards the bed, but before she had made it even halfway there she slipped and hit the floor hard, pain lanced through her side and she mentally berated herself for letting the pain affect her so badly. Struggling to stand she felt two strong hands come down on her shoulders and looked up in surprise at the Sub Commander's smiling face.
Fuyutsuki had been watching Rei's progress from the door way, not commenting. Rei was a determined character, Kozou felt he would be doing her more harm then good trying to help before she needed it. Using the Sub Commander as a crutch Rei was able to shuffle back to the bed and lay back down, her small reserve of energy spent.
"Do you want some water Rei?" Fuyutsuki asked.
She nodded slightly without saying a word. Fuyutsuki went into the restroom and got a paper cup, filling it from the tap he helped Rei sit up in bed and waited for her to finish before speaking again. "Gendo's will appointed me as your guardian Rei, you will be living with me for now on."
Rei observed the Sub Commander from the corner of her eye. "Why?" She asked. "My apartment is sufficient."
"Because Rei, you need to be someplace more suitable to actually living. If you get sick then what would I do? You are my responsibility now and seeing you hurt would make me feel terrible." The Old Professor reasoned.
"I have never had a problem with my health before sir, I will be fine." Rei protested in her normal quiet manner.
"You don't have your S2 core to fall back on anymore Rei you can get ill just like everyone else now."
The girl was quiet as she considered this, "Very well Sir." She blinked a few times as her eyes became heavy once more. Was being human, or reasonably close to such, really this limited?
Fuyutsuki watched her lie back down, even as she struggled to keep her eyes open. He placed a hand softly on her head. "Rest now Rei, your body is drained from this ordeal and will need to recover."
Rei didn't say anything as she drifted off into a dreamless sleep.

HHHHHHHHHHHHHHHHHH

"Ok, well, good evening everyone." Shinji said hesitantly as he took the seat at the head of the conference room table. Unlike Gendo, Shinji didn't see any reason to try and intimidate his own staff, that was going to take some getting used to, and so found a blandly furnished meeting room far more preferable to his father's now abandoned office.
"I've called this meeting in order to allow us all to share information and ideas. I'll be relying on each of you." Shinji's eyes locked with each person at the table in a very un-Shinji like way. "So I ask for your trust and best efforts." Sitting down each side of the briefing room table were Maya, Ritsuko, Hyuga, Aoba, Fuyutsuki, and Misato. The people he knew would be most involved in the operations of NERV. "I will now open this meeting, Dr. Akagi, would you please give your report on damages incurred upon the GeoFront during . . . Unit-00's actions yesterday afternoon."
Ritsuko stood up nodding as she scanned over the notes on her clipboard. "The GeoFront did sustain moderate damage, primarily the destruction of the armored defense door in place to lock down Terminal Dogma, and damage to the cage where Unit-00 was being repaired. Unit-00 has received no further damage . . . in fact . . ." Ritsuko hesitated.
"Yes?" Shinji asked.
"It appears that repairs to most of the biological components was greatly accelerated, this, was likely due to the presence of an S2 core."
"Too bad our EVA's don't have something like that in them all the time." Misato commented.
Hyuga nodded, "That's the truth."
Shinji thought it over and accepted the answer. "I guess that makes sense, please . . . continue."
"We believe we can move Unit-00's repair schedule up and have repairs completed by the end of next month but we will need to undergo a synchronization test to see how Rei's, physical changes, might have affected her ability to synch with EVA. Otherwise most of the damage done was minor, repairs can be completed in two weeks at most. More troubling are the back doors which set Casper against us but we have severed its external connections and are now doing a line by line check of the OS, we won't leave anything that we don't know about. All in all the damages incurred are well within what has been allowed for in our budget."
"That budget was accounting for Angel attacks." Fuyutsuki said nonchalantly.
"And this wasn't?" Ritsuko asked.
"Uh, good thank you for the report Ritsuko." Shinji interrupted. "Sub Commander Fuyutsuki will now brief us on the current status of Section Two." There was an awkward silence at that, what was wrong with Section Two?
Fuyutsuki soon explained. "To put it simply, we're firing the entire NERV security staff."
"WHAT!" Everyone save Shinji and Fuyutsuki looked shocked.
"Well yeah." Shinji said, "Think about it. They managed to lose track of me a fourteen year old, for three entire days. How can we expect these clowns to protect us from security risks." The room became silent as the entire command staff had to admit, that yes, losing track of a single kid in a town they all but owned, was pretty sad.
"Misato, that is why you will be put in charge of hiring replacement officers." Shinji said.
"Huh, why me?" Misato asked, dreading the increase in paperwork this would bring. Maybe I should ask for a pay raise. Come to think of it that wasn't such a bad idea, with Shinji as her boss she had a pretty good chance of getting the request passed.
"Because I looked up your files and when it comes to people outside of Section Two you are the only one with any actual military experience, I defer to you on this matter."
"Y-yes sir." Misato said awkwardly.
"We will need to select Agents based on past performance, the MAGI have already compiled a list of three thousand viable candidates, including ex-SWAT and SSDF personnel, we would prefer people with combat experience but anyone with other useful skills should also be considered I want to see the top two hundred on my desk by next week." Fuyutsuki finished.
"Wow, Commander Ikari is really rocking the boat isn't he." Maya whispered to Aoba.
"Yeah, just hope we don't lose our jobs."
Shinji coughed into his hand, "I'm sitting right here, I can hear you . . . You know that right?"
"Ugh, YES SIR!" The two bridge bunnies stiffened in their seats.
"I suppose with that out of the way, now would be the best time to inform you all of the situation we currently face. Doctor Akagi, please brief the Major and bridge crew . . ." Shinji's tone darkened. " . . . Don't leave anything out."
Ritsuko looked at him, and nodded solemnly, withdrawing a small handheld terminal from her pocket and dimming the lights. A projector activated on the back wall, painting an image of Terminal Dogma onto the conference room's screen. "I hope none of you have had anything to eat recently, this already upsets my stomach when I think about it too much . . ." With that said Ritsuko began.

They had all entered the briefing room with a vague idea of what they would see and hear about. But it did not prepare them for what they learned now.
She told them about Lilith, and they were shocked, having assumed that the crucified being deep within the GeoFront was Adam. She told them about what resided within an EVA's core, and they became violently ill knowing that human being's had not just died, but been imprisoned within these monsters. And then . . . she told them about Rei . . . and they were outraged at the sick mind that would twist a little girl into what the Commander had made of her.
Yet though it all, they did not blame Ritsuko, they did not blame Fuyutsuki, and they most certainly didn't blame Shinji. They blamed SEELE, and they blamed Gendo. Shinji had starred at the table top for the entire briefing, keeping his jaw clenched tight. He took in a shuddering breath as the lights came back on. "Doctor Akagi."
"Yes?" Ritsuko asked.
"Rei's . . . Rei's clones, the EVA graveyard, I want to see them, I want to see it all with my own eyes."
"Shinji, are you sure . . ." Fuyutsuki began gently.
"Yes." The voice was shaky but also filled with something, a strength that demanded Shinji do what he had never before thought he had the strength for.
"Sir . . ."
Shinji glanced up to see Hyuga and the other two bridge officers standing. "We want to see it too, we want to see it ourselves so we can know the truth." The other two bridge technicians nodded in agreement. There was no distrust in Hyuga's eyes, he trusted Shinji completely after the boy had revealed all of this, there was just the determination to see the truth for one's self. To have absolute evidence for one's self that one is not being lied to once more.
"You can if you think your up to it. I know it makes me feel sick just thinking about it. But . . . Rei is still the same Rei all of us have always known, so please don't think of her any differently." I just hope I can do that. Shinji was interested in more than just seeing the truth for himself, he wanted to be certain that he wouldn't think differently of Rei after starring her, 'Sisters' in the face. If he couldn't do that, he wasn't worthy of her friendship. "You are all dismissed, go home and get some rest people."
Misato looked at him worried as the rest of the bridge crew shuffled past. You don't have to take the weight alone Shinji . . . I guess I'll help Rei too, for your sake. "Come on Major."
"Hmmm, wha?" Misato turned as Hyuga grabbed her wrist and started to drag her from the room. "We have some work to do picking out the new Security Staff, we'll probably be pulling a couple consecutive all nighters getting it done."
Misato groaned as the Makoto dragged her off towards a mountain of paper work that she would need climbing equipment and an oxygen tank for if she ever wanted to see the topmost sheets.
Shinji stopped Ritsuko on her way out. "The Jet Alone trials are still scheduled for next week right?" A pilotless robot capable of fighting Angels sounded great on paper but Shinji had a bad feeling after looking over the information Ritsuko had shown him. For the time being she was going to overlook where she had gotten JetAlone's blue prints. Having piloted EVA against the Angels Shinji was sure JetAlone wasn't up to snuff as a weapon to use against them.
Ritsuko nodded, "Yes, do you want me to carry through with the original plan?"
Shinji paused and thought for a long moment, it would be nice to finish this up nice and neat, no lives would be lost either, that was always a plug. But . . . "Me and Fuyutsuki have been talking, we might have a better idea." He said after a moment and began to explain. When Ritsuko left the briefing room fifteen minutes later she was convinced Shinji's devious bastard genes were showing up now that they were in an environment to flourish. Who would have thought Shinji would come up with something like this, ah a man after my own heart. She thought humorously as she headed towards the elevators. Unit-01 would need to be prepared and the Sub Commander would have quite a few arrangements to make. Acting as Shinji's representative to the UN was going to be taking up much more of his time then the mere city council meetings he had been relegated to before. Which meant Ritsuko would be getting even more administrative work to do. No rest for the wicked and we're the wickedest of the bunch.

HHHHHHHHHHHHHHHHHHHHHHH

Rei looked up from the book the Sub Commander had given her to pass the time as a light knocking came from the hospital door, Shinji was smiling nervously as he held something behind his back. "Good afternoon, Sir."
"Please don't call me that, Ayanami."
"What would you want me to address you as?"
"Ikari is fine, or Shinji, i-if you want." He stuttered quickly.
"Very well, Ikari, why are you here?"
Shinji shifted uncomfortably, "I, uhm, came to . . . give you these . . . yeah." He held out the small bouquet looking suitably embarrassed for a boy his age.
Rei put her book in her lap and quietly took the flowers, head coking to the side curiously. "What are they?" She asked.
"Flowers . . . I just wanted to show . . . I wanted you to get well soon . . ."
"Flowers will not help one heal faster Ikari." Rei stated simply, and then starred at Shinji as he began to laugh, the laughter cut off when he realized she wasn't joking.
"Well . . . Yeah, that might be true, but they do show that people care enough to want you to be well soon."
"I . . . see . . ." Rei said hesitantly, "Your concern for my well being is . . . appreciated Ikari." She averted her eyes. "Thank you."
They fell into a comfortable silence. "Ayanami?" Shinji asked.
"Yes?"
"You won't try to do something like that again will you?" He said worried.
"Are you afraid I am untrustworthy?" Rei asked, she would not be surprised if he did, in retrospect, her actions seemed . . . stupid.
"N-no. I trust you Rei, I just worry for you as well."
"Again, I thank you Ikari." Rei said, blushing slightly, Rei's head bowed down as she starred at her lap. "But I am not worthy of such treatment . . ."
"Yes you are!" Shinji said, grabbing her hand and squeezing it tight. His eyes widened as he realized what he was doing and pulled the offending hand back, cramming it down into his pocket.
Rei hesitated before speaking, as touching as those words were she couldn't betray Shinji anymore then she could have betrayed his father. "You know about . . . the others correct?"
"Yeah . . . Ritsuko told me . . ." His voice suddenly filled with anger. "So what! you have a giant fish tank full of spare bodies, so what! If you died and they replaced you with one of them . . ." The words caught for a second but he pushed on. "I-if they replaced you, it wouldn't matter if the girl they gave us back had all of your memories, mannerisms, even your DNA, she wouldn't be you . . . And . . . I would miss you." He finished lamely.
For a brief moment Rei felt very close to finding the piece of herself that she felt was missing. Her lips twitched slightly. "I thank you once more Ikari."
Both of them were facing severe cases of elevated body temperature by now. "So . . . how long until you get out?" He asked, noting that Rei was not likely to be the one to break their uncomfortable silence. If anything she seemed to clam up even more when she was embarrassed.
"Three days, I am being kept for observation and bed rest." Rei said before pausing slightly. "I have had . . . time to think about what you told me."
"What did I tell you exactly?" Shinji asked a little confused.
"Your father, I have taken a great deal of time to consider it, and I must come to the conclusion that I did love him. And that I still do, he was my provider for the last eight years."
"Oh." Shinji felt his heart sink, and at the same time his blood heated as he thought about all of the things his father had done to her, how could Rei still honestly believe the man had cared for her?
"That is why I would like to ask you Ikari . . . Is it wrong for one to be sad when a loved one passes away?"
Shinji had to think about that for a long time. He could only vaguely remember the one person he had ever really loved, blurry memories of his mother were all he had to remember her by. But . . . he was sure that he would have wanted her back. And he did miss her, memories of his mother were the only time he could remember being loved.
"No, Ayanami, its not wrong for you to feel sad, you should miss him a little, you should think well of him. I-if you loved him." Shinji said hesitantly.
"I see, then, may I attend the funeral?" Rei asked.
Shinji was very quiet for a moment. "O-of course Ayanami." He was privately questioning whether his father even deserved the dignity of cremation. Shinji was tempted to just have the old bastard's corpse tossed into lake Ashino, preferably in small pieces.
"Is that all you wanted?" Shinji asked.
Rei paused for a moment before continuing, "Ikari . . . You are my friend now, correct?"
"Uhm, I guess." Shinji said before catching the deeply considerate look in her eyes. If you know where to look she does show her emotions. Shinji thought slightly entranced before answering more firmly. "Yes Ayanami, we're friends."
"Then . . . like you said, you would miss me if I died?"
Shinji's eyes widened, it wasn't something that he would have ever expected someone to ask. If anyone else had asked he probably would have gone off onto a long stuttering tangent. Instead he nodded, "I'd miss you a lot Ayanami?"
The girl's blush didn't get any redder then the faint pink already warming her cheeks but the words did serve to guarantee it would be there for a few hours yet.
"I have to go now Ayanami, I'll come by tomorrow . . ." Shinji's eyes widened, "Gah! I just realized I've missed the last two days of school, and we still have all of the announcements to make to the UN, and, and . . ." Shinji turned on his feet and tried to stumble through the door, instead managing to ram his face into the doorframe. Rubbing his jaw he grinned weakly, "I'll . . . see you tomorrow Ayanami."
The girl didn't answer instead watching as Shinji went shooting down the hall. Ikari will be a good Commander. Rei thought suddenly. Another thought surfaced unbidden. If he died . . . I would miss him. Rei gave a mental frown, that didn't seem quite right, but, it was sincere and the sentiment for now . . . was close enough.

HHHHHHHHHHHHHHHHH

It was turning out that being Commander had a lot to do with form and very little to do with function. Oh, he had the big decisions to make but the MAGI helped him a lot on the more mundane ones and Fuyutsuki was a great resource even as he taught Shinji how to make the decisions on his ow. But he also had to spend a lot of time doing frivolous things, like inspections, reviews of important documents and of course the city council meeting was coming up at the end of the week. Shinji had decided to sit in on it instead of Fuyutsuki as it fell on the day Rei would be moving in with the Sub Commander. As they walked down the corridor towards the EVA cage for inspection of Unit-00 a thought occurred to him.
"I've been meaning to ask, if we have all of this information why don't we just turn it over to the UN." Shinji asked frowning. It seemed simple enough, even if SEELE held ties in every major organization on the planet, if somebody revealed conclusive proof of their plans the masters would soon be hunted by their own servants.
"Because simply put, SEELE isn't stupid. They've long since had things set up to work against us in such a scenario. If we start revealing their plans it will be NERV that is left holding the smoking gun. We'll be wiped out, and SEELE will be left intact, and believe me, if there is a way to start instrumentality they will find it."
Shinji sighed, "It figures we can't get it easy. So are we ready for the JetAlone trials?"
"Yes . . . The UN Pacific fleet has agreed to conduct the live fire exercise, but they're using it to dictate terms to us on your authority." Fuyutsuki explained.
Shinji nodded, "What do they want?"
"They are requesting that you appoint one of us, either myself or Doctor Akagi to act as your direct advisor, they also want any actions you decide to take to be judged by a triumvirate of myself, Doctor Akagi, and Major Katsuragi." It was a pretty decent deal on the UN's part, frankly, they didn't want to get into the red tape that would be involved in contesting Shinji's ownership of NERV, considering the documentation involved was pretty solid. Either way, they at least knew somebody responsible would keep things running smoothly.
"Well that's no a problem, I was intending to do that anyway." Shinji said thoughtfully.

"Very well then Ikari, I have to make the arrangements for Unit-01's deployment. I assume you will pilot." Futuysuki said offhanded.
"Actually I want Rei to do it."
"Oh really?" Fuyutsuki asked with mild surprise. "Why do you want Rei to pilot?"
"Because . . . I want her to know I trust her, and its not like a higher synch ratio will mean much for this."
Fuyutsuki nodded, "I will have the necessary paper's drawn up. If Rei is fit to pilot by the testing day she will do it."
"Thank you Fuyutsuki." The Commander and Sub Commander stepped onto an elevator heading up towards the lower levels of NERV.

HHHHHHHHHHHHHHHHH

Seeing as how Shinji now legally owned NERV, and therefore was the employer directly or indirectly of some ninety percent of Tokyo-3's workers, one would expect him to be treated with a bit more respect.
"Shinji, where have you been for the last two days!" One would have expected wrong. Hikari Horaki, class representative and specialist on getting into other people's business.
"Uhm, I was just . . . just simulation practice, Misato want's all of the pilots to get in more practice." Shinji stuttered quickly, knowing how shallow his words were, hell he had only been in the EVA cage once in the last two days and that was when he had mobilized against Rei.
"Uhuh, where's Ayanami then?" Hikari asked suspiciously, then again that was her job. She had to keep up with all that little idiots who thought they could call in sick to get a free day off.
"Ayanami? She's uhm . . ." Shinji began hesitantly.
"Ah relax class rep, don't forget Ayanami's missing half the time anyways." Kensuke chimed, quickly pulling Shinji's ass out of the frying pan . . .
"Yeah, and besides you can have Shinji here take Rei's homework to her." Touji said, slapping Shinji on the back.
Hikari mentally shrugged and made sure to get the appropriate handouts for that afternoon before heading off. As soon as she was out of ear shot the stooges's eyes narrowed and they began their own interrogation of their latest member.
"What have you really, been doing?" Kensuke asked suspiciously.
"N-nothing, honest!" Shinji replied.

Both of his friends looked to one another and nodded in agreement with some unspoken fact. "Your lying." Touji said sternly, "Come on man tell us!"
"I-its nothing . . . just . . . my father just . . . died." Shinji admitted half of the truth, not really thinking as he said it. Most children would be in a state of great sorrow if they lost a parent. Shinji really couldn't care less that his dad was dead, especially after what he had seen and been told. And today . . . today he had to inspect the dummy plugs . . . and decide what exactly to do with them.
His friends were quiet for a moment, "Your father's dead?" Kensuke said slowly, "We didn't mean to bother you about it!"
"Yeah, sorry man." Touji added in, both boys looked ashamed for touching on something so personal.
"No, don't be." Shinji said, "We weren't ever that close. He kind of abandoned me after my mom . . . passed away."
Both of his friends looked unconvinced but seemed to accept his answer, partially out of understanding, partially to break free of the awkward situation they had just gotten themselves into.
"Hey wait, doesn't this mean somebody has to replace him as Commander of NERV?" Kensuke asked excited, then again the boy lived, breathed, and ate EVA it was his dream incarnate and that meant he was constantly harassing Shinji about it.
I just don't have the heart to tell him he's at the very bottom of the pilot aptitude list. Shinji thought somewhat ashamed out how funny he found his friends predicament. Actual pilots were rare to find, he had learned during one of Ritsuko's many briefings, but there were quite a few markers that could be used to test viability if a child was selected. Kensuke was behind nearly eight hundred other potential applicants. Including just about every other kid in there grade due to a combination of poor reflexes, bad eyesight, poor physical fitness, and 'psychological characteristics deemed dangerous in a pilot.' Whatever that meant.
"Uhm, well, I wouldn't know about that, I-I'm just a pilot." Shinji stuttered, yeah and you know he's gonna find out soon enough . . . Shinji made a mental note to have Ritsuko encrypt all of the data pertaining to his new status. He really didn't want Kensuke on his butt every other day wanting to see the GeoFront. As much as he saw Kensuke as a friend he couldn't bare that level of harassment, if at all possible he wanted to avoid the bespectacled boy finding out. EVER. In fact, if he did find out Shinji was almost ready to just live in the GeoFront for the rest of Kensuke's life.
"Man, I hope the new Commander decides to do some pilot shuffling, and maybe allow tours of the GeoFront, and . . ." Shinji was soon tuning the Otaku's long external monologue out with the same skill he applied to ignoring the teachers when he lectured about Second Impact. Not like he even know the real story. Shinji thought a bit more darkly. It was ironic, finding out all of NERV's secrets hadn't made him more depressed, it had just served to make him significantly more cynical. Oh well . . . tomorrow Rei would be getting out of the hospital. Shinji began to think about Rei, despite knowing her origins she was as much an enigma as ever. I'll help her move her stuff once she's well. Perhaps I should have Fuyutsuki move into one of the nearby complexes . . . Shinji dismissed that thought as just his male hormones trying to get the one girl he could remotely relate with someplace within convenient walking distance.
The bell rang and he had no more time to think, cough-scheme-cough. If one had been able to see some of the things that the heavily quarantined insane asylum section of Shinji's brain was coming up with they would definitely agree his father would be proud.
Someplace down in hell a bastard gets his horns.

HHHHHHHHHHHHHHHH

Happy thoughts were best left on the surface . . . That was what Shinji discovered as the elevator descended towards terminal dogma. This entire place reeked of the pain that had been inflicted through its very existence. It was the physical embodiment of an insane wish. And for that reason alone he wanted to destroy it, with each passing second Shinji was seeing that his father had been a filthy little soul who should never have been allowed to command his fear, much less respect.
He looked around at the others descending with him, Misato, Ritsuko, Hyuga, Aoba, and Maya, the Sub Commander, and, against his better judgement, Rei. It was the largest group to enter the lowest level of the GeoFront in years, yet even they, eight strong, couldn't shake off the misery that this place symbolized. The first thing Ritsuko had shown them was the EVA graveyard. "Do you have any idea how many failures we had before Unit-00 could even be made viable?" She asked rhetorically as she waved a hand at the skeletons of potential gods. "Billions, tens of billions of dollars down the drain because we could never perfect the system."
"But a solution must have been found." Misato said starring out at the remains, at a single EVA in particular, some of the muscle tissue was still left on this one clinging to the bone like parchment, one could see where a third eye lay hanging from its socket in the dead, never living to be honest, behemoth's forehead. "I mean, Unit-00 and the rest, the souls . . . their cores weren't finished right away, so that couldn't be it."
Ritsuko nodded in agreement. "Your right Misato. Making an EVA capable of simply living isn't that hard. We were able to construct a viable Evangelion by editing out the S2 core from the DNA." She explained, "S2 principal relies on the phase space of the AT field, without it the core breaks down any living tissue within proximity to it. Essentially, you need a soul in order to shield biological components against the negative affects of the S2 reaction. Of course without a soul it's just an inert mass of pseudo living tissue."
"So your saying these things all died because they didn't have souls?" Maya asked as they continued towards their final destination.
"That would be accurate." Fuyutsuki said, "Even after we were able to build Unit-00, 01, and 02, we still did not fully understand why removing the S2 core had such a significant affect. It was only after the absorption of Unit-01's test pilot that we began to research further into the AT field." Shinji froze stiff eyes dilating as it all meshed together like a well made watch.
Rei was the first to notice his hesitation, it seemed that all of the affection she had possessed for Gendo had transferred now to Shinji and then some, she had practically attached herself to the boy like a limpet never leaving his side save for synch tests and during her only recently ended period of enforced bed rest. "Ikari?"
Shinji's eyes were glassed over and distant. "Mother . . ." He whispered.
She flinched slightly, coming to a logical conclusion, I am not her, Rei thought quietly. She still did not know how much the Sub Commander had told him. She had nearly decided to say as much when Shinji continued on his own.
"It was mother wasn't it . . ." The entire group turned to Shinji who was now speaking with a cold voice. "Mother tested the EVA . . . She's the one who's trapped in Unit-01's core . . . isn't she!" He supposed he had known since Fuyutsuki had told him about the true nature of the EVAs, but he hadn't wanted to believe that his mother was there. It would be wrong to delude himself that way, surely it had just been some unlucky technician. Some unfortunate test pilot.
Kozou said nothing, he simply nodded his head slowly not daring to directly acknowledge the question for fear of setting Shinji off. The entire group was silent as Kozou spoke once more, "It was your fathers intention to initiate third impact, so that he could be with her."
"I . . . see . . ." Shinji said softly as Rei hovered over him becoming suddenly concerned for Shinji's well being. "Thank you Fuyutsuki . . . it's all making a lot more sense now." Shinji's eyes widened slightly as Hyuga moved to support him. Odd, he didn't remember beginning to sway . . .
"Are you sure you want to see the rest Shinji?" Misato asked.
He didn't answer, but his eyes did, they showed exactly how he felt and Misato could not deny him. Not on this.
The group continued coming next to a room that Shinji knew all too well, even if he had only been there once. "Ayanami's apartment." He said simply.
"Yes." Ritsuko agreed, "This was where she was born Shinji, from the water and light here." Everyone was silent as they starred at the small space, perfectly identical to the only home Rei had ever known. It was another level of control on Gendo's part. He had feared what would happen if Rei ever saw a purpose for her life. If her soul had ever found something beyond him. So he had done everything he could to stunt her development. It was largely through the use of Maslow's theory that he had achieved this. Rei had been given the necessities of life, but never had even the barest of true comforts. As such she had never seen past the second level of the hierarchy of needs. That was safety and security. Because of that she never realized the existence of the third level, the need for love and interaction with others.
Similarly Shinji though having reached the third level of the hierarchy due to Misato, had never reached the fourth level, Ego, which would have required him to develop self confidence. If either of these children had ever reached the fifth level. Self Actualization, the improvement of themselves, the scenario would have been in grave danger, averting instrumentality was perhaps the first event in human history, unlike wars, that instead of requiring humans to become more base in their needs, instead required them to step beyond themselves to survive.
Nobody in the room save Fuyutsuki realized this, and he was beginning to feel somewhat ill at the thought. He had allowed that bastard to cripple the souls of two innocents, out of all the people present that made him worse then even Doctor Akagi, most of them had not known, he had, and had not acted. Yui would forsake me for this . . .
"Now . . . Do you want to see them, Shinji?" Ritsuko asked again, coldly. The boy took a deep breath, this was it, what he had come here for, letting the breath out, he nodded slowly.
They were ushered into a large circular room, too dimly lit to quite make out the walls. Ritsuko walked to a terminal near the center of the room, one hand hovering over the lighting controls for the tank. "I believe you have all been informed about what you are about to see. If not . . . I suggest you leave now." With that said she hit the switch.
The entire room was bathed in orange light, and all were absolutely silent for a moment. Maya gasped and closed her eyes, Hyuga fixed his gaze on the floor after verifying what he had seen. And Aoba . . . well . . . he starred in a manner that would have worried the rest if they had been paying attention to him. They were not however, their attention was fixed on Rei.
To be precise, Reis, at least a dozen of them floating naked in the tank. At the sudden stimulus several had turned to stare at the occupants. Shinji felt ill as he saw their soulless red eyes, they reminded him, of dead fish eyes at the market. One of them glided down, pressing a hand to the tanks surface, and then began to giggle. The rest slowly followed as they studied their guests. It was those eyes though, those lifeless eyes, and the cheerful yet also hollow smiles that were plastered on their faces.
"These are what you wanted to see. We use them as spare parts for Rei and as cores for the Dummy Plug system."
Misato stepped back slowly trying to get as far from the walls as possible as Fuyutsuki clenched his fists tightly and forced himself to stare into the distance. He'd only come down here once before, he did not need to see it all again.
Rei however was possibly the worst affected in her own way. Shinji realized it as soon as she left his side, she went to stand by the door, already distancing herself from others, she was already expecting to be hated now. It was only natural, human beings despised that which was different from them. At best, she could be expected to be treated no differently then the Commander had treated her. At worst . . . She would be a tool, to be disposed of the moment her usefulness ended.

She didn't notice Shinji following her out of the room, neither did anyone else as Ritsuko was bombarded by questions about what exactly they were all looking at.

He stood observing Rei from behind for some time, and then he came to his decision, one that he had to make without any regrets. He doubted he was strong enough to do it, but it still had to be done, regardless of whether it was right or wrong. He couldn't run from it this time because all directions led to it.

Rei flinched slightly as hands dug into her shoulders, and turned her around forcefully. Shinji's eyes were confused, sad, ashamed, angry, disgusted? Rei did not know, she did not know enough of emotions to understand what she saw before her. What Shinji was really doing, was starring as hard as he could into those red orbs, he had to . . . He had to be sure. His grip grew tighter, she exhaled painfully "Ikari . . . You are hurting me . . ." Rei whispered tightly.

Suddenly the grip on her shoulders slackened the hands falling limply to Shinji's side as his head hung low. He'd seen it . . . There was something within Rei that made her different from her soulless doppelgangers. No . . . she hadn't changed at all, he was sure now. And felt ashamed for ever doubting it. Without another word Shinji headed towards the elevator, he had been wrong, he couldn't take what he had seen. He was going to need time to make sense of it all, and decide how he felt, if he could even do that.
The others came soon enough Doctor Akagi coming last as she shut down the lights, the clones would continue in there laughter for some time before finally settling down again. It was rare for something to stimulate their information starved minds. Rei watched as Major Katsuragi approached her, and suddenly hugged her tight. "I'm so sorry Rei." She said quietly, "So, so, sorry."

Rei's eyes were glazed as she seemed to look off into the distance, her body took control and she simply sagged into the embrace, barely supporting herself. Hyuga stood nearby watching concerned along with Maya both of them had come to the conclusion that they were guilty of ignoring Rei's predicament and so had no right to judge her even after what they had seen. Shigeru seemed to distance himself from the group after what he had seen, though primarily to avoid anyone noticing a slight . . . Bulge . . . In his uniform.

Fuyutsuki looked about, "Where is Shinji?"

"He has already returned to the lift. He will be waiting for us." Rei said without opening her eyes. This is very pleasant . . . Why was I not informed of this sensation. Rei wondered as she snuggled into the warmth of the Major's embrace. It was the first time someone had offered her emotional comfort and it was very much a new and wonderful sensation to her. She wondered if it would be the same to be embraced by a person of the opposite sex. Assuming similar intentions of course, Rei thought naïve was not unaware of the perverted nature of some members of the human race.

Ritsuko leaned up to the Sub Commander, "Why did you order me to keep Rei's human donor from them?" Ritsuko asked softly, voice filled partially with curiosity and partially with disgust. Fuyutsuki kept faced straight ahead and yet somehow managed to project his voice only to Ritsuko while doing so. "Just how closely related would they be . . . Honestly."

"Honestly?" Ritsuko said, "Including the use of Lilith Genetic material, editing to both genetic codes to make them compatible, the additional chromosomes, and minor genetic mutation due to the cloning process we used . . . Well . . . Not very." She admitted, "Well . . . Not at all . . ."

"Exactly, then why should we trouble the Commander's mind with more at the moment. He's assimilating enough as it is." Fuyutsuki had long given a relationship between Shinji and Rei thought on a philosophical level. It would have fascinated a Freudian he had to admit, but really even is Rei had been more closely related her hybrid nature rendered her sterile. Even if she had possessed functioning ovaries instead of the vestigial glands her S2 core had grown in their place, she would have been unable to conceive a child with anyone other then another Nephilim with similar genetic structure. At least theoretically . . . He hoped . . . He made a note to have the Magi keep a log of Rei's venereal exams. You could never be too careful. And she was after all a girl on the verge of womanhood.

HHHHHHHHHHHHHHHHHHH

Shinji remained quiet all the way home. He was still quiet at dinner, being Misato's night to kick she had admitted defeat just this once and ordered take out.

"Did you get the answers you wanted ?" She asked him concerned.

Shinji took a bite from his meal and then paused, "I did . . . But now, I'm not sure if I want it. Because in order to get it I had to betray my trust in someone who I promised to help."

Misato looked at Shinji and then came to a decision. "Do you know what my instructors told me during officer's training?" Misato said.

Shinji shook his head, Misato had never spoken much about her military career. "They said, Katsuragi, you're an idiot, don't panic about the little things as long as your troops come out okay you can always ask for there forgiveness when its all over. But if you let yourself go soft and be their friend in the middle of a mission you'll all end up dead . . . I think what he was trying to say is that you have to love the people you serve with but also have to be able to ignore that love so that you can act without hesitation to make the decisions that could save them. That's how an officer has to think Shinji."

The boy Commander starred at his meal. "I don't think I can do that though."

Misato just looked at him concerned before grinning. "Hay . . . You have the city council meeting tomorrow."

"Y-yeah." Shinji said, brightening a little as his mind was pulled away from its self abuse.

"Well, you'll have to wear your uniform, after all it will be your fist public appearance."

"Uniform?" Shinji wondered.

"Well yeah you didn't think that jacket your father wore was something he just picked up did you?"

Shinji suddenly didn't like where this was going. "B-but Misato why can't I just wear my school clothes I mean . . ."

"Oh no, you have to wear it Shinji, you'll just look so cute! Maybe I could go too it would be so adorable . . ."

"No, NO, as your Commander I order you to stop this!" Despite everything else, Shinji was still a kid, and he could still be teased.

HHHHHHHHHHHHHHHHHH

Ok anyways what I'm hoping to achieve here is Shinji having a kind of alter ego, not quite split personality but kind of along those lines. He can't run away, and he isn't wrong in believing it is his responsibility to see this through. So he will kind of have the strength of his convictions to him through. As for the Rei clones . . . Well . . . Something will be done for them. That is all.

(Authors Note: If you think of it this way, if Rei was created in reaction to Yui's absorption into unit-01, she can't possibly be fourteen. At oldest she could only be ten. This also fits with possible accelerated growth of the clones to their current state. Perhaps they could control her rate of growth in the tank similar to how they grew the EVA's.)