Still don't own anything. And I apologize but I've never quite figured out the layout of Misato's apartment so if how the groups are isolated is impossible then just chock it up to slightly parallel universe, yes that's it . . .

Chapter Three Living: Sister?

For Asuka, the whole situation was just too surreal. On her left, sat a nervous Misato, and an equally complacent wondergirl. To her left sat a somewhat happy though still a little confused Shinji, a girl who claimed to be his mother reincarnated in one of Rei's clones and an uneasy Gendo Ikari.
They were currently sitting around Misato's apartment. Yui had demanded to see how her son was living and seemed more or less satisfied. Gendo just looked uncomfortable but strangely content as Yui's slim hand lay on his own.
Shinji's dad had never struck Asuka as an actual human being, but now that she thought about it, their must have been some redeeming qualities in him at some time or Shinji's mother would never have married him. What had she expected, Shinji to have been born in a test tube?

She flinched slightly. Unfortunately Rei really had been born in a test tube. 'Well, that explains a lot.' Part of her wanted to laugh at the irony that Rei really was a doll in every sense of the word. A manikin that was able to walk and talk. But she suppressed it guiltily. She really wasn't sure what to think of Rei now. Her own past was dark . . . Rei's though was darker.
"So Shinji, why don't you tell me about those boys Touji and Kensuke, their your friends right?"
"Y-yes, their nice, they've been good friends ever since I met them . . ." Shinji froze, Yui's blood red eyes were inches from his, a wicked smile on her face.

"I advise you don't lie to me dear, don't forget I know quite a lot about your life. The images may be blurry but I distinctly remember you getting beaten up by one of those boys."
"Well," Shinji replied defensively, "He had good reason, his sister got hurt when Unit 01 one went berserk."
Yui's smile faded, she looked sad now. "I'm sorry Shinji, that's my fault." She said softly.
'What?' Shinji wondered, then the realization hit home on what his mother had been for the last ten years. 'She's the one who's fighting when EVA goes berserk she was trying to protect me!'
Everyone was surprised at what happened next. "Yui, people are bound to be harmed during battles." Gendo said gently, squeezing her hand. "That girl was as likely to be harmed by Shinji as by you in the fight. It was beyond anyone's control that she was injured."

"I know Gendo", Yui muttered quietly.

He face transformed going from sad to mischievous as she pulled Shinji up. "I haven't had anything to eat in ages, literally. I think I would like to try some of my sons cooking", Shinji found himself being dragged off to the kitchen by his mother. Gendo just continued to sit quietly.

"Commander." That word was whispered by the standards of a girl who spoke in whispers.

Asuka and Misato looked to Rei as she sat their quietly, she had kept her head bowed for most of the ride to Misato's home, and during the proceedings.

"Yes Rei." The Commanders equally firm voice replied.

Her head came up, and all three of them, Gendo included found themselves looking into eyes now filled with very uncharacteristic confusion. "What will happen to me now?"

Gendo did not hesitate to answer. "You will continue to carry out your duties as the Pilot of Unit 00", Gendo replied firmly.

The emotion vanished from Rei's face once more, "Yes Sir. Excuse me. I should go", Rei rose quietly and headed for the door.

"Hey, uhm Rei", Misato's voice was uncharacteristically quiet, it was the same uncertain voice she had used the first night Shinji had come to live with her when telling him how brave he had been. Asuka had heard the tone only a very few times by now, she mockingly called it Misato's sisterly voice.

"Yes Ma'am?"

"Why don't you stay, it's almost lunchtime. And I think we need to talk about all of this."

Rei paused for a moment, and then continued putting on her shoes. "There is nothing to discuss, you know what I am and have already come to your own conclusions about my nature."

She was almost out the door when Asuka finally snapped. She stood up strait, "Hay wondergirl, your Commanding Officer just told you to do something. Be a good doll and sit down!"

Rei turned at looked at Asuka. "I am not a doll", she replied.

Any other day Asuka would have simply kept tormenting Rei, but she had an objective today. "Oh really, prove it. Get back in here and park your genetically engineered backside wondergirl, we're going to talk about this."

Rei blinked a few times. Looked to Commander Ikari who did not seem to care one way or the other. She took her shoes off, and paced back to the couch.

"Rei, what do you think I think of you?" Misato asked, she really was curious.

Rei answered emotionless but honest. "For the entirety of our relationship I have been under your Command as a pilot. It is my purpose. As I am expected to enter combat, I am considered expandable both tactically and strategically."

"Rei . . . Rei, you are not expendable. Do you think I see Shinji or Asuka as expendable?" Misato shouted angry.

"Their circumstances are different, they are unique. There are ample replacements for me. If I die, my memories and soul will be transferred to the next. It has happened once since my initial activation fourteen years ago, and I expect it will happen again."

Misato gapped, slowly working her mouth. "What do you mean it's happened once?"

"When I was four years old, Doctor Noaka Akagi strangled me to death, and then committed suicide."

'Ritsuko's mother?'

"W-why?" Misato asked.

"I do not know, my most recent harmonics test had been three days prior so memories of my murder are not available. I was not reactivated until it was deemed time for me to begin learning the operation of EVA and basic NERV operating procedures.

"When was that?" Misato asked, why did she have a bad feeling about this.

"Four years ago."

Misato coughed, "WHAT!" She had met Rei about that time.

Rei seemed to be thinking the same thing. "Our fist meeting was six days after my reactivation."

Misato shuddered, Rei spoke of herself as a machine, her activation, not her birth, or even her creation.

And what about her education, Misato had never doubted that a very intelligent mind lay behind those eyes, but how the hell did you catch up on six years enough to function in only the two she had been given before being enrolled in school?

She looked menacingly at the Commander. "Sir, how could you do something like this?" Misato wanted to throttle the man.

The room had become silent, she wanted to yell at someone, probably Commander Ikari, but it wouldn't achieve anything, as much as she hated the man now. For what he had done to Shinji, his own son, and for creating such a wretched twisted being as Rei who had to suffer because thanks to the wishes of wicked men.

"Rei", Misato spoke shakily, "I want you to know, that I've always thought of you as being just as important as Shinji and Asuka. And knowing what you are doesn't . . . doesn't change a thing in my mind. Do you understand that Rei?"

Rei bobbed her head slowly. "Yes Ma'am".

Misato did her best to smile. "Misato".

"Ma'am?"

"Call me Misato off duty." Misato said, trying to show some of her old cheeriness.

"Yes . . . Misato", Rei replied. She got up to go again.

Asuka grabbed her by the shoulder and pulled her down. "Where do you think your going?"

"You wished to speak to me about your opinion of me. You have done that. There is no reason for me to stay any longer."

Asuka snorted. "If you weren't listening Misato asked you to stay for dinner."

Rei seemed to accept this and sat down again quietly between Misato and Asuka. Almost on impulse Misato pulled the poor kid into a hug. Rei seemed a little stiff, as if she was unused to people showing her affection. The sad truth was, that she was.

'This is . . . pleasant', Rei thought, 'Though not as pleasant as being close to Ikari'. Her mind wondered off to the first embrace she had ever been given, only an hour and a half before. There was much to consider, about her purpose, and, perhaps her wishes. 'My own desires. I will need to study them at length.' She thought as she melted into the Major's arms.

The entire room was ruled over by a comfortable silence now, the kind usually reserved only for libraries and churches, despite the presence of NERV's supreme bastard king. It stayed like that for over five minutes. Misato noticed that Rei had fallen asleep, the girls head was snuggled softly against her chest. It was kind of nice in a maternal sort of way. She forgot that Rei was a half Angel, a Nephilim. 'I should hate her'. Misato thought ashamed. The 1st Angel had killed her father, and from then on she had vowed not to let another little girl grow up without a father because of them. 'But I don't hate her, she's never caused me any harm. She's always so quiet. She doesn't deserve the suffering she's had to go through'.

Asuka finally got up and stretched. "I'm going to go tell the baka to make enough food for six." She decided aloud as she walked back towards her room, stopping by the kitchen long enough to shout in on Shinji her demand for lunch.

Misato's eyes turned to Commander Ikari, it took a few moments for what she saw to register. The Commander sat staring, Pen Pen stared back. It seemed like some absurd battle of the wills. Misato would have laughed accept for fear of waking Rei or agitating the man who was still her superior officer.

'Damn him', Misato thought bitterly. If only their was someway to get him arrested for this. But she imagined that any inquiry would side with Gendo on his actions if such methods were at their time considered the only possible means to thee ends. And Misato had to agree, bitter as it was.

'Rei needs somebody to care for her', even Shinji had done better with a little affection, 'I promise Rei, I'll try and help you'. Misato swore quietly to herself, it was all she could do for her. Gendo finally moved from his seat, grabbing his jacket as he went. "Major tell Yui that I wish I could stay, but I have to be going. There is much to be done if she is to be among the living again."

Misato nodded, "So are you creating a new false background?"

Gendo shook his head. "She's decided to use Rei's last name. We can tell people they are siblings, that will cut down on risks to detection by using an established paper trail". 'And SEELE hopefully will just think this is another Dummy Plug experiment'. Gendo knew that the shell of lies needed to pull something like this would be, by necessity, quite complex.

He paused before heading out the front door. "We will continue this later".

"Wark", Pen Pen responded.

Misato just blinked stupidly. Pen Pen looked at her knowingly for a moment and then waddled back towards the kitchen. She wondered how Shinji was doing.

Yui watched her son. The son she thought she would never again see in anything but a plug suit. He seemed happy when he cooked. He was doing something that he was good at, and he was content that he brought joy to others doing it. And that was what mattered, her son was happy. What more could she want.

Unfortunately, Yui was not a particularly good cook. She failed miserably to chop even the vegetables despite great care.

She stopped her butchery of the unfortunate carrots for a moment. She held the root in her hands. Feeling the texture, she closed her eyes to focus on the sensations.

"Mother?"

Shinji looked at her worried. Yui moved to reassure him.

"Its just been so long since I've been able to really feel anything Shinji.", she said, her voice quavering. She smelled the food cooking. Rice, fried vegetables, meat, and the sharp smells of spices. She wanted to cry as she realized how barren her existence had been of sensory input for the past ten years.

Shinji just looked at her nervously and accepted her words. He kept trying but other than seeing vague hints, he could not find Rei in that face. It was Rei's face and he could see that it was the same. But after over half a year of studying the strange albino he knew her better then perhaps anyone else. No that wasn't true, his father had known her better than him, he thought in, he didn't know what to feel when he thought about Rei now. What was she? Was she even a person?

'Is she really even alive?' He thought.

His depressed musing about one of the strangest people in his life was cut short by his mother's happy squeal.

"Ooooohh, and who might you be", she said in the manner reserved for extremely small children and adorable animals. She had her hands on her knees smiling as she studied Pen Pen.

Poor Pen Pen was confused. First his mistress had decided to bring home that odd man whom she called the Commander respectfully to his face, and sometimes the bastard king when she spoke of him in private. The man had dared to stare at him, attempting to beat him at his own game of intimidation. Hah, fat chance of that!

Now the odd girl that had come over once before was back. The one with the strange hair and eyes. She had been cordial enough when he had met her. Propping him up in her lap and being politely silent. He had watched that girl from his hiding place near a house plant, and the other girl that looked like her. This one was quite a bit more boisterous.

But then again . . . she did rub his head just the right way. He shook furiously for a few seconds and then waddled over to his fridge. He gave the girl a nod of acceptance and waddled in.

Shinji went back to work on lunch, stir fry was pretty straightforward and would fulfill the need to feed three or four adults and a couple of vegetarians. Which meant just about enough to feed Misato and Asuka on a good day.

"Um, Shinji. We need to talk." His mother said, not turning from her work as she spoke.

"About what?"

"Ayanami."

Shinji paused uncomfortably. "What am I supposed to think about her, I mean isn't me liking her like that, like, incest or something!"

Yui shrugged, "That's actually up for debate. Literally speaking she's your half sister." Yui agreed.

Shinji flinched as his own traitorous mind decided to make him feel worse. 'God, I groped her, I groped my own sister', he felt a little shaky and ill now.

Yui noticed this, she'd seen enough of her sons self hating nature to have a good idea it was him beating himself up over how he had felt and acted with Ayanami. She continued. "Shinji, think about it this way, most of the DNA that I provided is common to both Angels and Humans. And your forgetting just how inhuman her genetics is. Genetically speaking, while she is my daughter her relationship to either of us is barely within the same genus."

Shinji looked at her shaking his head angrily, "That doesn't change a thing. I've . . ."

"You've thought about her as any boy will think about an attractive girl." His mother said teasingly. "You're just going to have to take my words on faith Shinji. She's your sister only if that is the way you wish to see her."

"You're the last person I would have expected to say something like this", he mumbled as he focused on his cooking, trying to drive all thought away.

His mothers smile was sad, "Shinji I've spent my life in three different bodies so far, all of them different, nobody can go through that without becoming detached to certain things like pre-conceived notions of what constitutes a blood relationship."

Shinji just focused harder on his stir fry.

Yui saw she wasn't going to get anymore out of him, she was a little ashamed and part of her screamed that she needed to stay her and help her son. And . . . as much as she wanted to she couldn't put the blame for this entirely on Gendo. 'He had a good reason in his own mind. His quirkiness is why I married him', she reminded herself sternly. When he had been younger Gendo really had been a good man. She wondered how Shinji would have turned out if his father and been able to bridge the gap and love him in her place. An image of Shinji wearing dark sunglasses and white gloves flashed through her mind. It almost made her double over laughing as she went back to the living room.

Misato was laying quietly with the TV on low, Rei using her as a pillow in her sleep. "Where is Gendo?" Yui asked. The Major gave Rei a quick look, and then realized who was speaking. The voices sounded different, but only in the way identical twins would sound different.

"Oh, he said he needed to take care of some paperwork." Misato replied in a whisper, still afraid to wake Rei.

"I see." Yui took a seat next to Rei and combed a hand through the girls short azure hair. "I feel sorry for her", Misato whispered.

Yui looked at her. "It sickens me what my husband had done, I apologize", Yui replied sincerely. "But he had the best of intentions, maybe not honorable intentions, or selfless, but his reasons were good in his own mind. If you pity Rei, then I ask that you also pity him."

Misato looked at Yui, a woman and a mother who had been trapped once within the shell of Unit 01 and now within the body of a Nephilim. Shinji could barely remember his mother, but Misato could see where he got his kind and forgiving to the point of self hating nature. Obviously Yui hadn't been around long enough to give him a lesson in character building.

"I was thinking about my talk with Shinji." Yui began.

"Oh yeah, what did you talk about." Misato asked.

"He's a bit troubled . . . he's for the moment latched to the idea that he's been considering unforgivable sin."

"What's that?" Misato asked, she couldn't think of anything that Shinji would consider that could possibly be considered that disgusting. Well Pen Pen was acting strangely . . . oh god he wasn't . . ."

"Incest", Yui said simply.

"Oh", Misato said, thrown a little off. She looked down at Rei. "Oh." Their was an uncomfortable pause.

"Well, is it?"

Yui shook her head. "Not really, but he has the notion driven into his skull as firmly as Gendo's belief that gloves are cool."

"So, she's not his sister?"

"She is."

"Than it would be incest." Misato insisted

"No, not really."

Misato sighed, "Okay explain it to me then."

"It's a matter of philosophy over science, I suppose." Yui stared at the TV, a movie she hadn't seen since she was a teenager the first time, was on.

"Rei's genetic makeup is comprised of about fifty percent human and fifty percent angel DNA. Give or take a few percentage points."

Misato nodded dumbly.

"My DNA was the source for her human half, so if you want a philosophical answer. Yes she is Shinji's sister, but by the same coin that technically makes me his sister too." Yui continued, she seemed to muse on that one.

"Now like I was saying, Rei's angel half however pretty much dissociates her from the rest of the human race. Despite the similarities between Angel and Human DNA there are quite a few irreconcilable differences in their basic makeup which means that Rei's genetic structure had to be drastically altered. Due to her purpose most of those alterations had to be made to her human genome. So from the standpoint of their genetic relation they are not even the same Genus. So if we can get him around that block then her should be fine."

"Ah so it was bestiality", Misato said without thinking.

"What was that?"

Misato found Yui's eyes staring her in the face, looking very suspicious that she should by all rights be angry with that mumbled comment.

"Oh, nothing, s-sorry Mrs. Ikari, uh, how did you know about all this", she stuttered.

"Yui" She corrected. "And as for the filler, I asked Naoka's girl, she's a nice kid, a bit bitchy thought. I imagine she's angry I broke her nose."

"Uh, ok . . . Yui". Misato felt a little nervous. 'Scary, she could even intimidate the Commander. Probably why he married her.' She thought darkly.

She was broken off that track by the faint smile on Yui's face.

"What is it?" Misato asked.

Yui started giggling. "It's just that, when I was little, I always wanted to have a twin sister."

Misato stared dumbly, it was official the world was too strange a place to live in unintoxicated. She got up slowly, careful not to wake Rei as she propped the girl with a pillow.

"Where are you going?" Yui asked.

"Getting a Yebisu, I need a drink." Misato replied.

Misato was sure she heard a mumbled "lucky bitch", as she headed for the repository of her favorite beverage.

Dinner was served soon after. In Yui's opinion it was quite good.