Note: I don't own it people. Now on with the show. And please excuse if this chapteret isn't very good I just wanted to get past this part and move on to Yui's interactions with Shinji and Rei, and everyone else. Unit 01 will probably make a comeback in an equally interesting way. Oh yes and to all of you. THIS IS meant to be a Shinji Rei fic though its probably going to be a little awkward at first. Enjoy and Criticize my Suckiness!

Chapter Two: Mother?

Shinji was nervous, well panicking may have been more precise. He and Asuka had arrived on time. Misato had made certain of that . . . But as soon as they had stepped through the security doors a trio of Section Two agents had taken them by the arms and escorted now, hurrying them off down the winding corridors of NERV with Rei in tow close behind.

Shinji noted irritably that they did not bother giving Rei the same treatment he, Asuka, and even Misator, were receiving. He suspected a little guiltily that this was his father playing favorites.

They came to a stop in front of a door familiar to everyone present. Shinji had only been called here a few times. Mostly when his father was away on business by the sub commander.

They were all silent as the doors were opened, and then quickly shut behind them. There was the distinct click of a lock. The Section Two agents remained outside.

Shinji looked about himself, his fathers chair was turned at the far end of the room. A good twenty meters away. It was hard to even make any detail out from their place near the door. The dimly lit expanse of his fathers office seemed excessive to Shinji, even for his father. The man whose work involved building and commanding, humanities most powerful weapons.

"Major, Pilots, step closer", the Commander ordered, never turning his chair.

Rei did not hesitate to do as she was told, Shinji and Asuka were a little slower. Misato moved imperceptibly faster, getting slightly farther ahead than her two charges. Misato may not have known it, but she had very strong motherly instincts and something just didn't smell right.

The chair turned slowly as they approached with in five meters of the big wood desk. Gendo Ikari was there, fingers laced in his best scary retard pose. If it had been anyone else Misato knew she would have laughed. But the Commander seemed to have a talent for making even the most absurd gestures seem intimidating.

"Pilot Ikari, Pilot Ayanami, Pilot Soryu, Major Katsuragi". He chimed off as if daring anyone not on his short list to reveal themselves.

"Events within the last hour have . . . transpired that have led me to re-assess what information you should all be aware of."

Gendo Ikari was very good at keeping secretes, and though this was not the first time he had been required to reveal the truth, it was the first time that he had to do it gently.

"To be more specific, information regarding the dummy plug system, and how it relates to Rei."

Shinji could feel Rei stiffen slightly at his side. What did Rei know about this?

The dim lights of Gendo's office dimmed even further, engulfing the room in blackness. A holographic image appeared in front of Gendo Ikari's desk.

Yui, had apparently been giving this some thought. She had decided the would tell Shinji the truth about Rei, but they would soften it. Yui had been the one to tell Gendo what to say and how.

Images of EVA, and then a series of pictures of Rei Ayanami, growing up from child hood filled the holograms viewing space. It troubled Shinji, in the younger images he thought he could see love and happiness in those red orbs, appearing almost catlike in her four year old face.

"At the time of EVA's first initialization projects, several before unforseen difficulties arose. You see it is a half truth that only select children can pilot EVA.

Asuka seemed a little irritated at those words, she had lived her entire life thinking of piloting EVA as her talent, "So what's the full truth then?" She asked.

"First and foremost, the greatest necessity is that the pilot's Ego Border, conforms to a very tightly defined set of criteria. These conform very closely to the Ego Borders of the Angels."

"So are you saying the Pilots are chosen because they have something in common with the Angels?" Misato asked, this was starting to sound too strange. And what the hell was an Ego Border. She'd heard Ritsuko spout it a few time before . . .

Shinji tried to ask that same question aloud and only got a cold stare from his father.

"To be more precise, the criteria usually include that the Pilot has gone through significant emotional trauma, deeply affecting their psyche. Usually in the form of the loss of a loved one or . . . neglect."

Anger sparked in Shinji as he realized what those words meant. "IS THAT WHY YOU LEFT ME, SO I WOULD MAKE A GOOD PILOT!" He shouted.

His father ignored the outburst completely. Frankly it did not surprise Gendo that his son would react negatively to most of his fallowing words. And. That steadily more recovering part of him that was his once lost conscience was nagging that he was partly to blame.

"Secondly, EVA at the time of our initial activation attempts lacked something very important. That has been rectified in all of the currently functioning Units."

"And what might that be?" Misato asked.

Gendo lowered his glasses slowly, revealing his eyes. Then for the first time since they entered he answered the question. "A soul."

A chill filled the room. "Sir, what do you mean by that?" Misato asked, she was growing more uncomfortable by the moment. "It was discovered at a later date that Pilots best synchronize with an EVA whose soul has a strong desire to protect. Therefore, all of the souls within the current EVA's are from females, and all of them were mothers."

Misato looked shocked, Asuka looked like she was going to be sick, and Rei just stood their with her head down and her fists clenched. 'Why am I angry', she had never felt so intensely. 'Does it bother me that the Commander is going to tell Shinji about me?'

Shinji was pale. "Wha-what do you mean father, father your not saying that you . . ."

Gendo ignored his son's stuttered revelations.

Up until now he had told the whole truth, now the lie started to form, not so much lie as softening of the truth.

"At the time of the initial failures these conclusions had not yet been made. A stop gap measure was needed if we were to have a pilot available to fight the Angels. To put it simply, we needed a pilot that was capable of Synching with EVA. It was theorized that if certain Angel characteristics could be engineered into a child then that child would be able to synchronize correctly. However as research into this proceeded, new discoveries were made showing the importance of an appropriate Ego Border."

The Images changed from Rei and EVA to Rei and the pale bulk of a giant crucified to a wall. A lance embedded in its side.

"This . . . is the second Angel, Lilith." Gendo continued, their was a twisted smugness to his voice now. "And, Rei's mother."

"WHAT!"

The sound of three shocked voices was amplified by the cavernous expanse of the room.

"To be precise, Lilith provides part of Rei's DNA, with most of the rest coming from her human downer, Yui Ikari."

Shinji's legs bucked violently as he heard his mothers name, he found himself slowly edging away from Rei as if she was something unclean and demonic.

He didn't notice the single tear running down the side of her face.

"Why would you do something like this?", Misato had pulled her gun, though she wasn't certain whether to aim at the Commander or his pet Angel.

"Because, like I said we needed an appropriate ego border, and the only available at the time was Lilith. Rei is not merely born of Lilith, she holds within her a part of Lilith's soul, giving her a will that her sisters do not possess."

"Sisters?" Shinji asked feeling uneasy.

The images changed again. Now they were just Rei, or Rei's, over a dozen of them floating nude in LCL.

"Rei you see, is the core of the dummy plug system. The Autopilot we have developed for EVA. The clones are continuously updated during Rei's harmonics tests. Her clones also guarantee that Rei cannot die. She can be killed, but her memories are kept stored in the Magi for download into her sisters. And her soul will return to Lilith after death, making resurrection a simple process of re-distillation."

The way he spoke those words, he it sounded like he thought of Rei as a cheap beverage.

Asuka, Misato, and Shinji were now standing well away from Rei. In fact Shinji was edging his towards the door. He wanted, needed this to be some sick joke. No one was laughing.

The next words came from the least likely source. "Commander Ikari. Why did you tell them?"

"Because, Ms. Ayanami, Rei, as brutal as this is they need to know what you are. Or they might have reacted more violently to my appearance."

Shinji almost leapt from his skin as slim hands emerged from the shadow, turned him, and wrapped him in a tight embrace. He saw the azure hair on that head. It was Rei!

Yet he could still see Rei standing, and staring almost emotionlessly at the girl now hugging him so fiercely he thought his lungs were going to explode. Emotionlessly to anyone but him. To him she seemed, confused, shocked, and . . . perhaps . . . sad?

The girl loosened the hug and pushed Shinji's head up, pressing her own forehead against his, she studied his face, ran her hands down the sides of his head, feeling his shoulders and arms, and then holding his hands tight in a flurry of motion as if she was trying to size him up.

"Shinji, I know . . . I know you probably, don't remember me. And I'm sure you don't recognize me now." The voice was shaky and sad. 'What did you expect this to be easy?'

The voice was very much like Rei's though slightly louder and with a firmness that Rei did not possess. Something was so familiar about the way those eyes looked at him. This was one of Rei's clones, it had to be.

But those eyes, despite being red were not Rei's eyes.

And that face, despite being young and pretty, did not hold the innocence that he saw in Rei. It all looked so familiar. It suddenly drove home as impossible as it was like a pile driver.

"M-m-mother?" He asked uncertain.

She hugged him tight again, he could feel her shuddering slightly. She was crying, he draped his arms around her, but there was no strength left in them to tighten his grip.

"Shinji, Im so sorry Shinji, I never meant to be gone like that, I'm so sorry."

"How is this possible." Asuka whispered.

She had backed closest to Commander Ikari's desk, and her words were just within his ear shot. "The core of Unit 01 holds a soul just like all of the EVA's. To be precise, Yui's soul. She has been trapped inside of Unit 01 for nearly a decade."

"I remember", Shinji muttered sadly, he remembered his mother smiling before she had entered Unit 01's entry plug for the last time. And now, here she was right next to him, hugging him tight.

"So how did you get out of Unit 01?", it was again Misato. She didn't see how this all added up.

Yui pushed gently away from her son, "From what Ritsuko says, their was a glitch in Unit 01's dummy plug system, a one in a million hiccup during their testing and I was able to achieve a 400 synch with the dummy plug. My soul was transferred from EVA to the dummy clone in Unit 01's plug. It took me a while to get out of there, the plug design has changed quite a bit."

Shinji noticed now the bandages rapped tight on his mothers arms. "What happened?" He asked concerned.

Yui looked down at her arms. "Oh these. I got these getting out of Unit 01, just my own stupidity in the dark." She responded.

Shinji was too shocked to do anything but accept it at face value. His mother hugged him tight again, and despite her small frame, it somehow made him feel safe and protected.

When she looked into his face again Yui saw the haunted look in his eyes and traced it back to Rei. 'Damn, I guess we really didn't soften it up one bit. If anything this has made it worse. Maybe their isn't an easy way to explain it.' Yui decided she would have to just work with it as it was. "Ms. Ayanami", Yui spoke gently. Rei's head was hunched low, hiding her face, knuckled white, her nails digging into the palms of her hands.

Rei thought for a moment, 'Yui Ikari is the commanders wife, he seems to agree that this is Yui Ikari. The Commander seems to love his wife. So it would be appropriate for me to respond.'

"Yes Ma'am?"

"Come here"

"Yes Ma'am"

Shinji stiffened as Rei trudged up to him. He was still frightened and wanted to protest her proximity when his mother abruptly extended her hug, pulling Rei close to Shinji. He could feel her stiffen, then slowly melt into the hug. He could smell her, and feel her. Somehow he could feel that she was different, her body language was totally different from his mothers.

It made him a little uncomfortable. But his mother hugged him tighter, forcing him to stay. He didn't know what else to do. He just stood their, and accepted for this moment, that everything was ok.