Well, if you are here in America then happy thanksgiving. I figured I might as well post a new chapter for the day. Yeah, I tend to write the chapters with four thousand or more words so I apologize if it seems rather small. Also, this chapter can be considered a set up before I get into the story proper. Consider it the set up for the status quo moving forward.

Now as I usually do I like to thank the reviewers. So thank you rjcelona, S-01, Scattershot98, and Hellsink Bathhall for your feedback, thoughts, and questions. I also like to thank the readers along with those that favorited and/or followed the story.

Disclaimer: Neon Genesis Evangelion and Rebuild of Evangelion are the property of Gainix (?), Studio Khara and Hideaki Anno. I own nothing and please support the official release.

Ever since her rebirth from being killed Rei had felt a presence in the back of her mind. The blue haired girl couldn't explain it at first but soon she had found out why. That presence was the A.T. field of Lilith which she could feel thanks to her close connection to her. Naturally, this was a surprise to learn.

The bigger surprise was that she should actually have Lilith's soul so being able to communicate with her shouldn't be possible. Keeping this revelation to herself Rei soon learned why from her mother. Lilith had ripped out a part of her own soul in order to give them something to put within the clones. 'So, that means I am not what Commander Ikari wants me to be.'

To the outside observer, it appeared that she was all by herself sitting with just her thoughts. Really though this wasn't the case as someone was listening to her. "Your Commander kind of lied to you about a lot you know," Lilith while still too weak to talk for prolong periods felt that this was extremely important. As such she powered through the pain. "For instance, it wasn't him who created your clones but, his wife who I might add didn't actually love him anymore at the time she disappeared."

Any normal person would laugh. Especially if they knew Gendo whole plans. Lilith had an idea of it having just touched his soul once before during this time. The man was madly in love and wanted to be with his wife again. 'Then what is my purpose then?'

Rei should tell the commander about this but she wasn't so sure. "The plans of both the Commander and SEELE are based on misinformation and thanks to them Adam's spawn will be looking for me and him," Lilith was certain that Adam wasn't dead despite blowing up. If he was alive then naturally his children would seek him out and a means to wipe out her own. "I had fixed the patchwork of a body you currently inhabit making it actually healthy and eventually able to allow you to use your own abilities."

That was true as she didn't feel any pain from supposed defects. In fact, her LCL treatments didn't seem to do anything for her despite it being done to help heal her ailments. Ailments that were thanks to her being a clone hybrid. Lilith's action had done away with it even allowing her body to start developing things her previous body lacked. "I know what they are hoping to achieve and the disaster that it would become, their Human Instrumentality Project, as such I am hoping that you are the other two can stop it by breaking control to you three."

Rei looked up as her body showed a physical reaction to what was going on. There were two others like her? 'What do you mean?'

"The second and third children," Rei understood what she was talking about. There were two other children who could pilot the Eva's one of which she knew was in Germany and the other being Vendor's sons. "I managed, with a lot of effort, to turn them both into beings like you in order to make sure that there is no way for Third Impact to happen."

Continuing to look in front of her Rei processed this. 'What about the angels that we are supposed to be fighting?"

"They will still have to be defeated," SEELE very much had a limited understanding of the relationship between her and Adam. They did know that the two of them were of different seeds but they didn't quite understand it. "Both me and Adam represent different ideals that the First Ancestral Race once fought over and we weren't supposed to end up landing on the same world together."

The progenitor of humanity believed that the only reason Adam's spawn will be coming to her is that they will mistake her for him. If they manage to actually find and merge with the real Adam then they would be in trouble. While it was likely that his seed-ship was destroyed they would still be able to improvise a means to wipe out her children in order to inherit the planet. Their version of Third Impact was nothing short of the extinction and terraforming of the world to their ends. "The war will have to be fought and each one of them has to be killed."

The blue haired girl gave her a nod. She had to cut the conversation short as Gendo walked in. Today they were hoping for her to do her first harmonic test with Eva-0. The angels were for a few years from now but that didn't change the fact that NERV was to be ready for them. Several minutes later Rei was in her plug suit as she stood looking at the Eva that she was to pilot. Its metal coverings hid the fact it was actually made from Angel flesh. A fact, she remembered from her past clone.

Once she was inside she listened to the voice on the other side. The voice of Doctor Ritsuko Akagi the chief scientist of NERV. "Alright, we going to flood the LCL," Rei didn't react as the fluid filled the air around her. She knew better than anyone that it was breathable. "Alright, now let's get started."

As the test started Rei synchronization rate increased steadily. Inside it, however, she could felt vaguely aware of think. As soon as the sync started to pick up Rei's eyes shot out as she felt something around her. An unknown sensation started to boil up within her reacting to something that she didn't understand.

Outside looking over the computers Ritsuko started to notice the sudden anomalies. The scenes were going haywire as Eva-0 was starting to twitch and thrash around. Gendo looked at the actions in front of him before turning to Ritsuko. "What is going on?"

"I don't know nothing is responding to anything do!" Ritsuko had tried the emergency ejection but nothing was coming of it. "I'm cutting the power!"

Deep inside Eva-0 Rei opened her eyes as her suit started to tear apart. Behind her two wings shootout two pale white, opaque wings that looked almost like extensions of her own body before a the Rei let out a scream. Eva-0 stopped before turning off whatever happened that caused this ceasing as everyone moved into to remove a now unconscious Rei.

Lilith wasn't surprised when she felt Rei's awakening. What surprised her though was the fact that it had happened thanks to the harmonic test with Eva-0. The ancient being knew that it was made with Adam's flesh and forced in a soul from someone else. It was possible that the environment of combined with the synchronization it reacted with her physiology and awakened it. 'I guess she will need training in use it especially for the war ahead.'

This made her wonder about the second child and third child. Unlike Rei, their bodies were still developing into what they are to become. Lilith wondered if the same stimuli would trigger their own awaken or would it be something else? Stopping her train of thought she had to see if the effects of Rei's awakening had caused them any trouble.

Reaching out with her weakened A.T. field she did a sweep on the NERV headquarters. The scientists who deal with the Eva were looking into fixing any technical issues thinking something might have been off. Gendo the man Lilith was most concern about was taking this as a random event though he was going to keep his eye on it. 'At least she didn't sprout her wings in front of them.'

When they found Rei she was unconscious with her plug suit in shreds. Right now she was resting in the infirmary though if Lilith could tell it was more an aftershock from the sudden awakening. Her A.T. field had a low yet noticeable hum to it though it was hiding its true strength. Training her was going to be a huge hassle as she was certain that there was no place that Gendo wasn't going to monitor.

'Perhaps we could try theoretical training,' Lilith retracted her A.T. field as she felt herself grow tired. She has used up a lot of her strength and needed to rest for a moment.

Asuka spat out the toothpaste in her mouth as she looked at herself in the mirror. Staring back at her was her blue eyes which at a distance would seem normal to anyone. However, close up one would see that her pupils were oval shaped like that of a cat. The other difference was within her mouth. Her top pair of canines had lengthened over the years looking more like fangs than anything else, while the rest of her teeth seemed to sharpen as well.

These changes always stared back at her whenever she looked in the mirror. At first, they weren't all that noticeable and when they started to become so the personnel just chalked it up to side effects of Eva piloting. A few of them even commented that it made her look threatening.

For Asuka, these changes were barely an afterthought. The one pain was how sharp her 'fangs' and teeth were. She had actually managed to bite through any eating utensil she was given. Even metal forks and spoons were quick to break under them. It also made brushing them an utter hassle as they would cut off parts of the bristles if she wasn't careful.

Still, there were several benefits to them that she wasn't complaining. Though her other habits were things that the local doctors kept her monitored over after her first few tests. Thinking about it always allowed her. 'I mean so what if I was drinking the LCL fluid it was tasty and it's not like it was poison!'

Another thing that brought confusion was her inability to properly inject cooked meat. Whenever she did she had to fight the urge to throw up as her stomach couldn't take it. Raw meat was a completely different story as she not only could eat it without any side effects but she actually preferred it. The usual health issues were surprisingly missing. She had a mental chuckle at this. 'Guess I'm made of tougher stuff.'

She walked out and down the halls of NERVes German branch as she caught a few of the doctors having a conversation. "I am telling you this is all strange that she started developing like this are we sure we don't have another pilot for reference?"

"I don't believe so," The other doctor crossed her arms. NERV was disorganized at the best of times. At the worse, each branch was known to fight among itself. "Even then do you actually think they would hear their findings with us?"

Asuka crossed her arms as she looked at the two of them. It annoyed her that they were still caught up about her weird changes. "You know I can hear you!" The two of them were using English to talk to each other but Asuka understood what they were saying perfectly enough. "Verdammt, I get it already I act and look different!"

She didn't have time for this. It seemed like her changes are all that they talked about. So what they were the result of her piloting the Eva Unit? Asuka had made her choice long ago to continue even when they thought the effects were temporary. 'Honestly, it's not like any of this matters I'm not going to sport an extra limb or anything.'

The two doctors were left there as they watched her walk away. They both turned to each other as they looked at each other. Truth be told several things about her was starting to seem frightening to them. Besides the physical changes that could be seen it had appeared that she gained a degree of super strength. Finally, the last medical scan had picked up some kind of growth within her body. At first, everyone assumed cancer but that proved to be false when they tried looking for the signs.

She had grown a whole new organ. A completely new organ that seemingly served literally no purpose as far as they could tell. That didn't mean it wasn't vestigial or anything. By all accounts it could be doing something it's just they had no idea. "You know I'm actually scared she might try to bite out heads off," The female of the two paused at this. "And I mean that literally."

The other doctor turned to her with a raised eyebrow. "You are acting like she's some kind of monster."

"You don't think she is?"

"... No comment."

Shinji did not have the best of time after his mother died. His father abandoned him at a train station to be raised by his godparent. An old associate of his dad. A year later he noticed a change. His eyes had, something much to his confusion and that of the local doctors, developed Heterochromia. What else was neither of them were his old eye color. His right eye was a bright yellow while his left was a bright purple.

This didn't go unnoticed to the bullies at the school that he went too. This only got worse when his hair changed as well. No matter how he cut it the tips of it had turned into a bright grey color. They had spread a rumor that he had bleached it to look like even more of a freak.

The sound of the bell pulled him out of his thoughts as class was ending. Shinji picked up his books as everyone started to talk to each other about what they were hoping to do now that school was done. A few were talking about the possibility of heading off to play games, others to watch the latest movie, or just getting together. As Shinji walked out of the room he caught sight of the bullies who loved to bully him. He turned away hoping that they hadn't seen him. "Hey, Weird-eyes where do you think you are going?!"

Shinji stopped as he knew it was rather pointless to run. He had already tried and all that did was make it worse when they caught up to him. He turned to them as the stared at him with an intimidating look. "L-look I d-don't want a-any trouble."

A round of laughter escaped them at this. The leader of the trio placed his hand on his shoulder. "Really do does this mean that you wouldn't mind if we keep this then?"

One of the other two pulled out from their bag something that Shinji recognized. It was the bow to his mother's cello. Her cello was the only thing he had that belonged to her and he made sure to take care of it and everything that came with it. "H-how did you get th-that!?"

The shock and worry on his face were just what they had wanted to see. "We got it from your bag the other day figured it must have fallen in when you weren't looking," The one who held it in his hands pointed it at him. "I have to say this doesn't look like an actual bow how about we fix it for you?"

Shinji watched as the strong one of the group was handed the bow and before Shinji's very eyes broke it over his knee. The slippers of wood falling on the ground as Shinji looked at it his eyes fell on the now ruined piece of his mother's possession as they tossed it to the ground. "There much better don't you think Weird-eye?"

Shinji's mind looked on almost shutting down at this. For years he had put up with this. He had been bullied by them but never once had something like this happened. They had destroyed something his mother once owned. After a few seconds, he felt something snap in his mind. Before the knew it Shinji grabbed their leader and before everyone threw him into the lockers. Shock gripped them as they saw the dent the force of the impact had caused while Shinji looked over the bully leader.

No one moved as they just stared at him. The bully he threw into the lockers wasn't getting up as his body twitched in pain before them. As soon as he realized what he did Shinji froze in horror. 'What just came over me?'

Everyone who had seen this looked at him with fear. The remaining two bullies now cowered in fear at the act they had just witnessed him do to their friend. A few of the onlookers started to whisper to themselves. Shinji looked at his arms horrified at all of this. Finally, he couldn't take it and just ran out of the building.

Gendo sat in his office as he looked over everything. It was a year until the first of the Angels was destined to arrive. To years ago Rei had her incident with Eva-0 and since then they hadn't had another issue like the one from before. Rei was still making slow progress with her synchronization. After some thought, he had decided to let her wander off outside of the base and even was filling things for her to stay at her own place within the city. Under watch, of course, though he would allow her the privacy of her apartment.

Pulling out the reports he looked at the other things with his plan. His son Shinji was something he had put off for a while though with any luck things should turn out as he had hoped. "Did he start using contacts and hair dye?"

The image of his son's current appearance wasn't as he had pictured in his mind. Though his personality profile was, with a minor incident at his former school, as he had wanted it. 'Whatever weird quirks he picked up aside it seems that the scenario will play out as I hope.'

Placing it on the desk he looked at the report that the German branch gave him about their pilot. He suspected that a lot of it was hidden as was expected but it wasn't enough to know that everything was still as planned. 'I will just have to request that they transfer over then.'

Getting up from his desk he decided to take a walk across the headquarters. His first stop was to look at the Eva Units. More precisely he stopped to look the one housing the soul of his wife. It was fortunate that he had found all that she had been working on just after the incident. Now, thanks to SEELE he had the means to reunite with her.

Unknown to him someone was watching this. Rei looked at the commander almost feeling pity. The man had no idea how messed up Yui actually was due to her upbringing under SEELE. Lilith even dropped that by now whatever vestiges of a bond she once had with him was effectively gone on the part of her. Rei looked at the Eva-Unit herself as she thought about her relationship with the woman.

Yui was the one who had a huge hand in creating her body. Even using her DNA, and despite the alterations that came about due to Lilith's own, she had made sure she still looked like her. Rei could understand if someone thought that because of this that Yui was her mother or at least a parent. Knowing what she did, about how she had made her clones to fail and break apart, how her original intent was to be used as a cage for Lilith's soul, made her dismiss it.

If anyone was a parent to her it was the thing in the basement. The being who Gendo believed Rei housed the soul of. Gendo turned around and left without a word as Rei knew that he was probably going down below to talk with the crucified Lilith. A ritual that he did every few months.

Gendo stood looking at the crucified body of Lilith. Out of all the places in NERV, this one was ironically the most secure from eavesdropping from SEELE. Lilith was indisposed and seemly lifeless. As far as he knew he had Lilith walking around in the body of the clone that he had under his control.

"It's almost time for the Angels to come and with it, I only have to wait a year or two at most to be with Yui again," Gendo spoke to the giant in front of him almost like he was talking to someone.

The thing is while he was unknowingly doing so said someone couldn't speak back. Even then Lilith suspected that his reasons for talking to her was due to his declining mental health. Despite being an immediate threat should he ever find out about the truth Lilith couldn't help but pity him. 'You have no idea what has become of her and if you did I would suspect it would either crush you or doom us all.'

Gendo turned around placing his hand on his head as he rubbed his temples. "I just know my son will become such an annoyance to deal with when I call him in," Nevermind he will have to at some point get the second child to come to Tokyo-3. He couldn't have a wild card like that. "Still, hopefully, he'll be willing to help even if I have to force him too."

Unknown to him Lilith decided to take a look at what he had meant by that. If she could she would crush him with hands in a fit of motherly rage. He was going to purposely sabotage Rei training just before the day arrives in order to play on his son's feelings. 'Oh, you heartless son of a bitch I take back any pity I ever had for you!'

It was worse when she knew that Rei had to mentally suppress her ability to regenerate just to not arouse suspicion. His whole idea for manipulating his son was going to put her in needless pain. Gendo unaware of the killing intend coming off the rather enraged Lilith just went back to talking to himself. "I do wonder though if you are even aware of what I am telling you?" He adjusted his glasses at this. "Rei has shown no surprise or suspicious so I guess it's true that you're just a hollow shell."

'Oh, I am aware of what you are telling me and so will be my daughter,' Rei was good at not showing emotion. A fact which both helped her avoid suspicion but also scared Lilith quite a bit. Despite the awakening of her nature, Rei's soul was still so blank. 'You know it's actually a good thing that you abandoned your son I'm certain he would be a budding sociopath if he had you as a role model!'

As much as she would enjoy ripping him apart, and she was really starting to enjoy the thoughts of what she could do to him, he was needed. Fighting Adams spawn would be too much of a problem without the Evas and if they did find Adam then everything will die. Curse, SEELE and their need to poke at things that they shouldn't. "Well, It was nice talking to you Lilith and sorry for cutting this short but I have to get in contact with the committee."

He turned away to leave Lilith to the fate that he thought she was in. The ancient entity didn't react at all. No, she just saved everything he said for later. Both for Rei and hopefully for the other two children when the time comes.

Shinji looked around the strange dark and almost mist covered area. Confusion was in his face as he looked for any sign of why he was here and what was going on. A sound caught his attention as he looked around frantically for the source. Out of the darkness, he saw a pair an of glowing wings giving some illumination to the mist.

Shinji turned to it as an out like of something stared as him. Two glowing eyes stared back at him. One yellow and the other purple like his own. The creature they belonged too seemed to stare back into his own eyes before he got a look at the thing as it started to rise above him. His eyes widened as he looked at the gigantic creature before him. It opened its mouth and lunged right at him.

Shinji awoke with a fright as he shot up from his bed taking in deep breaths. As he slowly calmed himself down. His mind told him that it was just a dream and yet something about it felt so real. His mind replied the events over and over again as he felt a familiarity to the creature. "Was that me?"

It was the first question to enter his mind. For a second he dismissed it as utter nonsense yet, when he did he felt like he was lying to himself. 'No, none of this means anything it's just a dream.'

As we begin our story we'll have Rei already awakened and having to hide it. I also went with giving both Shinji and Asuka different mutation then just copying how hybrids usually looked in other fanfics I tend to have read. Oh, and what was Shinji dreaming about near the end? Well, it would be spoilers. Though I can confirm that each of the children have to hit a certain sync rate with their Eva's if they want to awaken their nature (though there are possibly other ways and Eva piloting is the first I revealed). Just don't expect the next to awaken next chapter or anything like that alright.

Cya all next chapter.