Two days until Christmas. I have been writing this story a bit more lately. It's not to say I don't write for my others as I am still writing for them. So no worries to anyone who is worried.

Thank you knight7572, and Scattershot98 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.

Rei awoke and soon noticed her position with her sister. The two of them close together arms wrapped around the other. Taking a moment to look at her Rei could feel that Asuka was like her also sleeping in the nude. 'This feels comfy,' Was this how siblings normally slept together? Rei didn't know as she never had a family. She was told the reason for why she was born and her purpose in life. That was it she had nothing else. Until it turned out that she did have a family member. 'I don't want to get up from this spot.'

As Asuka slept something crossed her mind. A silly little thought that had little consequence to Rei. Moving closer the girl's lips touched Asuka's. The redhead still in a dream-like daze returned Rei's kiss. A blush came over Rei's face at this. 'I feel… warm.'

Asuka's eyes opened weakly before they shot open. Her mind was racing at what was happening. She was kissing Rei and Rei was kissing her. 'Why am I still kissing her?!'

Finally, after a good second, Rei pulled off of her as the ice blue haired girl stared into her eyes. "Morning." Asuka shot back dragging Rei with her as the two of them fell off the bed. Rei landing on top of her as Asuka felt her leg graze her sensitive area between her legs. "Is something wrong?"

'We are sisters and we were kissing!' Asuka wanted to yell out at her sibling. Those words never left her mouth. Instead, Asuka wanted to forget that this along with what had happened. "It's nothing," The memory of her dream returned to her. "Let's just get ready for school."

Shinji awoke within a room that he had no idea what it was. All around him was an almost ground like room. At least that was what the appearance looked like. He got up from a cross-like object and raised his purple clawed hand? 'I'm looking at another of Lucy's memories.'

Floating to her was the purple colored Spear of Longinus. Her Spear of Longinus having it's colored customized by her preference. It opened itself as Lucy tapped it on the floor letting it excess the Seed-ships scanners. "No way!" Excitement filled her voice as she immediately raced to the opening. Lucy flew out as she looked towards a river valley that the ship was currently passing by. "They actually did it!"

She jumped to the valley as her A.T. field moved outwards slowing her down as she floated over primitives fields and farming villages. The start of a civilization. "Wait are they?" Shinji soon saw himself, or rather Lucy, floating down as her size changed growing smaller along with her Spear of Longinus. "Are they all women?"

As soon as she had landed in front of a village Shinji was greeted with what looked like a race of women. The one change between them and the humans of earth seemed to be large wings and a long whip-like tail but otherwise, they didn't seem that different. "Actually, they are a race if hermaphrodites," Shinji turned as he saw Lucy next to him. "I was experimenting with the idea of having several species reproduce like many plants, being both genders, and well, in the end, my sentient turned out to be one of them."

The memory disappeared as Shinji stood with her in front of him. The two of them were then seating across from each other. It was reminiscent of when they first truly met one another. "Shinji I been thinking about it but perhaps I should begin teaching you how to use my abilities."

"Y-you mean I can use them?" Shinji didn't know what she could do but so far what he had seen via glimpses and the fact that she was able to match Adam, the being who caused Second Impact. If he could use that level of power then… He had no idea what he would even do.

Lucy held up her hands to stop him. She could figure what his train of thought was. "First, I did a few years and your current form can only form a minor A.T. defense and feel emotions nothing more," Although Lucy was amazed that they could do even that. "As for my full power, it's very likely that if my body assimilated yours would need time to return to full power."

Even if her body was fully healed she didn't expect it to be able to use her full power. The process of returning to a severely weakened state did mean it had to get used back to using the god-like powers she commanded. "So, I'll just be learning how to use them for when they come back?" That made him look at her confused. "Couldn't you just give me the information due to us being you know the same person?"

"Tried that," Lucy was surprised by how separate the two of them were despite being the same. It was like a wall of will and a sense of self-existence between them preventing them from merging together. "There something blocking that kind of imprint learning."

There went the easy way. Shinji shouldn't be surprised. Even if things did look somewhat up, meeting his mother after so long, his father actually showing something of an interest in him and having someone to talk too, there was always drawbacks. He had expected to wake up and be told he was crippled or something. "How am I going to learn anything?"

Lucy motioned to the world they were in. "I can make a simulation of it while we are here within the subconsciousness," She showed as Shinji felt pushed back by a suddenly appearing barrier. "This way you can learn how to use your abilities instead of having to rely on just practicing while you are awake."

Thinking about that was he asleep? The last thing he remembered while awake was the feeling of something closing on his windpipe. The Angel's wipes crushing on Eva-01's neck and via synchronized pain his own. "Am I unconscious from the Angel attack?"

"Yes, your body is currently resting in the infirmary," Lucy wondered if this was going to become a thing with him. Both the times he fought the Angels of Adam he ended up needing medical care. "We're going to need to get you some combat training as well can't have you always ending up in the infirmary after every battle." She didn't have to tell him twice.

As soon as he opened his eyes he was greeted to the ceiling of the infirmary. Just as Lucy had said. He wasn't all that familiar with it but still. Shinji turned his head over to the side seeing his SDAT player on the nightstand next to him. It was the one thing his father had given to him if just indirectly.

He looked at the thing as he played one of the tracks. Lucy had once commented about it being rather limited in terms of music. Why an ancient being made with the knowledge and power to shape worlds was complaining about his choice of music was anyone's guess. He sat listening to it for a few minutes before looking at the clock. "Ten thirty-four."

It looked like he had missed school. Given how long he had been out the first time he wondered how many days had past. Getting out of his hostile bed he found his clothes in a bag. A few minutes later after having changed, he walked out of the infirmary. As he walked he was met with Kozo. "I see you're awake," Shinji turned off his SDAT and pulled out his headphones as Kozo took notice of the music player. "Your father wanted to speak with you as soon as you were up."

Shinji figured it was probably about him making contact with his mother. Following the Sub-Commander to his father office, Shinji took note of the rather sparse looking place. The one thing that did catch his eye was the weird graph or was it a tree? Surprisingly enough he felt like he had seen it somewhere before. 'That looks familiar to me.'

'I think it might be something of a symbol used by the First Ancestral Race.' Lucy was having trouble recalling where she had seen it herself. Given her vast life occasionally the little things would pass her notice. 'I think it's supposed to represent a theoretical framework of reality or possibly something to do with us, Progenitors.'

The last one seemed like an impossibility given there was fourteen of them. Whatever it was Shinji and Lucy could figure it out later. They stopped in front of his father. "I see that you are awake," Gendo turned his head to Kozo. "Thank you for bringing him to me but I would like to talk to my son alone."

As soon as he left Gendo and Shinji just stared at each other. Neither spoke as they looked the other in the eye, or in Shinji's case, in his father's glasses. For a moment there was perfect silence between them. Gendo adjusted his glasses. "You know the truth about the Evangelions I take it?"

Shinji gave him a nod. It seemed he thought that his mother had told him about it. "They are actually organic and are similar to the Angels."

That made things a bit easier for Gendo. He didn't have to explain one of the biggest secrets within NERV to him. "I hope you haven't told or are planning to tell anyone about it."

Truth be told he figured most of the staff had known about it. Although given that he a pilot of one of these things wasn't allowed to know about it did say a lot. "I-I won't," He was going to have to act like had just found out about this instead of being informed via the voice in his hand. "H-how did she end up in it?"

Gendo let out a sigh as the painful memory returned. Shinji it seems forgot all about it. He won't blame him. "She performed the contact experiment, a test to see if it was possible to synchronize with it, and in the experiment, there was an accident and she was claimed by the Eva."

He already knew this. Lucy had warned her the consequences after all. 'So he abandoned me because of the experiment,' He figured that was what happened but looking at his father he could see that the memory stung him. 'I guess losing mom broke him.'

"Shinji what I am about to tell you can not leave this room between the two of us," Gendo gaze hardened under his glasses.

Rei stood with Asuka as the two of them walked into the mall. Her sister had dragged her here in order to get her a much-needed upgrade in her wardrobe. Asuka would have done it a few days ago but the Angel attack had happened and the mall had been closed in the aftermath until now. "Alright, do what your favorite color?"

Rei had no idea what color had to do with her picking out clothes. "I have no preference."

Asuka wasn't surprised by that. She wanted to be but given how her sister was she knew this was likely the case. This did offer them an opportunity to try out and see about what Rei would like. "Let's start with the color blue then."

Her sister didn't respond. She simply gave her a nod in confirmation. A few minutes later it seemed that blue was, if not Rei's favorite color, then the color she most liked to wear as her primary one. Asuka had handed out several dresses for her and each one Rei would try on. Eventually after several visits of a few stores, and a bit of trial and error Rei had with her a few simple dresses and a nightgown. "Here how about a sun hat?"

Rei looked at the thing in front of her before putting it on. She never really had a need to wear something like this. Although her skin was slightly irritated from the sun given her albino skin tone. It was never much of a health issue thanks to her DNA from Lilith but having something to help with it would be nice. "It's acceptable."

After paying for it the two of them walked out as Asuka turned to notice that Rei had opted to wear the sun hat instead of putting it into her bag. For a moment her mind turned to her dream last night. 'Human Instrumentality Project.'

Something about it just sounded wrong to her. She had no idea what it was but a feeling deep within her didn't like it. The problem was how she was going to ask Rei about it. About something, she shouldn't know? 'I could say that I got it from a dream?'

While at first, this idea seemed stupid. Asuka soon realized that it made a lot of sense actually. If Rei and her did each share a piece of the same soul and they already had shared dreams then, of course, it was possible. As the both of them walked out of the mall to a quiet parking lot Asuka turned to her with a plan in mind. "Hey, Rei last night I had a strange dream," Rei turned her head to her sister as Asuka continued on. "One thing about it that stuck with me was something called the Human Instrumentality Project."

Rei's mind raced on what to do. She wanted to ask how she heard of that. Yet, Her words about it being a strange dream and their connection did open the possibility that it was due to her seeing her own memories. Remembering the Commander's wishes Rei figured that this might be the best time to see about telling her sister.

'... Your father is a complete idiot.' Shinji could feel heavily restraint on Lucy's part. After hearing his father's plan Shinji did have to agree with her. His father had told him about the Human Instrumentality Project.

He explained that it was a plan to return humanity to a more simple existence while merging their souls in a way to have each one strength dissolve each one's weaknesses. Gendo was planning to use the project as a means to free Yui from her prison within Eva-01 and reunite her with them. Just hearing this made Lucy wonder how criminally insane was these idiots were. The Progenitor knew that such a thing wouldn't make humanity whole nor would it removed their flaws.

The merged thing would be nothing but a zero-sum. Each of the strengths and the weaknesses would cancel each other out. In the end, the actions would only create a crazy barely recognized remnant of humanity. What also enraged her was the fact there was only one being who could have done this. The being she loved, Lilith. 'Oh, and never mind what such a thing would do to us!'

Unlike humanity who would be driven into a nimble near blink state both Lucy and Shinji would be able to remain separate. That is if the power of their soul didn't drive humanity into a permanent state of insanity while they are forced to be stuck on a barrier would in a sea of primordial soup. If they manage to get back Lucy body and assimilate it or return to it then they would be the only living thing on a dead wasteland of organic sludge. Admittedly in that scenario, there was a chance that they could undo the damage but depending on how hard and long it took at best they would only be able to save a fraction of what was.

While Lucy was mad at learning at the idiocy of this plan. Shinji was highly concerned about what it meant not only for humanity but for Rei and Asuka. "S-so, you th-think that this is the only way to get her back?"

Gendo answered with a nod. For his part, Shinji managed to block out the numerous curses that Lucy was yelling right now. Some of which likely came from her world. "Yes, I do."

'Shinji,' Lucy's voice was calm. A sort of calm that would unnerve anyone. 'We are going to tell Asuka about this.'

That caught Shinji's attention. It just seemed rather sudden that Lucy wanted him to tell the redhead about all of this. 'Why Asuka?'

Lucy, if she could, would be glaring at Gendo. The ancient being just knew what he had done. 'Shinji, only Lilith can perform this Instrumentality and I know for a fact that she wouldn't go for it,' Shinji wasn't liking where this was going. 'However, Lilith now has two other personalities connected to her in a similar fashion to us and while one of them is well adjusted and understanding of humanity, the other one has most likely been mentally conditioned by your father.'

Now he understood what Lucy was getting at. Rei was a piece of Lilith's soul. If she returned to Lilith then there was the possibility that she would take control and do what Gendo wanted. Asuka being the other piece of Lilith was the best chance they had at preventing that from happening. Still, the fact that Gendo had effectively been treating Rei like a tool was kissing him off. Especially, given he was likely going to try it on Asuka as well. 'I never knew I could hate my father even more than I do now.'

Gendo pulled out a NERV ID card that had his name on it. On it was his new rank as a Flight Lieutenant. Making Shinji effectively the highest rank Eva pilot. "Besides you and me only Doctor Akagi, and our Sub-Commander know about this," He handed him the card. "Do not talk to anyone but them about it."

"Yes father," Shinji answered as he pocketed the card. He knew that his father was likely omitting a large part of what was actually going on. Lucy pointed out part of it that his plan needed Rei and Asuka. 'Lucy, who do you think would want to do such a thing like Instrumentality to the world?'

The idea of some secret society popped into Lucy's mind. She had seen several such things happen before. Groups working from behind the scenes in order to control anything from cities to whole nations. It would make sense that one could have found clues either after Second Impact or perhaps even before it. Thinking about it the later seemed a bit terrifying.

Asuka couldn't believe it. Rei had told her a brief summary of what Human Instrumentality was. The returning of Lilithian life back to a primordial state. The merging of souls so that the strengths of each would remove their weaknesses. As soon as she had finished Asuka felt the urge to yell about how crazy it sounded. For some reason, Asuka felt that this wouldn't happen as Rei had explained it.

She kept quiet as Rei explained that it was her reason to be alive. A little voice within her head, a feeling that Asuka had within her, told the redhead that this was a lie. Only now that they were back in the apartment did she understand why Lilith had appeared in her dreams. This whole plan had to be the Third Impact that her mother's friend was talking about. The plan to use Lilith to permanently change the world. 'And my sister is being conditioned to accept it as her purpose?'

That didn't sit well one bit with the redhead. Rei shouldn't be treated as a mere tool. She was ok with the possibility of dying when all this was done. She clenched his fists as her mind turned to Gendo as rage boiled within her. "It's all his doing that bastard!"

"Who's doing?" She turned around to see Shinji. The son of the man she was currently angry at.

Shinji flinched under her gaze as her sclera seemed to turn black when she looked at him. "Your father," Asuka narrowed her eyes as she walked up to him. "Tell me do you know what your dad has planned for my little sister and me?"

Inwardly Shinji wondered if she was talking about Human Instrumentality. On one hand that did make this easier for him. On the other, the look she was giving him was terrifying. Shinji you were going to have to tell her anyway.'

While Lucy was true that he did come to tell her about it. Although looking at her glare made him want to rethink this plan. Feeling a nonexistent pat on the back from Lucy he figured he might as well do it now instead of later. That might just piss her off more. "Y-you m-mean Instrumentality," Asuka's gaze hardened as Shinji held his arms up at this. "Wait my dad only told me about it because I managed to contact my mother's soul with Eva-01," He started to panic at the end a bit. "His plan completely insane!"

Asuka paused as her anger give way to a questioning look. Did he just say that Eva-01, the giant robot that he piloted, had his mother's soul? 'Why would he say that about a giant robot…' Her mind put it together after a few moments. Robots didn't need to be put inside an organic fluid when in storage. They also didn't need to have certain people be able to pilot it. Furthermore, a robot shouldn't be able to replicate some of the things an Angel could do organically. 'But if it's not a complete robot.'

Her eyes widened before she realized her mother was talking about the problems of growing the Evangelions. It made a terrifying amount of sense. The reason the Evangelions could fight and win against the Angels was that they were made from Angels themselves. "You're mother's soul is in Eva-01?" Asuka froze up as the implication that this created cross her mind. Why she had been chosen to pilot Eva-02. 'Gott, bitte sag es mir nicht.'

Was that why her mother was so broken? Did that mean that Eva-02 housed her soul? Asuka shook her head pushing these thoughts out of her mind. She had to focus as the two of them had a lot to talk about. The revelation of the Evangelions being partly organic could wait. "You and me have a lot to talk about."

Yui was again bored out of her mind. Being locked within the body of an Evangelion with no way to move or do really anything, Yui had grown used to the feeling. Her first thought was to take a nap and sleep until a synchronization test. At least until she discovered something weird by accident.

She could project a weak A.T. field. Likely thanks in part to the S2 organ powering the Eva. Remembering how Lucy had used their A.T. field Yui tried to replicate the feat. She failed several times when trying to talk to Eva-00. At least that's what she thought. 'Maybe I am just doing something incorrectly?'

She almost wondered if she could use her A.T. field to talk to anyone. Yui knew that the Evangelion to the left of her was Eva-02. She had seen its pilot when they brought Eva-01 back to base. The girl that she made for her friend. 'Kyoko,' She did say that she was going to complete the first of the production models. A finalized creation intended to be used as the bases for Evangelions going forward. 'I'm sorry that this all happened to you and Asuka.'

As she continued to wonder what her old friend was thinking Gendo walked into the room. For a moment Yui debated if she should move her arm and crush him in her hand. With the S2 organ and a lot of concentration, it was possible for her to move her arm reach out at him. That is if she wasn't heavily restrained. 'I know the precaution is due to the S2 organ that Eva-01 is developing, but I can't help but feel like you did this so I can't crush you.'

Gendo looked on at the Evangelion. He was certain that his wife, well legally still his wife even though Yui wanted to not even think of herself as such, had taken notice of his appearance. "I told our son about my plan to save you," That and give him command over his fellow pilots. "He seems to be onboard with it."

'I highly doubt that,' Yui was certain that Lucy had already told him how stupid it was. It's more likely he was just faking it.

The Supreme Commander of NERV turned his attention over to Eva-02. He had occasionally been told by what little reports that the first production model as it was called would be perfect for the upcoming war. Yet, he knew it was just boasting done by the German branch. They had no intention of bringing it here until he basically took it. 'Perhaps I can see if there was some truth to Kyoko's words.'

You know even when Gendo is still somewhat not a total asshole I can't help but make things worse for him. Is that mean of me? Right, of course, not. I chose to not write an explanation from both Rei and Gendo on Instrumentality because you all very likely know what it is already and plus it would be repetitive. Speaking of which SEELE is not foolish enough to use one or two routes in their plan. I mean they now have three more ways to do it. If you can guess all three (excluding using Eva-01) then I'll give a shout oout to you next chapter.

Cya all next time.