Today is January the first. Happy New Year everyone.

Thank you Scattershot98, hornofdesolation, and Guest 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.

Gendo just sat in his office as everyone at NERV scrambled in the aftermath of the surprised Angel attack. The Commander rolled his eyes at this. Everyone thought it was an attack and he had as well. 'It wasn't an attack so much as reunification with us unknowingly housing its target.'

When that thing had merged with his son he saw the truth. Being that close to it and being conscious had allowed him to see when it's A.T. field entered through him. Yui's writing on something stopping Second Impact was real. 'Lucifer…'

The name wasn't in the Dead Sea Scrolls anywhere. Sure, he knew where the name came from in terms of the beliefs of the world. A commonly used name for the devil. 'In the same book that calls Adam the father of humanity,' He wanted to laugh but much like SEELE, he figured it was due to mistranslations from primitive man. 'The old men probably know things they aren't telling me.'

As for his son now turned daughter, at least that how he was calling it, he didn't know what to feel. From what he was able to recall Lucifer soul had passed into him/her when they were conceived months after having hidden in his wife ever since the aftermath of stopping Adam. Considering she had healed her and allowed Yui to survive in the environmental aftermath he felt somewhat indebted to the off-world Progenitor. He winced as he thought about his wife.

Yui had made Asuka, and Rei as well, to prevent Third Impact. A way to ensure that Lilith didn't fall into SEELE's hands. She even knew that Eva-01 would be demanding a soul. Yui chose her own to also ensure that Eva-01 couldn't be used as a means to trigger Third Impact. She was beyond pissed that he was literally doing the opposite of what she wanted. 'Even if she wasn't all instrumentality will do is obliterate humanity.'

The strengths didn't cancel the flaws. No, they both canceled each other and on such a scale that eventually everyone ceases to be. There was no joining, no greater consciousness, nothing but a dead world and blank souls. Gendo couldn't take this anymore. In one moment everything he had done was revealed to be for nothing. If anything he was actually making things worse for him. "Damn it!"

He slammed his fist on his desk before letting out a sigh in defeat. His wife hated him, he was running her plans, and he was effectively going to commit the greatest crime in human history. Reaching under his desk he looked at the bottle of sake. 'I am going to need a lot more than just this.'

He popped the cork out and went to work on the bottle not even caring about his usual one shot only rule. After he had drunk the whole thing he looked up at the ceiling. "What now?"

Mari looked all around before turning to Kaworu. For a second she felt something like a rush of water passing through her body. "Did you feel that?"

Of course, he did. It was a Progenitor signal and one which was familiar to him. The killer of Adam had become whole. "It's her," Mari was looking at him confused before he turned back to her. "The being that killed Adam has reunited its soul with its body."

"Wait, you didn't tell me that something killed Adam," Come to think of it she didn't ask much about where they came from. All she knew was that Adam shouldn't have been awakened and that everything after it was just a side effect of some people poking something with a stick to see what will happen.

Might as well be a good as time as any to tell his new sister the origins of life on this any many others. "It wasn't relevant until now though seeing how we are on it I think it's best to tell you how life came to be on this world," Kaworu took a seat as they were both waiting at the docks. Unit 04 was being moved with them both being moved with it. "Billions of years ago there was once a species who were at the time the only sentient race in the galaxy, masters of biological, technological and metaphysical understanding this First Ancestral Race was soon torn apart by itself until they reached a state were extinction was enviable."

To Mari that sounded like the commonly used Precursor Race. An ancient species who laid the groundwork for life that followed them. "Let me guess they sent beings like Adam out to make life on other worlds?"

Kaworu had a nod. "There was fourteen half held the Seed of Life the other half had the Seed of Knowledge each was sent out to colonize there own world."

Kaworu pointed to the workers around them. The buildings and the machines. Creations of the Lilin. "The Seed of Knowledge is the ability to change the works to your will," He pointed towards the ship. "Normally, Lilin can only barely swim in the water and would be able to use it to move but with the Seed of Knowledge they will eventually overcome the obstacle through tests, trial, and error."

That did sum up human civilization to Mari. Always moving forward, creating, and testing in all forms. From basic tools to things like computers all thanks to a drive to make life better. "Those born of the Seeds of Life have the power to naturally adapt to their environment there is no need to build a boat when you can simply float over the water."

As he walked Mari followed. Kaworu was recalling from the information that Adam had concerning the Seeds. It was one of the things that didn't seem to fade with him from his previous self. "Those of Knowledge share a similar design and form with each other, weak and yet familiar to each other as to foster cooperation."

"And those with Life don't have similar forms," Mari was starting to get it. The Angels differing looks and appearances was due to their own nature.

"Yes, each one is a collective in itself not one of many," Kaworu looked back at her. "Though each has a cost for Knowledge comes strive as the drive to create gives each member ambition and with its conflict," Another thing that was true about humanity. A history of conflict, wars, ambitions, suffering. The same power that allowed them to do great things also destroys each other. "For Life the cost is stagnation, there is no need to grow together, no great desires, and only basic ambitions."

SEELE when they were told the difference via their scrolls incorrectly assumed that holding both would eliminate the weakness of each. For a moment Kaworu felt possessed as he spoke recounting something imprinted in Adams very soul. "Having both only leads to eventual ruin as the First Ancestral Race discovered all too late."

"Earth was never supposed to have them both on the same world wasn't it?" Mari didn't need to see to know that he was right. She had a hand over her stomach as she knew that within her the war could continue.

Kaworu placed a hand on her shoulder. He may have only lived among the Lilin for a few days but he could tell that they were nothing like he expected. "The progeny are supposed to be shaped by the Progenitor, the Lilin have grown without Lilith guidance, and you now have Adam's ability to make Angels," He turned to her as a smile formed on his face. "Perhaps there might be a chance of peace between the Lilin and the new Angels within you."

A moan escaped her lips as she was opened her eyes were greeted to the medical ward ceiling. The memories of what happened played in her mind. As soon as she saw Lucy out the corner of her eyes she became almost possessed by the desire to reunite. Her hand moved to her stomach were the hand had pieced and where the body had entered her.

A blush formed as Shinji was aware of the changes to him or rather her. First were her slender and curvy body and her chest. Her breasts were rather, developed for someone her age, even bigger than Rei and Asuka's. The next thing of note was her hair. Somehow it was way too long. It went past her knees for crying out loud. Getting out of bad she noticed her shapely legs causing her blush to deepen. That and a certain part of her to hardened. 'Wait why do I still have that?'

Shinji was reminded when Lucy had asked him how she, then he, felt about being a hermaphrodite. It seemed she was being serious as now here she was. Reaching down she decided to see what changed. 'I only have the meat stick and the feminine parts…' Though knowing what she was now that probably was just on the surface. 'What do I look like?'

Finding a reflective surface she was given her answer. Her appearance was similar to her mother's. Her hair had grown a bit lighter in shape and her irises were now a dark yellow like Lucy's had been. Raising her hand up she saw her fingernails tipped almost like claws. Tapping the metal they seemed to dig in and with a small swipe, a scratch formed. Shinji continued to look on in surprise before a voice caught her attention. "You're up."

Turning around Shinji was met with Rei who looked at her. The two stared looking at each other. Yui's words on Rei were still fresh in her mind. The girl was made with her mother's DNA. Yet, Yui only stabilized it enough so she didn't break apart leaving all the mutations. "Yeah," Shinji blinked at her soft feminine voice. 'I really am this aren't I?'

"You are like me and Asuka," Rei's words were more stating of fact than anything else. She was right after all.

"Kind of," Shinji looked at her as she felt herself want to pull her in. She could see what she assumed was Lilith in her place. Shinji could feel the love Lucifer had for her and the desire to kiss her.

Rei herself felt heat rising up in her. Staring at the now changed Third Child was being something up in her. It was like something within her was telling her to wrap her arms around Shinji. "Kind of?" The both of them were cut off when Asuka looked at the new Shinji. "I want answers."

The whole base was still in an uproar about the surprised Angel attack. At least that what they thought was one. The MAGI system couldn't figure out what had happened after the merge. The blood type was orange which meant that the system couldn't confirm it either way. "I believe we all do." Ritsuko voice caught them as she along with a group of Section 2 was behind her. "However, until we can concern what happened Shinji," She looked at the now turned girl. "Will, remain here to see if the contamination is a threat."

That did not sound like she was going to enjoy this. Both Rei and Asuka walked out as Ritsuko stared at the transformed girl. Gendo while currently in his office had given an order to call him when Shinji awoke he was currently suffering drunken effects. This left Ritsuko to look at the boy turned girl with a mix of suspicion and curiosity. Perhaps it was time for a few tests.

Genetically speaking Shinji was similar to Asuka and Rei. The Angels DNA having spliced itself perfectly into her body. Unlike a hypothetical infection, this seemed like the DNA was made for her. 'Gendo did say that that it was after it's soul.'

Her, Kozo and Gendo were the only ones besides Asuka and Rei to know if the exchange. Their Commander had let them in on the fact that Yui talked about a being stopping Second Impact in her notes. If that was indeed the being in question then what did that make the Third Child? 'A vessel like the First and Second.'

There were other changes to the body besides just her gender. The first was an S2 organ that unlike the last medical scans of the two Lilith vessels was active. This meant that Shinji should be able to use an A.T. field of an unknown strength level. The second was the internal structure of her reproductive organs. She had the basic structure of everything a girl her age should have but she also had some of the glands that a male would have. Her ovaries, slightly bigger than normal, seemed connected to them and to the masculine organ.

Looking through a microscope she was greeted with the appearance of sperm cells swimming around. Shinji was rather hesitant to give her a sample but after some mild cozying and s bit of a threat, she produced the sample. "She's a biological hermaphrodite."

Speaking of the girl in question seeing how she still had Shinji's brainwaves and showed no threat to her as they did the tests Ritsuko felt it was best to declare that she was safe. The only problem was now getting her new clothes. Her old ones were no longer suited for her. Currently, Shinji was wearing the girl's school uniform along with a pair of bra and panties that would fit her that they had on hand.

'Lucy are you there?' Silence was all that greeted her. Not once had the voice that been with her on and off across her whole life replied since she had awoke. 'Did she disappear?'

As she thought about this she looked at her long mane of hair. She could really use a haircut. "Well, Shinji the only thing that remains for you is to see if you can still synchronize with your Eva," Although that might not be a problem. If Asuka and Rei could do it then she could as well. "Now, when you leave this room you will not tell anyone who isn't already informed of how you transformed ok."

Shinji didn't need to be told twice. Everyone was still jumpy about an Angel getting into NERV. The official story was that the pilot had done something that allowed him to kill the Angel while being turned into a girl. Either out of relief or some strong convincing everyone seemed to just buy it. "Can I get some scissors first?"

Half an hour later Shinji threw her arms up in defeat. No matter how many times she cut it the hair would just grow back right before her eyes. At the very least the hair in front of her head remained in a bob cut. She looked at the mound of hair on the ground around her. "Fine, I'll just wear my hair long."

Ritsuko who was watching this made a note to burn the hair for later. Still, it was amazing to see an Angel's regeneration factor working in such a short time frame. "I'll see about getting you some extra time in the showers and a special comb to help get the LCL fluid out," Thinking about it she might as well get one for each of the pilots. "I'll have to make some adjustments but we do have a plug suit that might fit for you."

Yui looked at the two Evangelion Units before her. She hadn't tried to make contact with each soul within them. Know that she did know how perhaps she could change that. It beat just being alone to herself. Reaching out to Eva-02 she readied herself to see what state Kyoko was in. 'Hello?'

There was a moment of silence. Maybe she couldn't do it like she thought. As she was about to pull back she was finally given an answer. 'Yui is that you?'

The two stood in a dark room. A projection of what was happening caused by their souls. Kyoko looked at her friend before wrapping her arms around her. "It really is you I thought you had died."

In a way she did. Her body had been lost and now all she was is inside of Eva-01. "The experiment didn't kill me but Eva-01 took my soul."

Kyoko shuddered at this. Eva-02 had taken half of hers while the other half was tossed into it at a later time. At least she was whole again. "So, how are you speaking to me?" Kyoko stopped as she realized it had to be her son or rather the thing within her son. "You learned this from Lucifer?"

"Yes, it's a thing where I project a certain A.T. field to a person and talk to them in a sort of telepathy," The real thing was more complex but it basically was as she said. She looked at her old friend noticing how like her she didn't seem to age. Perhaps this is what souls generally are? "It was a surprise to learn that my son was like Asuka."

Kyoko gave Yui a serious look. There was one thing on her mind right now The weird blue haired girl that her daughter seemed to have a connection too. One that looked suspiciously like Yui. "Yui, does Asuka have a sister?" Yui was taken back by this. "I saw her that girl that looked like you."

"You saw Rei?" Yui had already had a conversation with her son about this. Especially concerning her lack of care for the girl that she made. "Yes, she is made from Lilith as well."

Kyoko could see that Yui was distress by this. She tried to reach out to her but Yui turned away. "Kyoko you know when I made Asuka for you I…"

Suddenly Yui was forced back into her body as a small surge of pain shot through her being. Apparently, she couldn't hold that for long without being drained in a sense. 'Kyoko, Asuka,' She paused as she thought of the girl that she had left to her husband. 'Rei I'm so sorry.'

Misato looked at Ritsuko as she stood in front of Eva-01. She had been rather worried about Shinji after seeing the now transformed girl in the hospital bed. When Asuka started to complain about being unable to speak to her Misato knew that Shinji was awake. "You're having Shinji do a synchronization test after what happened?!"

Ritsuko turned to her with a simple nod. "Of course, given Shinji's sudden change it best we see if she can still synchronize with Eva-0," The faux blonde turned her head to the side the girl in question finally walked up to them. "I mean look for yourself she fine."

Shinji was kind of having some trouble with her new plugsuit. True to Ritsuko word it did need some modifications as it was hastily made. Her waist felt rather tight and it did squeeze over her shoulders. It did, however, draw attention to her chest thanks to it being a lighter shade of purple over her breasts. "This is a bit tight around my shoulders and waist."

The scientist made note of this. A few changes were needed to be made for her but overall it fit. Misato looked at Shinji with worry on her face. Like nearly everyone she had known that the Angel had done something to him before it was defeated. "Shinji, I have to ask how are you dealing with you know."

Shinji shrugged her shoulders. It was strange how quickly she was just accepting her new change from male to female, or rather a female hermaphrodite. Although given that Lucy was visibly female herself that might have explained it. Whatever the case Shinji didn't feel all that different. "I've accepted it," She looked down at herself. "I mean I am kind of stick now being almost girl."

"Almost?" Ritsuko whispered into Misato's ear about a certain biological change. Misato had a slight tint of pink to her checks at this. "Oh, well that is something for whomever she gets with."

The girl in question really wished Misato wasn't here right now. Shinji knew that this could lead to a whole different bount of teasing. A few minutes later she was within the entry plug as the test began. Subconsciously she reached out wondering if her mother was here. No response came as Yui just looked at her turned on keeping a distance.

Watching from the computer screen Mays looked at the number with a frown. The boy now turned girl synchronization rate was down resting at just about fourth three percent. "Shinji's sync rate was almost at a hundred and now it's less than half that."

There were several factors for that. The mental changes from altering gender were the first one to come mind, followed by her genetic alterations, and perhaps even changes in Eva-01. 'Perhaps Yui is having s hard time seeing her as her son, we daughter.' Regardless as the test continued her score showed no sign of increasing. "Alright, Shinji that's enough."

At the very least it was possible for Shinji to pilot Eva-01. That was one of Ritsuko's biggest concerns. Misato looked as she got out of the entry plug with her whole hair practically dripping with the LCL fluid. "She's going to need a haircut."

"Already, tried it just grows back until it reaches its current length." Which reminds her she had to burn the pile. Although she did wonder with Misato was going to try and see if she could prove her wrong.

In a secure location, an 11 appeared on a computer screen. SEELE member Eleven as they were know. The computer was equipped with a one-way camera as the member of the very real secret society that controlled much of everything looked at the sleeping scientist. "Doctor Hawkins asleep I see."

The doctor in question awoke with a freight. Falling out of her seat she pulled herself back up. Annoyed by being brought out of her dream. "I don't know what time it is for you in Japan but its the middle of the night here in Iceland!" She really hated being assigned here. After Second Impact Iceland was rendered a wasteland by the global effects. It was official under the U.N. Which made it the perfect place for SEELE to store some of their secrets. "Wait, we are you calling me?"

"Your report, you believe you might have been able to pull information from the salvaged White Moon's systems?" She gave a nod as she turned over to the pieces that SEELE was able to get from the first expedition after Second Impact. On first glance, much of it seemed like rock and maybe some kind of strange bone like coral. In actuality, it was a kind of pseudo-biological machinery.

SEELE had been trying to get information out of it even as their focus turned else were. With the confirmation of an interloper and Tabris disappearing it became more paramount that they find out anything useful. "I believe so let me see," She hadn't tested this. 'No time like the present.' A few moments nothing happened. "Come on you stupid thing…" Finally, something came on the screen. "It works!"

SEELE Eleven couldn't show it but this news brought a smile to their face. Who knows what secrets could be found from this. "Very good Doctor continue your work and you will be rewarded handsomely."

Kaworu sighed as he stood onboard the deck of the aircraft carrier. They were leaving port in the morning. Heading for Tokyo-3 and NERV. His mind turned to what he had said to Mari. As Adam, he didn't think peace was possible. As Tabris he had seen that the Lilin were not as he thought, and as Kaworu he now believed that peace was possible. 'For that be achieved my children, my siblings, have to die.'

That was a rather sober thought but a necessary one. Adam had imparted on them the desire for war with the Lilin. It wasn't done out of malice or hatred but out of ignorance and out of the idea that it was enviable. 'I do hope that the other one won't kill us when we meet again.'

Now seeing how I haven't gotten any names I will be using Shinji for the time being. When I do have a name I will tell you all either in the story or via author notes. As for updates this month might be rather slow in that regards. I apologize to everyone. I also am looking to update my other stories.

Cya later next time everyone.