So, yeah I am making another story. I had thought about this one after rewatching the series (and the Rebuild Movies) and I figured why not make one. So after three days, this story came into being.

This story will be more of an "Ultimate Universe" of the franchise. If you don't know tropes it means I would be using things from different continuities (like the manga, Rebuild, etc.).

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.

Pain was the first conscious feeling that she felt in… 'How long was I out?' The last thing she remembered was a warning system blurring. Something about an impact and then she fell unconscious. 'Why… why can't I move?!' Panic filled her as she managed to open her eyes. 'I'm still wearing my mask.'

She saw something happening to her legs. Being cut apart by some weird machines piloted by something. Lilith tried to reach out with her A.T field. The weak field managed to just touch the beings within the machines. If she could her eyes would widen in surprise. It was something made by her. 'By the pit!' This was the worse thing she could wake up to. Her own children ripping her apart for some reason. "Why are you doing this?!"

Her attempt to scream with her A.T. field failed on deaf ears. She was too weak and furthermore their own A.T. fields were so weak to pick up anything. All she would succeed in doing would be to scare them. A feeling of desire through her mind at this. She was stuck like this or worse. "So, how goes the extraction process?

Her attention was pulled to two other figures walking up to the pool of her blood. Reaching out with her A.T. field she managed to catch enough of their language to at least understand what they were talking about. Reaching into the older of the group she managed to see flashes of what he knew. The first was something called Second Impact, and Adam. Lilith if she could, would be wide-eyed at the fact another Seed had landed on the world. A seed that they awoke and nearly destroyed the world!

'By the pit, don't they know the threat that they unleashed on themselves!?' This wasn't supposed to even happen. They each were sent out into the void of space for different targets. Each had a target that should have been light years from each other. Even on the off chance that it did happen, they had the means to ensure that both sides didn't kill each other. That was no longer an option. 'I have to be free it's the only chance my children have!'

Lilith tried to link with her Longinus. Whatever was happening to her she could break it with it. The progenitor to humanity felt nothing coming to her. The all-purpose tool wasn't flying to her hands. It was destroyed by the impact. Panic consumed her before she pulled herself together. Perhaps her children had figured it out themselves? What she saw caused more questions. 'They are using me to create things to fight Adam's spawn?'

It sounded so wrong and yet if this was the only option that they had then what could be done? If they did manage to find her Seed-ship and her then it was possible that they could pull it off. The ancient being was content on this. If the greater good demanded it then so be it. At least her children would have a fighting chance against Adam's.

The next few weeks after the harvest Lilith just spent trying to extend her A.T. field. Gathering her strength she was able to see through the eyes of those working in the slowly being constructed facility. From what she had learned caused her pause. They didn't seem to locate anything from her seed-ship but her. At least from what they had seen. Though they seemed to have an understanding of some of the theoretical framework for many things that she knew about.

What she did see was them working on something. The designs for what could be described as a mockery of what she once was. A tool to fight the Angels as they called them. For a time Lilith while disgusted at what they were doing was content with the thought of the greater good. At least until she discovered the truth. The woman Yui, obvious to it, had explained what they were actually planning.

Lilith couldn't believe how badly they misunderstood everything. First, they thought the Dead Sea Scrolls, a corrupted warning made by her ships computers, was a means to a path to ascension. A means to either turn them into a hive mind or something. 'What next are they planning to fuse me with Adam?'

Her bitter thoughts aside Lilith was pissed at all of this. She had thought it was an accident that they had to awaken Adam. Nope, it turned out they were crazy enough to actually do it. That just brought them to how they had hoped to accomplish everything. 'A hybrid?'

Yui was getting to work on using her makeup and Lilith's in hope of creating a means to control Lilith. As she had planned her husband would find them active them and begin a means to set in motion both a plan to get her back and SEELE's while she got to complete her own plan. Speaking of Yui her plan was to become a god. 'Is everyone here crazy?'

As for their plan to control her, it was terrifying. They were going to rip out a part of her soul and stuff it into the clone. Lilith knew that such a forceful thing could render the newborn soul blank. A doll as Yui was hoping. Rage built up into Lilith at this. Her gaze soon caught sight through her A.T. field of Yui child. 'They are planning for him and two other children to pilot their abominations.' An idea crossed the mind of the ancient being. A fiendish and dare she say it mischievous. 'Let's see how they feel if I give the keys to them instead?'

It was rather complex yet so simple in the end. Using their own plans against one another. The first thing to do was to find a person to influence. A few caught her eye but the one that she had planned was the current physician. With some taxing actions on her part, Lilith was able to gain control of her. When Yui's child came for a check-up Lilith now in control decided to do a little change in his check-up.

"Now, before you go I have something for you." The possessed physician walked over to a syringe with water and something else floating inside of it. As she held onto it Lilith let out a low pained groan.

Seriously if this was the pain with only a tiny bit then she was dreading what was to come later. Turning back Lilith in her bored body looked at the little boy. It was hard to think that he had no idea the kind of insanity he was going to be thrust into. For a moment Lilith hesitated to what she was going to do. Mentally reinforcing herself she looked at him. "Give me your arm."

Shinji looked a the syringe in her hand for a moment before handing her his arm. Taking it she injected the fluid into him. When she was done she tapped his shoulder. His body shivered for a second after this. "Thank you now how about I get you something for being a good boy?"

Lilith turned around as she looked through the treats the doctor had for him. The syringe contained a tiny bit of her angelic DNA. Pointless on its own but with the near insignificant bit of her soul she had managed to rip off and left into him that would change.

Already his soul was assimilating it into his own. The change in his A.T. field would cause the small DNA proteins to be copied and assimilated it as well. The effect would alter his DNA and physiology but in the end, he would become something of a hybrid. Nephilim was the name for it. "Here we are," She handed the young child a candy. "You know your future will be rather interesting."

Altering the genetic structure of one of the clones was a huge choir as she tried into the room storing the clones. Once she did she looked over the genetic makeup of each of them. A glare formed on her face due to how many errors and problems they each had. It was like they were made to be unstable. 'Who am I kidding, of course, they were made unstable.'

It was easier to control them if they were biologically unstable. She looked at each of the clones and their lists. "Rei?"

If she recalled Rei was one of two names that Yui was planning to call her child if Shinji had turned out to be a girl. Lilith looking over the genetic code hardened her gaze. These clones had enough genetic material to look like her physically. The rest was altered due to wild mutation or was from Lilith's. If anything she was more Rei mother then Yui. 'You know I never had a child before.'

True humanity was her children but that was in a figurative sense. Lilith got to work stabilizing the genome of the clones. She hit into a snag one it turned out that it would take a lot longer then she had liked. At best she could get only one of them to be fixed up. 'Rei I is too genetically damaged though Rei II was able to be fixed.'

Fixing the genes was rather difficult to do. The vast patchwork left several unstable genes. Nevermind the problem of Yui walking in on her. As luck would have it she was finished as the still-developing soulless clone was finished. "There we go all better now," She erased the records of what she did from the computers. With the way security was in this place, she had to make sure there was no trace to be found. Walking out of the room Lilith caught one last sight of the clones. 'You're a true hybrid.'

In hindsight, she should have looked up just how far they were to Germany from her home/prison. Still, her goal to subvert the plans for their first three children. Pushing back her pain she walked into the German branch with a single goal being repeated in her mind. She looked around as she pulled up the map.

'Let's see I should go down here…' She stopped as she saw Asuka sitting on one of the benches. That made things a lot easier though she had an idea as to why.

Her mother was insane. Driven so due to her broken soul. SEELE was hoping that she would eventually kill herself so they can stuff her into the Evangelion they planned for her to pilot. "Asuka Langley Soryu?"

She looked up at her. The girl seemed to give her a questioning look before she noticed her name tag. As she spoke Lilith was grateful for her A.T. field being able to translate for her. "Are you the new doctor for mom?"

The ancient being felt rather bad about what was going on with her mother. However, She knew she couldn't fix what had happened. That could only cause more problems if she tried. "No, I am actually here to serve as the new physician," Taking out the clipboard that she had in order to play the part. "I was actually looking for you for your schedule check-up."

Asuka didn't seem all that happy with that. Lilith didn't know why and she didn't have much in the way of time to figure it out. Asus still went along with some minor fuss. Taking out the syringe she had packed she turned to her. "Now please give me your arm," Asuka extended her arm too her as Lilith injected the fluid into her. "Done so what do you say to a treat?"

Lilith placed her hand on her shoulder as she passed the sliver of the soul that she had prepared for her. Asuka felt a jolt go through her spine. She chose to ignore this. "No thanks."

Lilith groaned as she returned to her body the strain being almost too much for her. She took the time to let herself recuperate. Unaware to her as she was regaining her strength that now was the time that Yui choose to be absorbed into Eva-01. Those setting off events leading to his father abandoning him and learning all that Yui was working on. A plan formed in his mind. One which while ironically following both SEELE and his late wife's at first glance would have his own goals, not in others interests.

Lilith after regaining her strength in the last week knew that soon they were going to extract her part of her soul. They had managed to jerry-rig a device to do so. Lilith's A.T. field burned unto her flesh as she reached into herself. Unlike with the other two, this fragment she was about to break off was much larger. Lilith nearly fainted but in the end, she succeeded and ripped out a fresh blank angel soul from her own. Nearly blank as Lilith managed to edge something into it. The names of the other two and her mother.

As she felt this new fragment leave her Lilith felt herself fall back into a dream-like state. If she could she would have a smile on her face. Her actions had hopefully done what was needed to prevent this insane plan from coming into being. With her eyes closed, she entered into unconsciousness as her dreams were nothing but a mix of colors.

Nothing changed until she was vaguely aware of something. A minor touch on her A.T. field. An image formed within her dreams. It was close to her, close enough that in her half-conscious state that she could reach out to it. "Who are you?"

Lilith paused as she realized ho this was. It was the soul she had created from her own. The first child or Rei as the humans had called her. "My name is Lilith."

"What are you?" The question was one that had given Lilith pause. She didn't expect this to happen but it seemed that she was able to communicate with Rei even though her soul should be diverging from the piece of her own.

After thinking about it for a moment she responded to the question. "I am your mother."

So, to keep track we have SEELE, Yui, Gendo, and Lilith all having their own plans for the war with the Angels. Each one of them having goals that run counter to each other. Oh, and I picked a more unfavorable interruption of Yui motives because I figured if she is the daughter of someone in SEELE then she should be more like them in the thought process. That and because it's rather common practice (from what I have seen) for her to be heroic.

As for what Lilith's actions did to the first three children. Well, first off the effects of the DNA injects warps each of their genes (both human and angel) so there no genetic similarities. In case you were thinking about it.

I will be seeing all next chapter.