Here it is another chapter. Yeah, took me a bit to get it finished. I do hope you like it.

Thank you knight7572, emotheextremo, 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.

There was life on this world. Basic algae-like plants and something looking like insects but nothing else. A scan from the moon with the object in her hands was all that was needed to prove that it wasn't like them. This wasn't the world that she had landed on. Three years flying through the void and already five failures. Taking off again it continued to search even if it was coming to the end of the expansion zone.

A year later as it was about to give up as it reached the edge of the zone. Until it picked up the broken mess of a radio wave. Decayed heavily from the background radiation of space it was the first sign of life. Sentient life the rarest form in the galaxy. Following the signal in a years time, it passed by a primitive probe flying off from a yellow star. Hope began to fill it as this could finally be where it was searching for.

When it landed on the moon it looked out and saw a world teeming with life. The lights of cities could be seen from the night side of the planet. Holding up its spear it had to confirm it. It's or rather her voice was heard as a feminine tone escaped her mouth. "Yes!" Excitement filled her at this. "Black Seed-ship confirmed!"

It pointed the spear as it waited for communications to be set up. After a full hour passed its expression turned sour. Something wasn't right. That was when it saw the skies darkening and the wings if light shooting out from the south pole. Its eyes widened at the spear confirmed the activation of a White Seed-ship Terraforming device. "Two seeds landed on the same planet?!"

Wasting no time she jumped off the moon and headed for the south pole.

Shinji opened his eyes again as he realized that the train had stopped. He held onto the letter from his father. On it was just one simple sentence was written. Come to Tokyo-3. That was it more than a decade and only now did he actually want to speak to him. 'Talk about a terrible parent.'

The fourteen-year-old boy looked around for a moment before he realized it was just that voice in his head. Ever since he started having these dreams he has been hearing it. A feminine voice that spoke within his head. After a while, he just stopped worrying about why he had it. 'I've been hearing it a lot more lately.'

At this rate, he might just be going crazy. Given he was going to his father who left him with his uncle after a decade in hopes of getting something close to parental approval, despite every rational part of him saying it was impossible, he might as well be. After wondering for a few minutes he overheard the sounds of emergency. Planes flew overhead as Shinji was left questioning why.

'Is it an invasion?' The Second Impact Wars while having been done for over a decade still left a tense situation. Shinji couldn't think of anyone who would be attacking. Maybe it was just a test in case of war.

Walking to a pay phone Shinji put in a call to his father. 'You know he likely not to call you if this is an emergency.' The voice was back and it seemed to state what he was thinking. 'Assuming he actually does care about you at all.'

The automatic messaging system came on informing him that they couldn't forward the call. It was just like

Putting the phone back Shinji pulled out the envelope that came with his letter. Someone named Misato Katsuragi. Shinji looked at the photo of her with an arrow pointing to her rather generous amount of cleavage. 'You know she is rather beautiful,' Shinji had a blush after hearing the feminine voice within his head say that. 'If only your gender wasn't as is.'

He decided to ignore it as he continued to look out wondering where everyone was before hearing the sounds of explosions and artillery fire. In one of the buildings, he saw the reflection of a huge monster from the many windows. "Wh-what the hell?!"

'So, they are starting to awake.' It's official he was crazy as he had no idea what it meant. Before he could take off and run he had to jump out if the way as a car came racing to him before opening the door to the front passenger seat.

"Sorry I'm late," The woman driving the car removed her sunglasses revealing that it was Misato. "Now get in!"

Gendo looked as the Japanese Strategic Self Defense Force, and the U.N. both took their chance to defeat the Angel. Fifteen years since Second Impact broke the world. Yui wrote about them coming in her notes. 'The war begins just as you said.'

Looking at the footage it was almost painful to watch. Everything they threw at the creature was just deflected by its A.T. field. The look on the military leaders was amusing all things considered. They had dismissed him and told him that they would take care of the Angel. He had told them so. "Damn it!" The leader of the Japanese forces was getting frustrated at the seemingly hopeless situation. "Screw it drop the N2 now!"

The other two commanders, both from the U.N. force, looked at him for a moment before coming to an agreement. The planes moved out of the way and the military forces pulled back as a rocket carrying the strongest weapon in the JSSDF arsenal was sent at the Angel. A massive explosion lite up the screen. It seemed that the weapon had done the trick. "Yes!" The celebration was cut short as when the feed returned it showed the Angel still standing.

"The Angel's A.T. field has extended itself the damage it sustained is regenerating." A small smirk formed on Gendo's face at this. The fools were told that they couldn't defeat the Angel.

Gendo just watched as the Commander tried to see if they could do anything. After being shot down for his last crazy idea. Now it was time for him to take control of a situation as he should have. "Gentlemen I believe that my case has been made," The three of them turned to him as he adjusted his glasses. "You can not take out the Angel without my forces."

A sigh escaped the JSSDF Commander. He had rather not allow an organization with no government oversight, and a lot of freedom from its U.N. oversight, deal with these things. Yet, they didn't have a choice. One of the U.N. representatives decided to speak up. "Very well if NERV can prove that it can then you will have sole authority for any future incidents."

The three of them saw themselves out. No further words were exchanged as Gendo continued to look at the Angel. "We are down a pilot you know," He turned to his Sub-Commander and former teacher Kozo Fuyutsuki. "Rei is too injured to pilot if you recall."

"I know and that is why Misato is getting our new pilot." Gendo returned to looking at the Angel.

"Oh yes, your son Shinji." It had been a long time since he had seen the boy. Kozo was always curious as to why he had left him with his brother.

At that moment Gendo recalled the promise that he gave his wife. A promise that he had failed to keep. For a moment he wondered how he could make amends to her and for him. 'Perhaps I could order Rei to be with him?'

Almost getting hit by an N2 explosion was not something Shinji had expected to ever happen to him. Then came learning about the real case of Second Impact. Surprisingly enough when he read it he felt like he had both known it but also that the report was terribly lacking in understanding. 'At least the terraforming process was stopped before the worse could happen.'

'I know it must be going crazy because there is no way that I should believe that.' Thing is he had a feeling that all the voice had said was true. That the first Angel was attempting to terraform the world and failed but still caused Second Impact.

Misato stopped the car and turned to him. "Well, are you excited to see what your dad been working on?"

If he was honest he was still mad that he just left him. Sure he knew he was working on something but beyond that, his Uncle had no idea what. Shinji spoke almost a whisper as he figured that his father just wanted something from him. "Not really."

Having not heard him, or not heard what he said, Misato didn't comment on it. Instead, she pulled out a map of NERV which was given to her. The voice within Shinji's head was quick to pick it up. 'I am guessing that she is new here and has gotten lost several times before.'

That wasn't reassuring. Though looking at the map over her shoulder he could tell that the place was rather big and seemed to be built like a maze within the Geofront. 'How did something like this even get built?'

'By digging out part of an ancient spaceship that crashed into the planet.' That sounded like a plot for a sci-fi franchise. Once again though he knew it as fact.

After wondering for a few minutes Misato led him to a room which had a large purple robot. Shinji looked at the thing as for a moment he recalled seeing something like it. A blueprint for a thing looking just like it. Followed by several giant corpses huddled together in a graveyard. The voice in his head spoke with a rather sober tone. 'So, she actually did it giving up her own life over anyone else's.' Shinji felt like he didn't want to know what the voice was talking about.

"I see you didn't get lost this time," Misato turned as the head scientist of NERV, Ritsuko Akagi. She looked at Shinji noticing the similarities he had to Gendo. "So, this is the Commander's son the Third Child."

Shinji wondered why he was being called Third Child. Was this the reason that his father had decided to call him back? "He is," Speak of the devil and he will appear. Shinji turned to see his father walking up to him. "It's been a long time Shinji."

For more than a decade Shinji hadn't seen his father. Even now he didn't know what to feel as he looked at the man in front of him. In the end, he just spoke with mild annoyance. "Father."

Gendo adjusted his glasses as he looked at Eva-01. His wife was if her writings to be believed still vaguely aware of what was going on. Hopefully, he could convince Shinji to pilot Eva-01. "I will be brief I need you to pilot the giant robot."

His dad called him here after more than a decade in order to pilot a giant robot. He called his fourteen-year-old son to probably fight some monster within a giant robot. 'Actually, it's fitted around an organic center so it would be more accurate to call it a cyborg.'

He was going to figure out how the voice knew all of this. If it even was a voice that is. "You called me here just so that I would pilot your robot and fight that thing out there?" Shinji didn't know why he expected anything less from him. "Forget it I'm not piloting that thing!"

There wasn't a change in expression on Gendo's face. He knew that his son was likely to harbor anger at him. If he was being honest Gendo believed it was rather justified. Sadly he didn't have time to explain himself to his son. He turned over to Kozo. "Get Rei it looks like my son refuses to pilot."

Kozo seemed hesitant for just a moment before nodding. Misato looked at Gendo like he was crazy. Ritsuko had to make sure she heard that right. Shinji was confused until he saw Kozo wheeling in an injured girl on a hospital bed. 'He can't seriously be thinking of letting her pilot the robo-cyborg in her condition.'

Rei opened her unmanaged eye as Gendo walked over to her. This was deceitful, and while he could just have her soul put into another clone body, he rather not go through with that right now. "Two my son is useless I need you to pilot Eva-01."

The girl didn't complain and just gave a weak nod before trying to get out of her hospital bed. She immediately fell out and was caught by Shinji before she could hit the ground. She stared at him with her one eye while Shinji looked at her. A sense of familiarity came over him as suddenly both he and the voice spoke in his mind at the same time. 'Lilith.'

For a moment no words were said as Shinji picked her up and placed her back on the hospital bed. Turning to his father he gave him a cold look. Gendo looked back as he almost for a moment swear that his son's eyes turned a dark yellow. "I'll pilot but you haven't to promise me that you won't do that to her ever again."

That worked a lot better then he had expected. Although Gendo could have sworn Shinji's voice near the end had started to sound feminine. 'It's probably nothing.' He adjusted his glasses before turning to Ritsuko. "Get Eva-01 ready for launch we have our pilot."

Gendo watched the recording again before once again realizing that he messed up when it came to Shinji. The first half of it was simply the Angel just toying with the untrained pilot. Then to both his shock and the Angels Eva-01 began to beat down on the Angel rather savagely. Gendo winced as he had a terrible feeling that Eva-01 was picturing him. 'I just realized my wife is currently able to crush me in her hands.'

When this all ends he is going to be in so much trouble. At least there was nothing physically wrong with Shinji this time. He made a note to get his son some training with a gun and self-defense. If this happens again he would only be digging himself deeper. Not like he wasn't already in a lot of crap as is with her.

With the video over there then came the issue of what to do about Shinji's living arrangements. Gendo kind of lived at the base as it is. Forcing Shinji to live here was out of the question. Misato had an apartment with two spare rooms. 'Ritsuko commented that she did live in a mess of an apartment.'

It was better than putting him in the one building that NERV owned above on the surface. Only Rei's room was even close to liveable and that was taking a very loose term of the word liveable. Even he is not dumb enough to realize that doing so would enrage Yui further. So left with these options he chose the lesser of three evils. The door to his office opened up as Kozo walked in with several old files and a dairy. "You know I went and retrieved the old designs that Kyoko had for Eva-00 at Ritsuko request and I stumbled on Kyoko's old diary before she had transferred over to the German branch."

His wife's old friend and colleague. Kyoko was possibly the only one, besides him, that he could see Yui telling about the notes that she had. For a moment he wandered back to the removed pages in his wife's journal. 'What are the odds that it is in her diary?' Slim but if there was a chance he might as well take it. "I'll see to it that it gets delivered to her daughter."

Kozo gave him a nod before handing the diary over along with the key. As soon as his Sub-Commander was gone he unlocked the diary and looked through the pages. A violation of the privacy of Kyoko that it was he had to see if it was there. Finally, he landed on the pages he was looking for. After reading it he closed the diary and looked at the image of his wife on his desk. 'You had a proof of concept for Rei it seems.'

On one hand, it seemed like this complicated things. Rei was needed to return to Lilith in order to cause Third Impact as he envisioned it. Finding out that his wife made another vessel for part of Lilith's soul meant that plan would have to be thrown out the window. 'Or perhaps not,' Depending on how he went about this he might be able to get both of them to perform Third Impact though how that would go about he was still unsure. 'Asuka Langley Soryu.'

He was going to to get her sent here as soon as possible. Gendo couldn't risk SEELE figuring out that his wife had done. He almost wondered how Rei would react to all of this. If the writings are to be believed then he wondered how she would react to meeting her half-sister.

Shinji saw himself in a dark room with a light appearing over him. For a moment he wondered how he got here and where here even was. "You are within your soul," The feminine voice from before was heard yet again as Shinji saw a chair. "Well, actually our soul."

In front of the chair was a woman. Her skin was purple her hair was both dark grey and light blue each on one side of her head. Her eyes had black sclera, dark yellow with cat-like pupils. A third eye rest on her forehead with yellow sclera and purple iris, and a red pupil. Out of her back were two large demonic wings. She wasn't wearing any clothes but it wasn't like it was hiding anything. She had almost the same anatomy as a doll. Still, her body was drop dead amazing with ample breasts almost the size of Misato's and a figure that was one most models would kill for.

Pushing away his teenage thoughts. Shinji caught sight of her fingernails which were more like claws as she motioned him to the seat in front of her. When she opened her mouth Shinji could see that in place of canines she instead had fangs. "Take a seat and I'll explain everything."

He stared at the being in front of him for a few moments before taking the seat. This was just so weird as he felt like he knew her and what is even stranger he felt like he was her. "Who…" He looked at the demonic looking lady, "Wh-what are you?"

The lady in front of him just looked at his confused expression before rolling her eyes. "As said before I am you or well if you want I am your past life, other self, and soul among other things," Around them the darkness gave way to show a broken purple figure touching his injured mother. "I transferred my soul after fighting the Seed of Life that ended up on your world in hopes of surviving while my body entered into an emergency healing state," Next showed Shinji being born. "When you were convinced you ended up becoming the vessel for my soul," She stopped and looked at him. "Well, now our soul."

Shinji looked at the woman or rather himself as the scene around them just turned into a star sky. She was supposed to be him? He paused as he realized where the voice in his head was coming from. "So, I'm some kind of what?" She called him a vessel for her soul so does that mean he wasn't a person. "An empty shell just to house you?

"No that is your body," She showed him, himself only with an emotionless look about him. "It is a shell to hold us," It was waved away from the two of them. "You are apart of me a separate personality within the realm of my soul as such if you want to get technical you can say you are and I are two parts of a greater whole."

Silence came over them as Shinji disgusted what he had just learned. The being in front of him was himself. That made him question if he should consider himself a boy? "Where did you come from?"

The lady stopped wondering how to explain this to him. She could easily fill him with the knowledge but he wasn't that developed for it yet. As he was apart of herself she would rather not destroy him and damage herself. "Let me explain while using a tale," With a snap, they saw themselves in the galaxy. "Billions of years ago fourteen seeds were sent out into the galaxy by an ancient species known as the First Ancestral Race," Before them were fourteen orbs seven white and seven black. "Half of these were known as the Seeds of Life and the other half the Seeds of Knowledge, each one representing a fraction and philosophy of the First Ancestral Race," The seeds were then scattered around as Shinji watched them landing on world after world. "Each one had the tools to turn whole worlds into paradises of life and civilizations in a time where life was rare in the galaxy and even now complex life is a rarity."

Shinji watched as from each one the barren world was changed. He noticed that the worlds were the black seeds landed became similar to his own. Though the life forms did look strange and somewhat alien he could at least make out what they were when compared to animals and planets on earth. The worlds were the white ones landed were utterly alien. Strange crystals, floating gases housed in rocks, and honeycomb-like things were just some of the more mild creatures.

Two of the seeds, one black and the other white, continued to float before they both landed on a world together. The world soon turned into the earth as it is Post-Second Impact. "There was only one thing no world was allowed to have both seeds as just like it had done before with the First Ancestral Race," The image of the Angel long with military troops fighting it appeared before them. "The two would clash and the world would be driven into war at best and at worse," A dead planet was shown before Shinji.

All of this was true. Somehow he knew that this was all real and that he had once taken part in it. The dream of him staring out on a newly formed planet. A question arose on how they fit into all of this. "Alright, so what does this all have to do with you?"

"Oh, that's easy see me and the others like are God-like entities meant to both create the life on these new worlds, teach them, and a whole lot of other things," The images ceased as they were within the dark room with just the two of them seated across from each other. "I am a Seed of Knowledge much like Lilith the progenitor of humanity."

With everything said Shinji was starting to get an idea on everything. That thing that had attacked Tokyo-3 and that he had fought. It was from the Seed of Life the thing that caused Second Impact. The voice in his head was of a Seed of Knowledge that had fought it and was his soul. "Wait, what is your name?"

The lady in front of him actually looked surprised by this. Perhaps she had expected him to just know her name given he was her and she was him. Maybe it was an effect of him being a separate personality. She had a embarrass look on her face at this. "Oh, I guess I just assumed you knew my bad," She pointed at herself as she gave him a wink. "My name is Lucifer, but you can call me Lucy."

Shinji as a lesbian female Progenitor Angel within his head and as his soul. I am just going to add that issue on top of you know all the ones he is feeling right now. Also, the foreshadowing is out and I want to hear how you feel about my take on the new dynamic that the pilots will have. I think I just did something unique.

Cya all next time.