Disclaimer: I do not own any part of Evangelion

Thanks go to my pre-readers Dennisud and Deacon Joe

Chapter 3: Discoveries

Gendo walked in through the main gates of NERV that morning like he had every morning for the past 10 years. He had come very close to losing his son and daughter yesterday and now Ritsuko said there was something wrong with Unit-00. The reason this bothered him so was the fact that she felt he needed to know about it right away.

He walked through the halls of NERV Headquarters, nodding a brief hello to the workers who passed him on his way to his office. As he approached the door to his office, the men outside it in black suits stiffened slightly. When he was but a step from walking into the door, it whooshed open and he walked inside, the door closing behind him. Inside, he was greeted by several scanned images of religious texts in their original arcane script. The images were being projected into space just before the walls, and were nearly as tall as he.

Walking over to one in particular, he began scanning lines of script, until he found one passage in particular:

"And the champion shall defeat the Twelfth, the sky shall rain blood, and the Beast within the champion shall reveal itself. The Beast shall stand in the sight of the Almighty, in the blood of the Twelfth, victorious."

Pondering the meaning of the text versus recent events, Gendo walked over to his desk and sat, hands before his face.

Shortly after sitting down, his desk beeped, announcing a visitor on the other side of his office door. Turning off the projections, he opened the door remotely, allowing Dr. Akagi entry.

"Doctor, you have something to report on the status of Unit-00?"

Dr. Akagi walked forward past the inscription of the Sephirothic System in the floor, and right up to Gendo's desk before beginning: "The special control systems we installed 2 months ago have disappeared."

"Explain."

"I can't at this time. We're still running scans to determine where they went, but from what readings we've gotten so far, it's as though the systems never existed in the first place."

"Is Unit-00 safe to use?"

"Normally, I would say no, but..."

"But, what Doctor?"

"It would seem that the overall design of the Unit is slightly different from what we have stored in the Magi. I can't begin to theorize on what effect those changes might have on the Unit's operation."

"Very well. Continue your analysis until you have reached a definite conclusion."

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Shinji sat at his desk that morning wondering how he had messed up so badly. After trying to cover up after freaking out when he was told that Asuka and he were going out, he had tried to explain that he just hadn't thought that it had been that long. Asuka had simply stormed off ahead of him without looking back. With Asuka almost breaking into a run in front of them, Shinji and Rei had had some time to talk more about what was happening to the world around them.

------------- Flashback -------------

"The Asuka I know would never have been acting like this."

"Commander Ikari and Major Katsuragi have not been acting normally either."

"How many people do you think have changed?"

"Possibly... everyone, except us."

"But wouldn't it make more sense that only we changed?"

"Explain."

"Well... What if the Angel did something to our minds? Like giving us false memories maybe... How would we know that this is the way things have always been?"

"That is possible."

"So what can we do about it?"

"I do not believe there is anything we can do."

-------------End Flashback-------------

When Shinji finally caught up to Asuka at the school, she hardly recognized his existence except to tell him to 'Buzz off.'

Lunch time arrived and the students all either got up to get their lunches from the cafeteria, walked out the door with their friends, lunches in hand, or just stayed in the classroom sleeping or talking and eating with friends.

Rei would usually just stay in the classroom, staring out the window, until the majority of the class left, before going to the cafeteria herself to buy her lunch then sit outside to eat. Today however, two other girls in her class came up to her, one looking rather impatient, the other curious.

"You coming with us or what Rei?"

"To do what?"

Hikari smiled, thinking Rei was joking: "To go eat lunch of course."

Rei turned back to the impatient redhead standing over her, "Are you not going to go eat with Shinji-kun?"

Asuka reared back as if Rei just slapped her across the face, but blushed all the same. "Why would I want to eat with that baka? The fool couldn't even remember how long it's been since we started going out."

Hikari looked thoughtful for a moment, then: "What did he say exactly?"

"What does it matter what he said? The fact that he didn't remember says everything."

"Just tell me." Hikari asked

"Fine. He kinda freaked out when I told him how long we've been dating, and then he tried to say something about not realizing it had been so long."

"And that's it?" Hikari prodded.

"Yeah, pretty much..."

Hikari looked thoughtful for a moment considering what her friend had told her, then: "Have you considered the possibility that he's enjoyed himself so much in your company that he really DIDN'T realize how long you two have been going out?"

Asuka was about to make a biting refusal about that when her friend's words finally sank in. When they had, she just closed her mouth and hung her head slightly.

"Didn't think so..." The Class Rep sighed and shook her head.

Asuka immediately glared at her friend: "What's THAT supposed to mean?"

Rei chose that moment to put her two cents in... "She is merely pointing out that more often than not, you are too selfish, haughty, and stubborn to realize others' feelings before your own."

Both other girls' jaws dropped at their friend's words as they just gaped at her.

"What?"

Normally, Shinji would've been awake and chatting with his friends over the local network, but today, he opted to sleep through class. When the lunch bell rang, he woke with a bit of a start, but calmed himself quickly. Mentally gathering the scattered bits of his mind, Shinji began rummaging through his backpack for the lunches he made earlier.

When he found them, he pulled out the three boxes. He didn't know if this new Asuka still had him make her lunches, but he figured he'd be better off if he made her one whether she wanted it or not. Looking around, he spotted Asuka, Hikari and Rei together, the two former girls staring open-mouthed at the third in some sort of shock as Rei looked questioningly at them.

He got up and walked over to them, figuring that this would be the best time to try to give the girls their lunches without getting beaten to a pulp for interrupting something.

"Um, Asuka? Rei? Here are your lunches if you want them..."

From the look of it, Asuka and Hikari were snapped out of their stares by the boy's interruption, but didn't seem to mind too much. Asuka seemed angry at first, but calmed enough at the prospect of food to not rip his throat out.

After getting their lunches, Asuka practically drug Hikari and Rei out of the classroom behind her attempting to get out of Shinji's presence as Rei thanked Shinji on her way out.

"Yo, Shinji!!! You gonna eat yer lunch or what?"

Even if the people in this world were different from the ones he remembered, he couldn't mistake that voice or tone for any other. Smiling, he realized that if he didn't get to eating his lunch soon, Touji would do it for him.

As he walked back to his desk, he saw that his two friends had set up around it and were munching away at their own lunches.

Without bothering to finish his mouthful, Touji asked the question that was on his mind: "So why's the wife mad at you Shinji?"

Shinji didn't quite catch the comment, but answered it anyway: "I don't know, I think I said something wrong on our way to school..."

After the bespectacled one finished his mouthful, he put his two cents in: "Huh... well it doesn't take much to piss her off to begin with though, so I wouldn't be surprised if it was something small."

"You're probably right... Still I think I should find a way to make it up to her..."

"Hmm... Hey, speaking of making things up to people, how are you going to apologize to Hikari for ogling 3-E's Geography teacher yesterday Touji?"

At this, Touji nearly choked on his food, but managed to swallow it before making his retort: "I don't know what you're talking about... I may have been checking her out, but I see no reason to make it up to Hikari."

Touji's friends' only response to this was to laugh.

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Later that afternoon, Shinji and Rei returned home to an empty house. Neither of them were unused to this, so they just went about their business.

However, seeing that this would be a prime opportunity to speak with Shinji about the changes in their friends and colleagues, Rei left her room and patiently made her way down the steps to the foyer and then continued to the kitchen where her 'brother' was working on his homework.

"I believe I have come to a decision about our situation, Ikari-kun."

Startled by her stealthy approach, Shinji jumped a little at her sudden voice, but soon managed to calm down enough to ask her what she meant...

"Um... I don't understand..."

"I believe that the changes in our surroundings are for the better as you observed earlier this morning."

Shinji laughed slightly at this... "Of course you would, Asuka doesn't hate your guts any more... Now both the old and the new Asuka's hate me..."

Rei cocked her head slightly, wondering if he really was as blind as he seemed, or if she was just more perceptive than him.

"I do not believe that Sohryu hates you Ikari-kun."

"And what makes you say that?"

"She seemed rather ashamed at lunch when Hikari-san and I confronted her about it."

This new piece of information hit Shinji like a ton of bricks... ... Well, maybe not a TON of bricks, he'd be dead if that were true, but definitely like he had been hit in the face with A brick...

"She... She did?"

"Yes, I believe she is beginning to feel sorry for not thinking before she reacted."

"Hmm... thanks Rei." Shinji said to his new sister.

"You are welcome... Shinji." And with one nod she turned and went back to her room.

In a rare moment of insight, Shinji realized what had just happened and smiled. Perhaps this little unexpected happening would have some good points after all...

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Later, Shinji had finished his homework, and was preparing dinner for the three of them, when his father came home, apparently exhausted from a full day of work.

"Heya, Shinji, is your sister home?"

"Yeah, why?"

"No reason, I was just wondering why you're cooking and not her."

This question made Shinji slightly nervous as the wrong answer could possibly give him and Rei away as not being the ones that everyone here knew so well...

"Um... she didn't feel like cooking tonight, so she told me how to make a few things..."

"Huh... alright, that's not very common for her, but I guess it's understandable." Shinji made a mental note to mention to Rei later that she's the main one to cook for the family.

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A leisurely dinner followed, after which, Shinji went up to his room to 'catch up on some reading.'

Shinji, after closing the door behind him, sat down on the bed, opened the drawer in the nightstand, and withdrew the journal he had found there the night before. Opening it, he laid back against the headboard of his bed, and began to flip through the pages until he found the first entry in the book that seemed to be about Asuka. He found it about halfway through the entries, and began to read it in earnest...

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Journal, April 12th, 2009

Today, dad was visited by some people from Germany. I don't really understand what they were talking about when they went to talk in the living-room, but they brought their daughter with them.

She has red hair like her mother, and her name is Asuka. She and Rei became quick friends, giggling as they played up in her room.

Later, she came into my room, wondering what I was doing all by myself. I told her that I liked being alone for a while, but she didn't believe me. She actually came over and drug me out of my bed and into Rei's room to play with them.

I had fun, more fun than I thought I'd have with girls, but I won't lie about it. I think I like this Asuka girl too. While we were playing, she said she'd be around while her parents were here on business, so we'd get to play together a lot.

Bye for now, Shinji Ikari

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'So, we've known each other since we were children...'

Shinji scouted forward through the entries until he found one that caught his eye.

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Journal, May 10th 2009

Asuka left today, I hope I'll get to see her again someday. I probably will since our parents seem to be friends.

Rei's really sad about losing her friend, but I think she'll get over it eventually. Dad was telling her that she'd see Asuka again soon, but I don't really think that it'll be soon. Probably not until we're older. At least that's what I think.

Bye for now, Shinji.

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The next few entries were few and far between before the mass of entries from just recently and didn't really say much of anything other than routine or mundane things.

Of course, they were mostly routine or mundane things that involved Asuka.

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Journal, July 17th 2015

She's back! I had started to think that she wasn't coming back. I'm glad she's here. I got to see her as she was being transported here from Germany on the USS 'Over the Rainbow'. Apparently, she's the Second Child I've heard so much about since I became the Third Child.

The trip wasn't all fun and games though, an Angel got the idea to attack the convoy we were traveling on. Asuka came up with her own idea to attack the Angel in Eva-02... while at sea! Anyway, I'm not going to get into details since I'd rather not remember them, as they're simply too embarrassing.

Rei was ecstatic when Asuka got back, apparently for good this time. They're out getting reacquainted right now, they invited me to go along, but I figured that they'd enjoy a girls' night out.

Besides, I'm sure we'll be seeing her a lot from now on.

See you, Shinji...

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'Wow... I never thought I'd hear myself be THAT happy about getting to spend time with Asuka...' Continuing through the journal entries, he reads about happenings during the most recent Angel attacks, and other happenings between them.

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Journal September 4th, 2015

We almost lost Asuka today, She was fighting the most recent angel inside Mount Asama. Anyway, in order to beat it, she had to tear part of her cooling pipes away and shove them into the angel's mouth. She managed to kill it, but her cable wasn't going to last long enough to get her back to the surface.

Misato ordered me to stay where I was because we couldn't afford to lose two Evas and two pilots. But I jumped in anyway... I couldn't afford to lose her, and I'd be damned if I was going to sit there and let her die. Misato chewed me out later for disobeying her orders, but after Asuka found me, I honestly don't remember much after she smothered me in a hug for what I did for her.

Except... I remember I asked her out at some point between then and now. I just hope I didn't get myself in over my head...

Bye, Shinji...

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'Hmm... so that's how this whole dating thing got going... Which reminds me...'

Pulling out a pad of paper and a pen, Shinji begins writing a letter to Asuka:

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To Asuka:

I know I messed up yesterday. I'm sorry that I forgot about how long we've been together. I know I hurt you very badly when I said that and I want to make it up to you.

I know this letter is short, and may not sound as sincere as it should, but I've never written a letter like this before. I've never felt I needed to.

If you feel you can let me try to make amends for what I've done, meet me on the roof of the school after classes end.

I'm sorry,

Shinji.

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With a sigh, Shinji put the pen down and folded up the letter. After a few quick glances around his room, he realized he had no envelopes to put the letter in. Shinji left his room and went downstairs to look for those ever-elusive envelopes.

After finding some which his letter would fit in, he took one, put the rest back, and headed back up to his room. Once there, Shinji neatly stuffed the letter into the envelope, sealed it, and wrote 'To Asuka' on the front of it.

Glancing at the clock, he saw that it was quite late. Before going to bed, he put the letter to Asuka in his backpack along with his laptop and other school supplies. He performed his 'Evening Ritual' and put the journal away before he turned off the lights and got into bed.

TBC...

-----Author's Notes-----

Oi... Even longer than last time... I won't say I'm sorry for this since I'm not. I do not live to write, and therefore, updates to my stories will happen whenever I have free time in which I feel like writing. And this last semester at college was arguably the most tedious and stressful one I've had there. As such, I didn't have much free time to start with, and the free time I did have was spent either sleeping, playing some form of computer game or RPG, or reading other fanfics.

Also, it didn't help that I wrote myself into a corner that I had the hardest time getting out of during that lunch scene. As I stated earlier, this fic already has a fairly well-developed storyline beyond this chapter, but if anyone has a suggestion for how this story could evolve, just send me an e-mail or include the suggestion in a review, and I'll try to get back to you if I'm thinking about using your suggestion to augment my timeline. And please, only serious suggestions... jokes and insults only annoy other readers who want to know what others think about this story and take up space in the reviews area.