Disclaimer: still don't own anything.

Author's note: I know this is going slow but bare with me I don't like to post things if I don't feel that they are done. Yes I know Kaji is supposed to be dead, and I know that Nerv is the one that is supposed to kill him and that it is highly unlikely that he would just be walking around Nerv without a care in the world. That will all be explained later.

Chapter 2 About time.

Two Months later.

Fuyutski was pondering his next move and decided to move his knight.

" Not much going on lately huh Ikari"

Pawn. " It seems so, there is no scenario now"

Rook. " Then what will Nerv be used for?"

Bishop takes knight. " What it was originally planned for, a combat unit under the control of the UN."

Pawn takes pawn. " Is that wise?"

Knight. " The old men are lost and there is no use for the instrumentality project. It failed and is being cancelled"

Bishop takes knight. " That will surely anger Seele"

Queen takes bishop. " Yes and they will surely attack in retaliation" he looked up with a smirk "Checkmate"

" Indeed"

Across town in a classroom sat Rei staring out a window as usual when her laptop beeped at her.

And how is our precious Shinji today?

Annoyed she just ignored the message. Her computer beeped again.

Hey Wondergirl don't ignore me!

This time she decided to answer. What do you want Pilot Sohryu she always called her by her professional title because she felt that there was no feeling of friendship between her and the second.

Oh did I get the commanders doll wound up. I want to know why you keep going to see that idiot. 'Doll' Rei hated being called that.

That is of no concern to you. With that she shut her laptop.

Toji was leaning back listening to the teacher for a change however his usual speech did not. He was droning on about something involving the years after the 2nd impact when Toji heard a chair scoot back. It was Asuka " may I be excused?" she blurted out. Before the teacher could answer she was gone. Toji saw the address of the message Asuka was typing before she shut it off. 'Hmm...'

Beep. Annoyed Rei opened her laptop once again.

So what did the red headed devil want

Do not concern yourself with it Mr. Suzahara

Toji was dumbfounded. How did you know it was me?

You and Aida are the only ones that call her that and Aida is asleep

Toji turned around to see that Rei was right. ' Weird she didn't even turn around. Hmm...'

It's about Shinji isn't it? No answer.

You do have a thing for him don't you?

Once again Rei shut her laptop. ' I knew it' Toji thought with a smile.

"How's Asuka doing?" Misato was standing in the observation room over looking the synch test plugs.

" She is doing quite well" Ritsuko turned to Maya " increase the depth"

" Yes Ma'am" Maya sounded

" She is fully capable of piloting and her synch tests are improving ever since her reinstatement" Ritsuko said with optimism.

"..."

' She's not going to ask about Rei?' she frowned at this thought ' I bet she hasn't even read her medical test file' " That's enough testing for one day you two are released" Misato turned and walked out immediately.

"Bout time" Asuka blurted

Rei just quietly exited her plug and returned to the dressing room where Asuka was already dressing. They both dressed in silence. Rei was buttoning her shirt when she felt a presence behind her. She turned around to see a very angry German.

" Look Wondergirl nobody ignores me, when I ask you a question you answer it"

" The question was of no concern to you..." *THUD* her wind left her lungs when Asuka's fist slammed into her stomach. Asuka then reached back and slapped her to the ground where she then kicked her in the stomach.

" I'LL TELL YOU WHEN IT IS OF MY CONCERN! You just do what you are told understand!" Asuka then turned and stormed out.

With yelps of pain Rei sat up clutching her stomach. She now felt lost and alone she needed to see someone, and that person was Ikari. He would help her understand. She collected herself and wiped her tears, she was once again ready for the outside world.

Misato was on her way to see how Shinji was doing. For the last month she had been avoiding Kaji not being able to think straight about him. ' How did he come back he was supposed to be dead' the last word stuck in her mind causing her some discomfort. 'Just like my father' she dwelled on her thoughts not noticing the new passenger on board the elevator. ' I got to snap out of ...'

" Why have you been avoiding me?" the question was simple but it threw Misato's mind into a frenzy.

" Major?" the long bit a silence caused Rei to question whether or not Misato had heard her at all.

" Because I don't know what you are" came a soft reply

The answer confused Rei. "Rei Ayanami the designated pil..."

"That's Bullshit!" Misato exploded. This scared Rei into backing up against the door. Misato in turn closed the distance and slammed her fist right next to Rei's head. Rei was now very scared.

" Your not Rei Ayanami the designated pilot of shit! You're just a damned monster, an angel! Just a fucking angel!"

"But..." tears were starting to form under Rei's eyes.

"Shut up! I don't want to hear it from a fucking doll! Its because of you my father is dead, it's because of you so many people died, you are the cause of Shinji's condition! All you are is a fucking doll that people can use, something for Gendo's sick game! You do anything you're ordered to! You probably kill Shinji if ordered to!"

*SLAP*

Rei's hand was shaking after she struck Misato across the face. Barely audible whimpers escaped her mouth and tears were threatening to fall. The elevator stopped and Rei rushed out past a surprised Dr. Akagi.

"Rei! What's wrong?" She turned back to see a very guilty looking Misato Katsuragi. "What did you do Major Katsuragi?" The last two words had venom to it. All Misato Could do was look at the ground with guilt.

"I see. Well this could not come at a worst time" Misato looked up with a questioning look. " Oh you didn't know? Oh that's right you have been avoiding her this entire time. Well maybe it's time to act like a fucking adult instead of a beaten dog!" she shoved a file into Misato's gut and instructed her to read; she complied.

Date: 12 August 2016

Subject: Rei Ayanami

Results: We have found that the Subject has been having a period. This is in result of a newly found uterus in place of the S2 engine that was there before. In further test it has been confirmed that all Angel DNA that was originally used in Rei III's original genetic makeup has reverted to human DNA. In affect Rei cannot project her AT field nor can she regenerate. Her synch ability with the obsolete dummy system has also been degraded to an unusable degree. Her piloting skills however have not been affected.

Conclusion: Ayanami is no longer classified as level two material and has been reclassified as Rei Ayanami employee of Nerv and Evangelion Pilot. Her birth date has been entered into the database as 07 December 2001.

Signed

Dr. Ritsuko Akagi

Misato now felt more guilt for what she just said. Ritsuko stood there with a look of disappointment and disgust when her phone rang.

"Hello.... yes sir" she hung up. " The commander wishes to speak with you"

Rei ran down the hall and into Shinji's room. She sat against the floor with her back against his bed. 'They all hate me. The second, the major, all of them...' Her knees were pulled up with her arms across them. ' Even Ikari-kun' Rei began to cry freely now. On top of the bed a young boy began to stir.

Misato stood unnerved in front of the commanders. She knew she was in trouble but just how much she could not say. The commander sat with an opposing glare aimed directly at her.

" Major Katsuragi what is your position here at Nerv?" he coldly said

She flinched. "Operations officer of Nerv..."

"And caretaker of the pilots" he interrupted "is that correct?"

"Yes..."

" Then how do you explain your recent actions towards the first child?" She didn't answer.

" These actions are absolutely unacceptable and will not be tolerated is that understood?"

" Yes sir..."

" If these actions do occur you do know you will be dismissed from your duties..." she nodded "...permanently"

The none to subtle hint didn't faze her. " Yes sir"

"What are you going to do about this situation major?" the sub-commander asked.

Misato stood and thought for a short while. ' I need to show Rei that I don't hate her but what' it was then that she remembered something that Shinji said about Rei's living conditions. "I propose that the first child be moved into my apartment"

The commander's eyebrow quirked. " And this is to accomplish...?"

"To show her that my actions were not called for and that I ...did not mean ...it"

'This will help her with her current dilemma' Gendo thought " the necessary actions have commenced and remodeling of your apartment will take place shortly...and Major just what game am I playing anyways?

Misato's eyes grew wide. ' Did I say that?'

"Yes you did say that" Gendo knew what she was thinking. He smiled to himself. " I know what you know. The project was a failure, everything is being either salvaged or scrapped. We will now report as a combat unit and only as a combat unit to the UN directly. Everything you think is happening is no more do you understand?" she nodded. "Dismissed"

"Yes sir" with that she turned and left.

After the door closed Misato let her breath out which she was unconsciously holding. "Wow... I hate it in there" she heard some snickering ahead of her. She looked up to see a smiling Dr. Akagi. Her eyes narrowed "what are you laughing at?" she barked.

"Hey calm down I hate it in there too" Misato eyes just narrowed more " Ok look something happened and you nor I know what. All the projects are useless or destroyed there is no instrumentality anymore. It failed"

"That's what the commander said" anger still audible " I still don't trust this"

" Look that's over with now...friends?"

The major studied the doctor scrupulously then stuck her tongue out at her.

Ritsuko chuckled "ok then..." She thought for a bit "What are you going to tell Asuka?"

Misato's eyes grew very wide.

Inside the office a rather angered Gendo Ikari stood over-looking the Eva cages.

" New reports regarding the second branch" the professor said effectively getting the fuming Ikari's attention.

" Complete loss there is nothing of use that can be salvaged" he continued

" Anything on its whereabouts this entire time?"

" One of the investigating team was quoted in saying that it " Been to hell and back" further investigation on our part shows that that remark isn't far off from the truth"

" What is the Eva's progress?"

"Unit-00 is behind schedule do to failures in the organic reconstruction of the head, Dr. Akagi's team has been working rather hard on its reconstruction"

" Give them the day off tomorrow"

" Huh?!?!"

" You heard me, tomorrow will be a minimally manned day"

"What brought this on?"

" The Third just woke up we do not need everyone studying him, just the essential people"

" Yes sir. You going to go...?"

"No" he interrupted then paused."... too many people"

The old teacher smiled. "Of course"

Shinji was trying to make shapes out through the mushy haze. He could hear soft crying but he couldn't locate where it was coming from. He looked up and saw a ceiling that was becoming all too familiar.

" I hate that ceiling" all at once the crying stopped. 'Where the hell...?' he sat up and looked around to try and locate the source.

' Hmm...' He heard a door open then saw a young blue haired girl leaving in a hurry " Hey wait ... Ayanami!" she stopped "where you going?"

Rei turned and faced him, her neutral impression like a rock was ever present. " To inform the medical staff of your condition" she lied.

'She's lying' Shinji thought. He didn't know how he knew he just did. " Umm...ok I just thought...." he trailed off as he lay back in his bed

Rei's turned and walked back to Shinji's bed. "Are you feeling well?"

"Yes... how long have I been sleeping..." then something struck him " oh my God the fight, is everyone alright? Misato, Nerv, Asuka!" he sprung up fast and Rei put her hands on his shoulders to try and calm him.

"Everyone is fine. Nerv suffered no damage and all personnel were accounted for, and you have been sleeping for four months," Rei calmly informed.

" Oh thank God" he relaxed slightly then looked up at Rei, she was looking down blushing slightly. "What's wrong?"

" You really should stop doing that Ikari" confused Shinji followed her eyes and noticed that he wasn't exactly covered.

"AYE!!" he scrambled quickly to cover himself. " Sorry"

" No apologies necessary" her blush deepened as she turned to leave " I'll go inform the staff of your condition" 'He needs to stop doing that'

"Thank you"

Rei stopped dead in her tracks " for what?" she softly said

" For being ...here"

If she was facing him he could see her mask completely break for a few moments. She composed herself and, while blushing deeply, she left.

'I'm such a pervert' he thought as he awaited the inevitable barrage of questions, doctors, and well-wishers.

Author's Notes: No comment.