Disclaimer- don't own it

A/N Thanks to all of my Readers and Reviewers. You guy's and gals rock

Shinji ZERO

Chapter 3

Shinji and Rei

Misato, Rei, and Kaoru followed Ritsuko into the bowls of Terminal Dogma. Their destination was a small lab which bore an odd resemblance to Rei's old apartment

"So what is it im suppose to find out Ritsuko"

"Would you like to tell her Rei, or do you want me to"

"I will tell her Doctor, Major until now you have not been allowed access to any files pertaining to me, which will now change. I was created years ago from the DNA from the 2nd angel and a human donor named Yui Ikari"

"What"

Misato couldn't believe what she was being told, Rei was a lab experiment

"Yes I know this must be hard but understand, I did not chose this, Commander Ikari ordered my creation"

Misato's expression was a cross or pure horror and total anger

"Does Shinji know any of this?"

"Yes I informed my brother last night"

"Brother"

"Yes, I carry approximately 50 percent of Yui Ikari's DNA. There for I am Shinji's half sister"

"The reasoning behind this was simple Misato" Ritsuko added

"We needed a core component for the dummy plug system"

She pointed to a set of double doors against the far wall

"In there are the last of the plug cores and your answers Misato"

Misato Rei and Kaoru followed Ritsuko into the large circular room, the Clone Room

'Ah the daughters of Lilith' Kaoru thought to him self

About an hour ago Unit 00 had been moved to the main holding area with Units 01 and 02. As Shinji slowly regained consciousness he at first thought it had all been a horrible nightmare. 'Thought to soon' the thought, realizing he was still in the restraints. However the feeling of a lukewarm liquid up to the level of his knees caused him to open his eyes.

In the main control room Maya was telling her fellow Bridge Bunnies Hyuuga and Shigeru about the day's events when Shigeru noticed that Unit 00 had powered back up

"Sir, power levels are rising in Unit 00"

Fuyutsuki, now the commander of Nerv, inquired

"Is it attempting to leave the cage?"

"No sir it's just standing there"

"good, 'im going down there, Major Katsuragi and Dr Akagi should return momentarily, tell them to meet me in Unit 00's cage"

"Um…yes sir"

Misato couldn't believe what she was being told. Nerv's every secret had been placed at her feet. Rei's origins, Instrumentality, Kaoru's revelation that HE was the 17th angel It was all to much

"So let me see if I understand this Nagisa, you're the 17th but because Adam was in Commander Ikari's hand he died with him so you're harmless now"

"It is as you describe it"

"I…I need to let this all settle in, after what happened to Shinji, and now all this"

Ritsuko nodded

"I know how you feel Misato, go home and get some rest, at least 5 hours. I'll call you if I need anything or anything happens"

"Alright, I just need to sort all of this out"

Misato quietly headed out of terminal dogma and headed for home, Ritsuko looked at Kaoru and Rei

"Rei you should go to, you need to rest as well"

"No thank you doctor, I will stay with my brother, is there any way you could arrange a synchronization test for me"

She thought for a moment

"Yes I think so, it shouldn't be so difficult. Why do you want to try Rei?"

"I wish to speak to my brother; this would be the most expedient way to do so"

Kaoru nodded

"Yes that is so, however I believe the second child may also benefit from such an undertaking"

Ritsuko tilted he head to the side

"How so"

"The light of Shinji's soul still glows brightly inside Unit 00, it along with his obvious affection for her could serve to aid her recovery form Arael's light"

The older woman nodded

"Yes that shouldn't be a problem, so what will you do now Kaoru or should I say Tabris"

"I will live as a lilum, with Adam destroyed our life source is ended. We angels of Adam will no longer live eternally; therefore when my day comes I shall pass along, as all lilum will in their time"

"Though you still have your abilities"

"Yes, they are a part of me that I can not be rid of"

Ritsuko nodded in acceptance of his answer

"Alright, we should head back to the bridge and prepare for the sync tests with Unit 00"

The three left for the bridge. Unexpectedly leaving Rei's sisters, who thanks to Tabris's presents now had souls of their own, a lot to think about.

Shinji stood in the cages, his new body, or Eva Unit 00. He looked out into the cages at the other Eva's. His mother in Eva 01 was still asleep, though he had talked to her a few times since the accident. Unit 02 however hadn't said a word to him, so he decided to make first contact.

"Umm…excuse me"

"Yes" she answered in a monotone voice which reminded Shinji of Rei.

"Umm…what's your name?"

"Why do you care?"

Shinji could tell she was depressed, he remembered what had happened to Asuka at the hands of the 15th angel. This person must have gone through something similar.

"I umm…just wanted to talk to you, my mom's asleep and I'm kinda…getting lonely"

She sighed

"Yeah I know the feeling, Yui and I talk sometimes but I never really get talk to anyone new"

"Well…I'm here now"

She brightened up a bit

"How did you get in there anyway?"

"My father, he tricked me and got me to test this damn thing"

"I know the feeling, my husband; well ex-husband did the same thing. I didn't even get to say good bye to my daughter"

"What's your name?"

"Kyoko Zeppelin Soryu"

"Soryu?"

The pair spoke long into the night about their lives and by the time he fell asleep again Shinji knew he had found someone who truly could understand him

The next day Ritsuko, Misato, Kaoru and Maya sat in the control room of the cages watching as the Technical staff prepared for Rei's sync test with Unit 00. She had originally had her reservations about the tests but all indications showed that Unit 00 was more than ready to sync with Rei. Her plug was lowered into place and locked into the Eva

"Ok Rei were now beginning synchronization"

"Yes doctor"

"Maya lock in connections 1 through 236"

Maya looked at her monitor as the connections locked into place

"Connections locked ready for final connections"

"Do it"

"All connections locked, Rei's sync now at 67.5"

Ritsuko nodded

"Rei how is it"

She sat back and smiled, something no one in the room had ever seen

"Very comfortable doctor"

She closed her eyes and concentrated her thoughts

Are you there brother?

R-Rei?

Yes brother I am here

Oh thank god, it's good to hear your voice

As it is to hear yours

Yeah

How are you

I'm fine actually; I've been talking to either mom or Kyoko so I'm not really lonely.

Dr Akagi and Major Katsuragi have been at HQ nearly every moment since your accident

I can hear them when they come into the cage; I just wish I could talk to them

They are working on a system using the communications system

Ok, umm rei

Yes brother

Would you mind if I try something

What is that brother?

I…want to see if your can talk to mother

Rei couldn't help but smile a bit

Of cause brother, I am curious, does she see me as her daughter

Yes, im going to try now ok

Yes brother

For a moment everything was quiet then rei heard a voice she didn't recognize

Are you their Rei?

She smiled again

Yes…mother

It's good to hear your voice finally

As it is to hear yours mother

Its sweet you're already calling me mother

I carry your genes, you are my mother therefore it is only reasonable for me to call you such

Thank you, when this is all over, if Naoko's girl can free us, mabe the three of us could try to be an actual family

I would like that

Ok, i'm going to go for the time being, goodbye my daughter

Goodbye for now mother

Rei relaxed until she heard Shinji again

I'm back little sister

That is the first time you have ever call me that

Oh umm…sorry

Do not apologize, I enjoy it

You're welcome

Shinji, Dr Akagi will soon attempt to see if Pilot Soryu can sync. Nagisa has informed her that you may be able to help her

I'll try but, how does he know

Kaoru Nagisa is the 17th angel

HE"S THE WHAT

Rei cringed

Do not shout brother, it hurts

I'm sorry rei, but Kaoru is the 17th angel

Yes, but he is harmless at this point

But how

I shall explain, In order to keep him under control the commander had the 1st angel placed into his body, when unit 01 destroyed him Tabris's goal was destroyed as well

Tabris

Pilot Nagisa that is his name

Shinji reflected on that for a moment

Tabris

Yes, now I must go so that the attempt with pilot Soryu may attempt to sync

Ok, bye sister

Be well brother

Rei opened her eyes, she was still smiling. Though it felt like longer the whole conversation took only a few moments

"Dr Akagi Shinji is ready for pilot Soryu"

Ritsuko tilted her head to the side

"You've been talking to him"

"Yes"

Misato butted in, worry resounded in her voice

"How is he Rei, is he ok"

"He is well; he has been spending time with our mother"

"Your mother"

"Yes, Yui Ikari"

As Ritsuko and her staff prepped Asuka for entry a group of girls walked through Terminal dogma toward the location known as Heavens Doors. Each of the 7 girls bore an extreme resemblance to Rei, though differences were starting to show. Differences like changing hair color, eye color, body shape and facial structure. With in a matter of days each would look unique.

They all walked up to the doors which slid open as their approach. Inside stood their objective, the crucified 2nd angel Lilith. The group of girls stopped at the edge of the LCL pool at the angel's feet

"Why are you here my daughters?"

The gentle voice of Lilith called; the girl at the front of the group stepped forward and spoke up

"Mother we require your aid"

"In what matter my child"

The brother of our sister Rei requires aid, he has become entrapped inside of the human construct called Evangelion, Unit 00"

"Tell me of this matter and we shall aid him"

The girl told Lilith of how Shinji came to be trapped inside of Unit 00. How his father had betrayed him to the machine and how Unit 01 had finished him. They also told her of Adam's fate and Tabris's new allegiance to his friend at which she seemed slightly pleased

"So Adam has been destroyed and his angel Tabris has placed his allegiance to my children, this is good"

From the LCL in front of the girls strode a young woman with long white flowing hair, brilliant red eyes, and pail but soft skin. She had a well developed body over which hung a simple white robe tied with a sash at the waist. It was Lilith in her human form. Each of the 7 girls hugged their mother. After which Lilith laid out her plan

"Now my children, we shall help your sister save her brother and the others trapped inside of Evangelion"

One of the girls asked

"How mother"

"Come closer my children and I shall tell you"

A/N Well that's chapter 3. What are the clones and Lilith planning you ask you'll have to read and find out in chapter 4.
Next chapter- Asuka's sync test with Unit 00
Will it help her come to terms with everything that has happened to her, or will it do more harm than good.

till then
later