Disclaimer- don't own it

A/N Rei will be a bit OOC in this story, but that's because I'm still using Rei 2 and not Rei 3. Sorry the last chapter was kinda rushed; all I needed to do was establish Rei and Kaoru's presence.

Shinji ZERO

Chapter 2

Death and Rebirth by Unit Zero

A few weeks had passed since Unit 00's self destruct. Dr Ritsuko Akagi and Sub-commander Fuyutsuki looked out into the cages where a second Unit 00 was nearing completion. Normally it takes a month or two to build an Eva even with the parts on hand as in this case. However enough of Unit 00's remains had survived the explosion to expedite the re-construction. The Eva, which for the moment only had its A-Type equipment (no shoulder plates), was sporting its blue coloration despite Dr Akagi wanting to return it to its original yellow.

"So how long until its ready" the sub commander asked the bottle blond

"Its core just arrived, its S2 organ was installed yesterday, so we should have it in and ready by test time tomorrow"

"Good" 'now lets hope Ikari doesn't pull anything' he thought

Gendo Ikari, AKA supreme bastard of the universe, sat in his office going over the final stages of the new Unit 00's initial activation test. By tomorrow morning the unit would be ready for the first test pilot. Rei would no doubt volunteer but he still needed her to accomplish his goals. The 2nd was to unstable to even sync much less control it in the fashion he needed. The 5th was also unsuitable; his score was too high to sacrifice him. That left the 3rd child; he was a thorn in his side already. Unit 01 was far too valuable to the committee to risk it's lose to the 17th angel when it arrived. Rei or the 5th child in Unit 02 would be more than enough. Or, he smirked, the 5th in Unit 02 and Rei in Unit 00. Rei was stable; she would follow his orders, even after she discovered what he had done. Or so he thought anyway.

"Yui I will be by your side soon"

Shinji sat in Unit 00's Entry plug. To say he was nervous was an understatement. The last time he was in this Eva it tried to kill him and he ended up back in the hospital. But this time it was different, the Eva was a clean slate, no one else had even set foot in its Plug.

He sat back and though of the previous night

Rei staying in his room

Sleeping on the other side of his bed

And Rei's confession

She had told him of her past, her 'creation' by Nerv. At the time he was scared, but that faded with the realization that she was as frightened as he was. Her emotionless mask was off; she didn't care at that moment.

"Rei…you mean you"

"Yes, I was created by Nerv from the DNA of the 2nd angel and Yui Ikari"

She was crying, though she wasn't crying as a normal person would, she was silent and her voice was still monotone and even, but Shinji could see tears running down her cheeks and onto her side of the pillow. Shinji closed his eyes and thought for a moment. He want sure he could handle this and kept repeating his old motto 'I mustn't run away' to himself. He opened his eyes, she was still crying. He needed to know one thing

"Rei…are you trying to tell me…that…you're my…sister"

She nodded

"Please do not abandon me"

Shinji then did something that shocked even him; he wrapped his arms around her and pulled her closer to him

"I would never abandon you…baby sister"

Hearing those words were all Rei could ever have wanted. Shinji, no her brother, had accepted her. He wouldn't leave her. He would stand by her side when ever she would need it. And even in the times she didn't think she did, he would be there. And what's more, that's what he believed.

Yes his life was now more interesting with a half angel sibling.

"Shinji were ready to begin"

"Roger"

In the control room Misato, Ritsuko, Commander Ikari, the Sub-Commander, Kaoru, and Rei stood watching the first activation test for the new Unit 00. Maya and the other Techs monitored the Eva as the startup procedure began

"Connecting main contacts"

"Now beginning insertion"

Unit 00's entry plug was inserted into the plug socket

"Monitoring sycnro graph"

0.8

0.6

0.5

0.3

0.1

"Border line cleared, now beginning pilot synchronization"

"30, 44, now at 50 percent, 60, 76, 78, 80, now stabilizing at 83 percent"

Misato looked on, beaming with pride "Shinji's amazing isn't he"

Kaoru nodded "yes I agree, his skill is impressive" 'then why am I feeling uneasy' he thought

Suddenly Unit 00 began to strain against the restraints in the test chamber; Maya noticed his sync ratio skyrocket as the emergency alarms began to blare.

"Ma'am his sync ratio is at 95 and rising"

"Cut the connection, eject the plug" Ritsuko commanded

"The connections won't terminate and the plug eject signal has been received but ignored"

"What's his Sync ratio at" Misato asked in a panic

"276 and rising, that's imposable it should have gone berserker by now"

Ritsuko couldn't believe this, this Eva was a new one it shouldn't... her thought caught her. A new Eva, a new core, and untried core 'damn you Ikari your going to use Shinji for the core component aren't you, well im not going to let you' she was broken from her thought track by Maya

"Ma'am Unit 00's S2 has become active"

"Shut it down"

"All signals are being rejected, Sync ratio now at 345 if it goes any higher"

Misato looked on, she knew what would happen if it breeched 400

"It's the same"

"The same as what" Kaoru asked

"During the 14th angels attack Shinji's sync ratio jumped passed 400 and he was absorbed into the Eva, its happening again"

At that moment Unit 00 ripped free of its restraints. It stumbled forward and fell to its knees clutching its head. With teary eyes Maya called out the sync ratio

"The Sync Ratio has leveled at 407, we've lose vitals on the pilot"

Ritsuko shook her head, she looked at her monitor and confirmed

"His Ego Border is gone, were to late"

Rei couldn't believe this, just the night before she had found her brother, only to lose him less than a full day later. Suddenly the alarms began to blare again. Maya reported

"Ma'am the plug ejection signal is now being accepted"

Ritsuko became frantic

"No abort ejection"

Too late, the entry plug rocketed from its socket in the Evas back. It hit the ceiling with enough force to crush the Entry Plug. The group looked on in horror as the LCL and remains of the plug fell to the floor below, everyone that is except Commander Ikari who wore a slight smirk, which Rei seemed to notice. Underneath her emotionless façade Rei's anger was at its boiling point. Yes she could take the way he treated his son, yes she had come to understand why Shinji didn't trust his father, and yes she herself had begun to question him. But this was too much, this was her brother, this was where she drew the line

"Major Katsuragi may I have a word with you"

"Rei now isn't…"

Rei grabbed her wrist and dragged her off to the corner of the room

"Alright Rei alright, what do you need"

"My I see your weapon please"

Misato was a bit talked back by this

"Why"

"I can not say as yet"

"Umm… I don't really think it's a good idea Rei"

"It is necessary Major"

"Ok, just don't do anything stupid"

Misato pulled her 45 from her holster and handed it, handle first to Rei. The quiet girl nodded her thanks befor rejoining the group. No one noticed her even pull Misato to the side, save for Kaoru who could tell what the quiet girl had planed. She walked up behind commander Ikari. In that brief moment a horrified Misato saw what Rei was planning to do.

Shinji definately wasn't having a good day. At first the activation test was going just fine, and then he got this mind numbing headache and blacked out for what seemed like a few seconds. As he started to come to it felt as though he had somehow found his way out of the Eva and on to the catwalk, maybe. He was on his knees that he knew, his eyes were still closed and his head was still pounding. He called out to Misato and the others, but got no answer.

'Communications must be down' he thought.

Then he decided to open his eyes, and immediately wished he hadn't. For a moment he was blinded by bright white light. He waited for a moment for his eyes to adjust before he opened them again. Again he wised he hadn't, for the body he was staring down at wasn't his own, But Unit 00's. He blinked a few times, hoping it was just his eyes playing tricks on him and that he was in the entry plug still. Then he noticed the shattered Entry Plug and puddle of LCL surrounding it. Then it his him, He had been absorbed again, by Unit 00 this time. He collapsed forward, his head coming to rest on the floor of the test chamber. He pulled his arms, well they were his now anyway, to his chest and simply sat there in shock. Then he heard some kind of commotion in the room above him.

Everyone in the control room had their eyes glued to Unit 00. That was until they all heard the cocking of a pistol. Commander Ikari heard it to, then he felt s slight pressure in the middle of his back, he knew it was said pistol though is user was a surprise, it was Rei.

"Why did you do it commander?"

He knew at this point he was in trouble, if he made any aggressive move Rei would fire. He knew her well enough to know she wouldn't do something like this and not go through with it.

"Why what Rei"

"Why did you Order pilot Ikari to test Unit 00 knowing it was untried"

"Because his usefulness was over"

"I believe you were mistaken"

Before anyone could react the retaining wall separating the test chamber from the other Cages collapsed. The commander used this distraction to quickly knock the gun from Rei's hand and grab her by the throat

"You dare to point a gun at me Rei, I made you"

She was struggling for breath

"You dare interfere with the scenario"

Rei's vision began to darken

"You will be replaced, goodbye Rei"

Befor he could finish the job the wall separating the control room from the test chamber was ripped away. To his horror, there stood Unit 01 its mouth open slightly. He droped Rei and stepped back. The Eva reached into the control room and plucked him out. He sat in the Eva hand looking up at it

"Yui"

In that moment Kaoru sensed exactly what he had come here for, Adam, he was close. Then he noticed him, he was inside of the commander some how. He also knew Adam, along with his mission, was doomed

Unit 01 closed its hand, the sound of crushing bone and squashed flesh could be heard. Unit 01 droped the remains of Commander Ikari, Which now resembled smashed hamburger, to the floor of the test cage and smashed them under its foot for good measure. Kaoru just shook his head, his mission was over, and Adam was dead, as was Commander Ikari for that matter.

Shinji was frightened beyond all description. When the wall collapsed he had scooted back a bit so he wouldn't be hit by any debris. Now he had scooted all the way back against the wall. Eva Unit 01 had just smashed through the retaining wall, ripped its way into the control room, extracted his father who at that moment was strangling Rei, and crushed him into ground meat. So of course he was afraid.

Misato and Ritsuko were at Rei's side. Ritsuko confirmed that she hadn't suffered any damage but instructed one of the technicians to take her to the Infirmary anyway just to be safe. Kaoru walked over to the now destroyed window and looked into the test chamber.

Eva Unit 01 approached Unit 00 which had scooted back against the wall opposite the now smashed retaining wall. Shinji closed his eyes and waited what he thought would be a painful end at the hands of the berserk Eva. Instead he felt a hand softly touch his cheek, well what you could call a cheek on Unit 00, which was followed by a soft soothing voice

"Do not worry Shinji; he'll never hurt you or Rei ever again"

The voice was one he knew well; it pained his very soul to hear it. He had only heard it a few times after all

"M…Mother"

Shinji opened his eyes; Unit 01 was kneeling in front of him with its hand still in place. The hard and cold expression of its eyes had softened

"Come on Shinji lets get you stood up ok"

"Yes mother"

Unit 01 helped Unit 00 to his feet; she then guided him over to the remains of the restraints

"Let's get you put back into the restraints so Naoko Akagi's girl can take car of you"

"Ok"

Unit 01 Helped Unit 00 dock back onto the surviving restraints

"Now you go on to sleep ok Shinji, they'll take good care of you"

Shinji could feel his eyes getting heavy and drifted off to sleep, still held in place by the restraints. Unit 01 turned and headed back to its cage. In the control room Dr Akagi was baffled by all of this. Apparently the souls with in the Evas DO have conscious control to an extent.

"ma'am Unit 00 has powered down most of its systems but the backups and the S2 are still online and were getting a backflow signal that, well, looks like a REM signal" Maya Reported

"An REM signal, what does that mean" Misato asked

"Well…" Ritsuko walked up to the now missing window "…it means the Eva is dreaming, if it is an REM signal"

"So, Shinji is in control of it"

"Not exactly, more like the Eva's body is now his own"

"Just what the hell are you saying Ritsuko"

At this point the Sub-Commander piped in

"Doctor, I suggest you show her, and take Rei and Kaoru to"

"Yes sir, com with me you two"

The pair followed Dr Akagi to the infirmary. Once they had found Rei the party of 4 descended into Terminal Dogma and Nerv's biggest secret.

A/N Well that's chapter 2. Killing Gendo like that was fun, even if it was a bit much.
The next chapter will be a bit calmer though and expect the return of Asuka.
Thanks to my readers and reviewers. And sorry if I rambled a bit im trying to be more descriptive.