Not Going According To The Scenario

Chapter 1

A New Life

Disclaimer: I do not own Evangelion or its characters or Anything (So don't Sue I have nothing good anyway).

2023 AD Japan

It was a nice sunny day in the in mountains in the country side of Japan and it had been nice and sunny for over the month as well. The seasons and weather had become unpredictable after 2nd impacted and had all over the world but so far for this area it had been good most of the weather had been nonstop rain but from what some of the leading scientists in the world had said that the planet was slowly returning to normal and for the small community that lived in the mountains it was nice to see same hot sunny days. Most people in the town were going to the big lake that was in a valley surrounded by 3 mountains it had been the best place that Shinji had found to hide and live a somewhat normal life he had tried to live in the U.S. for 4 years and had been a political refuge and given asylum in the U.S. and had been working for the U.S Army in Research and development but that only lasted so long.

4 years Later NERV had came to the U.S. after they had been looked all over the world for Shinji thanks to the CIA and NSA and had finely found out by a NERV Spy that had found him in the U.S. working in a U.S. Army Research and development base that was setup where NERV's Fourth branch had been. NERV had demanded the return of Shinji Ikari from the U.S. back to Japan as he was listed as a deserter and was to be returned to Japan for his court-martial

2020 AD U.S. Army Research and development base

Lieutenant General Jack Simmons had been having a bad day he knew this day would come but it had come to soon he had hoped that the CIA and NSA could keep NERV from find out where they had been hiding one Shinji Ikari, The head Doctor of a top secret project known as Project A to People with the right clearance.

Shinji had over the years had been working on his Doctorate and had several degrees in Computer science, Theoretical physics, Applied mathematics and several other degrees And with an IQ of over 160 he had completed 3 degrees before his 14 birthday before his days at NERV he had also secretly been doing more degrees well working at NERV most people didn't know the real Shinji he had been acting for those years at NERV only two people had known the real Shinji in Tokyo 3. One was Kozo Fuyutsuki NERV's Sub Commander who had payed for all of Shinji's studies and all so kept them secret so NERV never Knew how smart he was and second person who knew was a girl known as Hikari Horaki or the class rep like his old friends like to call her.

She had found out from her sister Kodama who had seen him years before at the Tokyo 2 university he was one of the youngest students ever to go to the university and she had heard about him having almost finished 3 degrees at the time and had helped her a few times as they had some of the same classes.

There was beep from the intercom on the Generals desk "Sir, Major Ikari is here"

"Send him in" the jack said

Shinji opened the door and closed it be hide him "General you wanted to see me" Shinji Said

"Yes we have a problem"

"What is it General"

"We were contacted by NERV Japan and demanded you be handed over to them"

"What, how"

"We found a technician that seems to have been working for NERV to spy on us"

"Do we know what projects NERV knows about and if anything about project A was leaked?"

"No, he had only just started here 2 weeks ago and only had a low clearance level and he was caught before anything about project A could be leaked but we don't know if he told NERV about any other projects we are still questioning him"

2023 AD Japan

Shinji was sitting by the lake side bar where most of the Adults where watching their children play while having a drink and a bit to eat. Shinji was enjoying his chips when a young girl about 9 years old with brown hair and blue eyes came running up to Shinji and jumped up and hugged Shinji almost knocking him and the seat over.

"Daddy"

"Jessica, having fun with your friends"

"Yes, Daddy can I please go to a sleep over at Sarah's house tonight please"

"If it all right with Sarah's parents then I don't see why not"

"Thanks Daddy" Jessica hugged her dad and run back to the lake

Shinji just smiled and thought back on how his life had change 6 years ago when Jessica had come in to his life.

It had been 5 years since Shinji had adopted Jessica he had found her 6 year ago when he was working for the US Army in a small town that had been wiped out by something that he had always feared might happen the town had been attacked by what was recovered to be an EVA using it's AT field to crush the town the army had tried to stop it but nothing could get past it's AT field.

It was when Shinji was looking at some of the damage Buildings that he thought he heard crying as he went closer to one of the collapsed buildings he could hear more crying Shinji called for help and he and the other soldiers spent over 2 hours digging though the rubble by hand due to there was no way any equipment in their after the attack and could only get to the area by helicopter. In the end they found a 3 year old girl that had been trapped under the rubble of the collapsed building. Then when Shinji turned 18 and he could adopt her he did she had stayed with him after that day he found her but Shinji was not old enough but only had to wait a year so Shinji had been given special permission to have her stay with him and she had stayed with him ever since and that was one of the reasons for working on project A to stop something like that from happen again.

Shinji's cell phone started to ring and he picked it up to see that it was Jack Simmons he picked it up "jack what can I do for you today"

"It seems the project is ready for testing" Shinji shot off his chare when he heard that

"Really they weren't meant to be ready for another 6 months when will the tests be done?"

"6 weeks, will send a jet to transport you and Jessica to the base near the test site"

"When will we be leaving?"

"4 weeks"

"Ok bye" Shinji hung up and looked over to the lake it had been over 5 year of hard working even when he moved back to Japan and hid in this small community NERV didn't think to look for him in Japan they still thought he was in the US. The US had an old lab complex which was used in the war it was built in a hidden cave in one of the mountains and had a large house that had been built near an entrance right in to the complex for the people working their when it was used.

He had been working on Project A in Japan for 3 year and had finely finished a working prototype only 6 months ago and had sent it to the U.S. Army's Research and development bases where they made 5 other prototypes based off his design and made some mods to try and improve the base prototype. They had 5 prototypes all with different mods for testing and they could see if all their hard work payed off and see which one worked best and see where they could improve in the design.

Shinji found Jessica playing with her friends Shinji told her that he would pick her up tomorrow afternoon Shinji hugged her and said good bye and headed for his car as he was driving home he had no work to do and Jessica was over at her friends for the night and there was something that he had been meaning to for over 7 years and it was time he paid her a visit and it was only 2 hours by car to get to Tokyo 3 and who would know who he was anyway 'how much trouble could I get into I'll only been in Tokyo 3 for a few hours' thought Shinji and there were some other things that need to take care of like an old friend that had been one of only 2 people he had opened up to and shown his real self to.

Most people who knew Shinji would say he was a hard worker he had soon after moving to the area had started working as a teacher at the local school due to the small community they were hard to find teachers so when Shinji had started sending his Daughter to the school and was told about not having enough teachers so Shinji worked part time at the school teaching math and science and it was the perfect cover so most would not think of him of have a nice sports car he had two car's one for work and the other for going out.

As Shinji got in to his sports car and started the 2 hour drive to Tokyo 3 he remember the day he had left Tokyo 3.

2016 AD

It had been over 6 month since the 9th angel had attacked Tokyo 3 and week since Shinji had found out what his father and a group Known as SEELE had planned for the world. He had hacked it to the MAGI one night and had been looking over file and reports for projects that didn't look right he was smart and found some projects that were highly illegal and from the data he found there was something big going on and the UN didn't know about it.

It had taken weeks of hacking to find out what NERV was up to and he had to find out if it was true so he went to the only person he could trust one Kozo Fuyutsuki. Kozo Fuyutsuki was like a father to him he had helped him out with his schooling and made sure he always had what he needed and had kept his schooling secret from NERV.

Fuyutsuki had told Shinji everything he knew and how Gendo and SEELE's sick scenario was not going according to the scenario as the angels where late in attacking should have all come within the year and how the German branch of NERV had refused to release unit 2 and the pilot to be transferred over to Japan after the 5th angel had attacked and how all of them had their parts to play in this sick scenario and how he had been for years trying to find away to stop them but this far had no way of doing without winding up dead and also about Rei and how she was related to him.

Shinji had feelings for Rei but not in the romantic sense but like a brother and sister he had made up his mind to leave it would derail his fathers and SEELE's scenario. It was a hard choice to make but he made the choice to leave. It would take one of the keys needed for this so called Human Instrumentality Project to work with him gone they would not have means to fully awaken unit 1 and the unit would not for it to work for anyone but him and it was hard he had just found out Rei was his sister but with him gone and his plan to destroy all her clone's and making it look like a computer glitch and with that same glitch corrupting all the data on how to make new clones would set them back over 10 years and would keep Rei safe from just a replaceable item as the commander sore her. He would have rather he keep her safe but he couldn't ask her to leave with him she was still close to the commander and would report him to the commander and it would also force the third branch to hand over Eva unit 2 and its pilot to Japan as much as Shinji didn't want his NERV to have another Eva unit it was the only way to keep Rei safe so she wasn't fighting alone.

From what he had heard from the report he had found in the pilot had been training all her life he could not find any more info on the pilot due to the third branch kept all information about the second child on a secure system cut off from the rest of the NERV network it was done after NERV Japan tyred hacking in to their system to find out where she went to school and lived.

It was this that had cursed the third branch to up security on any information on the second child and also upped the amount of security to watch her if NERV Japan tyred anything.

Shinji left a day later with the help of Fuyutsuki he was on a plane to the US where he would be granted asylum and would given the rank of captain in the army and could lay low till NERV stop looking in the US for him this was all thanks to Fuyutsuki he had been a professor before working for NERV and had kept in contact with of some of his old students witch happened to be high ranking officer in the military and had been told about Shinji they had more than agreed to take him in and help stop NERV.

2 Hours later just outside Tokyo 3

It was dark when Shinji pulled up to two be gates the area was like a desert with no living trees and it was like this place was surrounded by death Shinji thought. Shinji hopped out of his car and walked though the big gates walking past all the makers and stop at one that had Yui Ikari 1977-2004 it had been over 7 years since he had last visited her. Shinji lad down a bunch of flowers "hi mum sorry for not visiting sooner but I haven't been able to risk NERV finding me and I have a daughter to worry about now. Jessica She 9 year old I just wish you were here to see her. I am sorry I cannot risk bring her here NERV doesn't even know I 'm in the country let alone a daughter I have to go now buck I hope I can come back with .Jessica next time. Bye mum I love you"

Shinji then walked back to his car unaware of the black van with tinted windows that had been lessening in on him the whole time.

Author's Notes:

I just came up with this hope you like it and I have updated my other story I redid chapter one so have a look I am working on more chapters as we speak and any Beta Reader would help me out a lot hope you like