Neon Genesis Evangelion: Conspiracy Chapter 9
30th December 2000
Japanese Government Facility - 2330hours

"What is the status on Adam?"

"He is... stable at the moment, we currently have him sedated and our computers are also tracking the other specimens. We are ready to move onto phase two of the operation, if you would like to come with me, Director."

"Of course."

The director stood up and took one final look around his office and smiled at the man who stood at the other side of the room. A light from one of the choppers overhead shone through the window illuminating the entire room, he took a step forward and made his way out into the corridor, continuing his conversation with the man.

"Is Keel still here?"

"No Sir, Keel and the rest of the committee left just over an hour ago."

"So they are not staying to see the beginning?"

"They are watching from a location outside of Tokyo 3, just in case one of the specimens returns."

"Of course, they would want to play it safe."

They made their way into one of the facilities laboratories, this laboratory was the largest within the facility, along the walls were tanks filled with an orange liquid and inside were various humanoids in different stages of growth. The director stopped when they passed by one tank, inside was a fourteen year old girl, her blue hair shimmered in the orange liquid. He reached up and began typing on the keypad next to the tank, the man accompanying stopped and looked at him.

"Sir what are you doing? SEELE's instructions were to leave everything here and resume the genetic modification procedures elsewhere."

"SEELE aren't here are they?"

"No but still we can..."

He was cut off suddenly when the director pulled a gun out and pointed it at him, he turned to face him. The director spoke again this time sounding fiercer.

"If you wish to stop me go ahead, I think you'll find however that the people left here are under my command and not SEELE's."

"Sir if you do that I'll have to inform Ke..."

The sound of the shot echoed around the laboratory as the man slumped to the ground, blood pouring from the gunshot wound. As the director finished putting in the commands on the keypad another person stepped into the area, this time a brown haired scientist. She looked at the body on the floor and then to the director and smiled.

"Did he try to stop you?"

"He threatened to tell Keel"

"Unfortunate, I'm sure he would have made a good test subject for Project E."

"You will have plenty of test subjects later Naoko, why are you here?"

"I came to find you, Fuyutsuki is at the chopper with my daughter. We're preparing to leave the facility."

"Tell them I will be along in a minute, there is something I must do."

Naoko looked at him and then to the tank he was opening, a look of disgust appeared across her face, but she quickly disguised it. She turned and made her way out of the laboratory, leaving the director and the person he was helping out of the tank.

"Rei, we're leaving."

"Yes sir."

He took off his jacket and gave it to the young girl to put on and they quickly moved out of the laboratory. A few moments later they were outside on the roof of the facility, a chopper waiting for them along with three other people. Naoko, a young blonde haired girl and an older grey haired man. The man stepped forward and spoke to the director.

"Director Ikari, quickly, we don't have much time."

"Of course Fuyutsuki, I was just getting Rei."

Fuyutsuki looked down at the Blue Haired girl who was wearing only Ikari's jackets and frowned slightly.

"Ikari, you know Keel will not be pleased with this."

"Of course I do, but we cannot afford to leave Rei behind. She is the key to project E."

"I understand, was a survivor chosen?"

"Yes a young woman, the daughter of one of the head scientists here, Dr Katsuragi's daughter. All has been taken care of and the beacons are set up, all we have to do now is activate Adam."

"Doctor Akagi has the Magi system logged in and ready, we will activate when we reach the outskirts of Tokyo."

"Lets proceed then."

16th May 2015

Katsuragi Residence - 1720 hours
"2015 marks the fifteenth year since the ‘Impact Incident' a deadly explosion which took out most of Old Tokyo. It is believed the explosion was caused by a malfunction at the Gehirn research facilities in the heart of Tokyo, however even to this day scientists have not been able to return to Tokyo due to the radiation that surrounds the area and the city itself.

The Japanese Prime Minister has recently made preparations for a special memorial service on the 30th December to mark the 15th Anniversary of the incident many are calling the biggest disaster in human history. The entire city of Tokyo was turned into a ghost town with no survivors...."
Misato switched the TV off and threw the remote down to the floor sighing to herself.

'Yeah...no survivors except one.'

She made her way into the kitchen and pulled another beer out of the fridge, she gazed over towards Shinji's room as she took a seat at the table. Despite them living together again she had barely heard from Shinji since they got back from the Over The Rainbow. She had seen him at NERV but they barely exchanged words, Misato knew it was because of what Asuka told him.

'He's just like he was thirteen years ago, shutting himself away and not talking to anyone, he's barely spoke to me at work and he only comes out for dinner. He's twenty seven not fourteen, he needs to learn to deal with this.'

Misato stood up and made her way over to the door, she tapped on it lightly and spoke through it.

"Shinji, I'm coming inside."

There was no response so she slowly opened the door and peered inside, the room was just as tidy as it was when Shinji arrived. She looked over towards the bed and looked on in shock when she realized Shinji was not there. His possessions were still in the sports bag on the bed but Shinji had left. Tears burnt the back of her eyes as she looked around whispering to herself.

"No... don't do this to yourself Shinji."

Wiping her eyes on her sleeve she made her way back into the kitchen and picked up her cellphone dialing in Asuka's number. It rang for a few times before she picked up.

"Hello."

"Agent Sohryu, its Katsuragi have you seen Shinji today?"

"No, you guys still won't let me go back to work remember, something to do with the injuries I got and subsequently healed from."

"Sorry I forgot, have you heard from him at all?"

"No. Why what's happened?"

"He's run away again?"

"What do you mean again?"

"When I first took him in thirteen years ago I quickly found out that if something was troubling him he would run away from the problem. He did it a few times before I finally managed to convince him to face his problems, but after what you told him I think he's started again."

"How do you know he has run away, maybe he's working late or something?"

"No he wasn't at work today, he wasn't here when I woke up, and his stuff is still in the bag on his bed, he hasn't been in there since yesterday."

"Well he's an adult it's up to him, if the idiot is going to do that then it's up to him."

"I know but I just get the feeling he's in trouble."

"Have you tried contacting him?"

"Yeah, but his cell phone is switched off."

From the other end Misato heard Asuka sighing heavily.

"He's probably with Wondergirl."

"Wondergirl?"

"Yeah Agent Ayanami, I'm going to start calling her that because I'm still wondering who the hell she is and how she got away with attacking me."

"Agent Sohryu please be serious I'm worried about him, I think what you said to him messed him up."

"More than he already is you mean?"

Misato was now nearly shouting down the phone, trying her best not to break down.

"Agent Sohryu!"

"Okay I'm sorry, but I'm not taking the blame for saying that. He needed to be told if I didn't tell him, no one else would have."

"You were too blunt though, you saw what he was like on the flight back."

"Look I'll meet you at the offices okay? We'll see if he's been there, but you need to stop treating him like a kid, despite being an idiot he is capable of handling himself."

"I suppose you're right, I'll meet you there in half an hour then."

30th December 2000
Streets of Tokyo -2350 hours

A huge explosion rocked the street as a young Misato Katsuragi stumbled out of her apartment block. She looked out towards the center of the city, entire buildings had collapsed and smoke poured from those still standing. She stumbled onto the street and was suddenly swept into the crowd of moving people, all of them racing in a panicked frenzy trying to get out of the city.

As she tried to keep up with the crowd she felt something shoving her out of the way, she quickly fell to the floor screaming out in pain. She scrambled over to the side of the street as best she could to try to avoid being trampled on by the thousands moving through the city. She looked out towards the center and saw a huge pillar of light hovering over a building, she blinked and then looked on in fear realizing just what the light was hovering over.

'GEHIRN... FATHER!'

She rushed back out onto the street and tried to make her way towards the light only to be dragged along by the crowd again. Suddenly the light vanished and the sound of a huge explosion tore through the sky, everyone on the street began screaming even louder. Misato stood on watching as flames and smoke rose from the area where the light previously was.

'No... please don't let it be GEHIRN'

Several more explosions sounded off all around her as she tried her best to fight through the streets towards where Gehirn was located. All around her people were screaming, women, men, children, all of them screaming and running. She moved onto one of the main roads and straight into another crowd of people, a white flash tore through the sky causing everyone to stop and stare towards the center of Toyko. Two of what appeared to be lightning bolts were coming down from the sky, they broke into what seemed to be wings. Misato looked up at this beautiful yet disturbing image, more explosions tore through the city, this time even closer to Misato's location.

A huge sound was heard overhead as a light swept through the street, similar to a helicopters spotlight. Misato covered her eyes as the light shone directly in her eyes getting closer. A rumbling sound could be heard above her as the light stopped moving directly over the street. Everyone at that moment looked up at the huge object which was above them, Misato being no exception. She closed her eyes as she felt herself being pulled upwards by some strange external force.

'What... What is happening to me?'

17th May 2015
NERV Offices - 1750 hours

Lightning flashed through the sky as Misato brought her car to a halt in the NERV carpark, she stepped out the car and looked across the parking lot and noticed Asuka's car parked nearby. She breathed a sigh of relief and quickly made her way into the building and down towards the offices. When she opened the door to the office she found Asuka stood over by Shinji's desk looking through documents and sipping from a cup of coffee. She looked down as Asuka's bandaged hand from two days ago and frowned.

"Agent Sohryu, glad you could make it."

Asuka turned towards her and nodded and then looked back at the documents before taking another sip from the cup. Misato watched her unsure of what to say instead she just watched the woman as an uneasy silence fell upon the room. It was eventually broken by Asuka speaking.

"He's been here."

"How do you know?"

"All the files from the recent cases Sachiel, Shamshel, Ramiel even what just happened to me on the Over The Rainbow were all here on his desk. He's got profiles of both Gendo Rokubungi and Gendo Ikari, I know what you're going to say but I'm still not taking the blame for him running off, would you preferred for him not to have found out?"

Misato looked at her and shook her head as a tear rolled down her face.

"Agent Soh... Asuka I'm sorry for blaming you... I just... I don't know what to do..."

Asuka looked at her and felt uneasy as the woman broke down crying before her, she walked over and put her arm around Misato and led her towards one of the seats in the room.

"It's alright, I'll find the idiot even if I have to travel all around Japan."

Misato looked up at her and looked at her quizzically.

"You don't have to do all that..."

"No I do, because I'm sure as hell not getting stuck here with you being depressed and me having to work with Wondergirl, at least Shinji hasn't attacked me."

Misato wiped her eyes on her sleeve and looked at Asuka smiling slightly, Asuka however was still frowning.

"Thank you, I really appreciate this."

"It's alright don't get upset over it, like I said the idiot can handle himself."

"Asuka why do you keep calling him an idiot, from what you said the other day when you got back from the Over The Rainbow you were starting to agree with some of he said."

"That's not the reason, the reason I'm calling him an idiot is because of what he done."

She couldn't help herself but a slight grin crept onto Misato's face as looked at Asuka.

"You're concerned about him aren't you?"

Asuka immediately turned red and replied back fiercely.

"Don't be stupid Misato, I'm only helping you so I don't have to get randomly attacked by Agent Ayanami. Yes, I said I agreed with some of what he has said but that doesn't mean I'm going to start getting concerned about him because of something like this."

"He likes you, you know?"

Misato grinned as she watched Asuka growing even redder then before, despite her concern for Shinji it was providing her some relief teasing Asuka like this.

"Well so he should, after all to be able to work with someone like me... hold on a minute what do you mean he likes me?"

"He told me the night he was came to live with me after his apartment was burnt down, he said he was worried something might happen to you and that he was enjoying working with you. It was he who got the chopper to come and pick you up from the Over The Rainbow as well, he was with Rei in the ambulance but when he heard something had gone wrong he left and immediately had it fly out to help you."

"That doesn't mean anything, I'm sure any other Agent would have done the same for the person they worked with and what do you mean his flat was burnt down?"

"He didn't tell you?"

"No, he hasn't spoken to me since I told him about his father."

"On the night you left Tokyo 3, a car pulled up outside Shinji's apartment block and broke into his room. Agent Ayanami was able to rescue him and bring him to my flat but the people burnt the entire block down in the process."

Asuka thought for a moment and looked back to Shinji's desk and the documents on there. She glanced through the Shamshel documents looking for something, Misato shot her a confused glance when Asuka threw the documents down in frustration.

"They're gone."

"What are?"

"The documents of the liquid samples we took during the Shamshel case."

"What, how? Do you think Shinji took them?"

"I don't know I want to see Shinji's apartment block."

"Do you think he'll have returned there?"

"No, but I want to see if something has been there."

Shinji's Apartment - 1800 hours
"Agent Sohryu I don't think NERV are going to be too happy with you stealing that lab equipment."

"I'll pay for it later, besides I'm not stealing it, we're investigating the disappearance of an Agent."

Asuka shot Misato a cocky grin and stepped out of the car and looked at the building in front of her. Just as Misato said, it had been practically destroyed after those people burnt it down. She wondered just what they had used as the smell of the fire still hung heavily in the air, mixed in with the dampness from the pouring rain. Asuka made a personal note to get out of here as soon as possible. She ran into the alleyway where Misato said Shinji and Rei had been attacked by two of the men. She got down on her hands and knees, looking around the debris from the building, Misato followed her, wondering what the red headed girl was planning.

"Agent Sohryu, what are you looking for?"

Asuka withdrew the equipment she had brought with her and began collecting from what seemed to be a small puddle of orange liquid. Misato asked her again what she was doing.

"Agent Sohryu, what is that stuff?"

"I don't know, but it's been present at most of the cases me and Agent Ikari have worked on. It was present at the Sachiel case, the Shamshel case, and it was on the ship when I was with Gaghiel. I've ran so many tests on it but the results are always inconclusive, from what I can tell it's very close to human blood but there's something inside it that makes it different."

"Like what?"

"I don't know, I was recruited to NERV before I finished all my medical training."

"Shinji said you had a degree i..."

"I do but...it's a long story. Anyway I'll take this sample hopefully it'll give me the same results as the others."

"What happened to the other samples?"

"Stolen or went missing, on the Over The Rainbow there was an entire laboratory consisting of this stuff though. It was labeled as LCL in there, I took a sample but I gave it to Shinji when I surfaced on deck."

"Why?"

"I knew I was going to end up in hospital and didn't want to risk it being stolen and I knew I could trust him with it. Of course now he's gone missing so I can't run any tests on it."

"I see, but why didn't you trust the hospitals?"

"I hate hospitals, it was in one where my mo..."

Misato looked on as Asuka stopped herself mid sentence, if Misato didn't know any better she could have sworn a look of sorrow appeared on Asuka's face, but it soon turned to anger.

"It doesn't matter, I just don't like hospitals and after Shinji's father appearing so coincidently in the last one I thought it'd be best to let him take care of it."

"I see, so what do we do now?"

"We get this sample back to a safe location, my house. Besides that, I don't know, maybe Shinji will have retur...."

Asuka was cut off by the sound of her phone ringing, she pulled it out of her pocket and looked at the caller ID on the screen and looked in shock when she saw who it was.

'Shinji Ikari'

She answered the phone and put it to her ear only to have the person hang up immediately. Just as Asuka was about to tell Misato what had happened the phone went again, only this time telling Asuka she had a text message, this too was from Shinji and only contained one word.

'Home'

Unknown Facility - 1500 hours
Kaji looked out across the car park from his spot under the entrance, he smiled when he saw the person stepping onto the tarmac and moving towards him. As he watched the man he threw his cigarette to the floor and stamped it out.

"So we finally meet again, Shinji Ikari."

Shinji looked at him and moved into the facility as well.

"Agent Kaji..."

"Please, just Kaji will do, it's been a while."

"That it has, what was the important thing you wanted to tell me about?"

"First of all there is something I want to know, why weren't you at Misato's last night or at work today?"

Shinji looked at him and then stared down at the floor, speaking quietly.

"There was something I needed to think about, have you been watching me?"

"I've been assigned to Tokyo 3 and I heard from people that you had barely been seen. Misato will be worried about you."

"I... It doesn't matter, there's nothing she can do, and anyway I need to sort this out on my own."

"That's where you're wrong Shinji, you need people you can trust and people who trust you."

Shinji looked up and began shouting.

"And who trusts me? Misato only acts the way she does because she was my guardian, Sohryu thinks I'm an idiot and I don't know anything about Ayanami. I was even last to know about my father being who he was."

"Shinji I didn't want you to find out that way, that's why I asked you to come out here. I wanted to apologize for you finding out the way you did from Asuka, she always was a little blunt."

"It's alright, if she didn't tell me like that no one would have, I just...why did he have to be there, why didn't he say anything to me?"

"I don't know Shinji, but I do know something that might help you find out."

"Is this the real reason you called me out here?"

"Yes, there's a case you might be interested in."

"So that's it huh? What's the case?"

"Fifteen years ago two people, twins to be precise, went missing from their home on the outskirts of Tokyo. Their parents moved out of Tokyo on the day of the impact incident."

"I see, what about it?"

"Well yesterday the twin girls returned to their home, their parent's new home. Not a scratch on them or anything and no memory of what had happened to them."

"Unusual, but why would I be interested in it?"

"Well a few reasons, on the day of the incident their parents reported seeing strange lights in the sky, second and probably the strangest the twins have not aged a day since the day they were abducted. They vanished at the age of nineteen and they both returned having not aged a day since then."

"That's..."

"Impossible? Highly improbable? I know, but it's happened."

"Ok, so what's the third reason?"

"Their parents knew your father."

2nd January 2001
Medical Facility - Unknown Time

When Misato came too she was staring straight into two bright lights, she turned her head and found herself inside a hospital room. She attempted to lift herself up off of the bed but immediately went back down due to the immense pain around her back and stomach. As she propped herself into a sitting position a nurse entered the room and shot her a look of shock.

"You're finally awake! We were afraid you'd never wake up."

Misato looked at her and spoke softly.

"Where... where am I?"

"It's alright, you're safe now."

"What happened to me, how did I get here?"

"There was an incident in Tokyo, we found you on the outskirts and brought you to this medical facility."
Misato felt pain at the back of her head as all the memories from that night ran through her mind at once, she felt herself freeze up as the nurse continued speaking.

"More will be explained later, it'd be best for you to just rest for now."

She was met with silence, the nurse made her way over to Misato and took a needle from the tray.

"You've been asleep for near enough three days now Miss Katsuragi, when you were recovered you were badly injured. This injection should help relieve some of the pain, the doctor will be in later to explain more."
Misato was still sat in silence as the nurse began to inject her with something. She looked down at the needle, still unable to speak, she could smell the stench of the liquid being injected into her.

'It smells... like blood'

A slight tingling sensation was felt in her arm and it quickly raced around her body, she felt her eyelids growing heavy as she sank into sleep once again.

Asuka's Residence - 1830 hours

Asuka pulled her car into the driveway and looked across, just as she expected, Shinji was standing there on the doorstep looking at her. She got out the car and stormed over to him with a furious expression on her face.

"Agent Sohryu I..."

He was unable to get his sentence out before Asuka slapped him across the face, he brought his hand up to his face, feeling where she slapped him and looked down away from her.

"I'm sorry for what happened..."

She slapped him again only this time she spoke afterwards.

"The first one was for Misato, the second one was for me. Now you may speak."

Asuka looked him directly in the eyes, noticing slight tears forming and a hint of sadness across his face. He reached his hand out towards her but he immediately brought it back and spoke, his voice breaking up.

"Agent Sohryu... Asuka... I'm sorry I can't say anything more than that."

"Is that why you're here, to apologize?"

"No... well yes I want to explain what happened but I..."

"Explain inside, despite what's happened I don't want you to die of pneumonia out here."

"Thank you."

Asuka frowned and unlocked the door and they both stepped inside into the house, she took her jacket off and hung it up. She stopped Shinji before he got any further into the entranceway.

"Give me your jacket, shirt and trousers."

"What, why?"

"They're soaked through, idiot."

"But what will I wear then?"

"Well I've got a dress upstairs that'll suit you if you'd like that...."

"I don't think so, I'm fine."

"See this bag here, they've got a change of clothes for you, Misato thought this might happen and had us stop off and pick them up from a store. What did you think I'd go out looking for you and stop to do some shopping for myself along the way?"

"You were looking for me?"

"Yes, Misato was worried about you, I personally didn't care. Now hurry up and get changed."

"Here?"

"No, on the moon, of course here. I'm not letting you get all that water in my house."

"But... but...oh alright then."

"Good, I'll go make you a coffee and then you can tell me why you decided to be an idiot."

Shinji began to unbutton his shirt as Asuka turned towards the kitchen, a slight grin on her face. She paused when he heard him calling her.

"Asuka... thank you."

"What for?"

"For... never mind."

Shinji quickly changed out of his clothes and put on the new set Misato had gotten him, a few moments later he went into the kitchen to find Asuka pouring two cups of coffee and putting them on the side. She turned and looked at the clothes she had picked out for him, of course she wasn't going to tell him that. It was nothing too grand but it made a change from the same black trousers and white shirt he always wore. She pointed him towards the main room and she took a seat, she watched Shinji as he nervously looked around.

"You can sit down you know, the furniture isn't going to eat you."

He smiled and took a seat, as soon as he did so Asuka began speaking.

"So where did you run off to?"

"I just had some things I needed to think about, it was about my father."

Asuka looked down embarrassed slightly.

"Oh."

"Thanks for telling me, if you hadn't I don't think I would have gotten to know."

"Well that's what I'm there for, you're the one who looks for the outlandish explanations and I'm the one who puts it bluntly."

He laughed and took a drink from his coffee as she continued.

"So why did you come here, of all the places I didn't expect you to end up here?"

"I can't face Misato yet, I need a bit more time and besides I wanted to return something to you."

"What do you mean?"

"The vial you gave me, it's in my jacket pocket still, I thought you might want it back to analyze or something."

"Oh right."

"I also met up with Kaji today, he contacted me. He gave me information on a new case, he also said it might help me find out more about my father."

Asuka glanced at him and sighed.

"Is that really why you're here?"

Shinji sat back in the chair looking dejected, what he had said didn't quite come out how he had hoped it to.

"No, I... sorry."

"Three."

"What?"

"That's three times you've apologized to me in the space of ten minutes."

"Sorry..."

"You did that on purpose."

He smiled, "I know."

She smiled briefly but questioned him further, "Why?"

"Why what?"

"Why do you want to find out about him?"

"He abandoned me with my uncle two years after my mother vanished, I want to find out why, I want to find out why he was there in that place and why he couldn't even say anything to me. I want to tell him... never mind."

"Do you hate him?"

Shinji looked around the room and nodded slightly, Asuka moved over to his seat and nervously put an arm around him. She smiled at him and changed the subject.

"Well, seeing as you've got a new case, and I owe you one for upsetting you I guess this means I'll have to go back to work."

"You don't have to rush back and besides, you didn't upset me I just...."

Asuka ginned and quickly interrupted him off.

"I know, but I want to get back to work, my talents go to waste sitting around at home besides, I can't imagine you'd get anywhere without me."
Shinji smiled and turned slightly red, he looked away, hoping Asuka wouldn't notice and spoke quietly.

"Thanks."