Hey you!

Don't tell me there's no hope at all
Together we stand.

Divided we fall.

Pink Floyd – Hey You

3rd December 2015

Resistance Base

He rounded the corner and continued straight on. For a brief moment he paused, thinking he could hear a low rumbling in the distance. Quickly he calmed himself down. There was nothing there, just like the last time he'd thought he'd heard something and the time before that and the time before that. It was just his nerves, he thought to himself, high tension brought on by days of patrolling and drinking too much caffeine.

He stopped as he got to the camp entrance and sat down, yawning as he did so. He wondered how long he would have to keep doing this. Of course he knew the reasons why, after all it had only been a matter of days since the incident in Tokyo 3 and it was firmly etched into his mind. So many questions had arisen from that incident. Some about himself and some about those on the other side, why did they agree to it? Why was Keel so quick to attack? What significance did Misato's child have to this whole scenario? Why did he agree to let Misato join them on that trip? Was it because he really believed Keel wanted a peaceful solution or was it just because that was the easiest option?

It couldn't have been because of Keel. He knew what Keel was like. Shinji had expected it to have been a double cross. After what had happened previously both to himself and others, everyone should have known better. So why did they even agree to it? Was it desperation or was there some other hidden motive that Shinji didn't know about?

'I've been kept in the dark about everything it seems. They choose to feed me what they want and when they want. When it's convenient for them they'll tell me something or I'll discover what they want me to. I wanted to find the truth but it's not the truth, it's someone else's truth packaged up for me. When I found it it was too late and now, I'm stuck in this, people making me out to be some sort of hero who's going to lead them in a fight against Keel...all because I have some serum I never asked to have in me flowing through my veins...'

He paused for a moment collecting his thoughts, there was so much running around inside him. He had never really had a moment to stop and think like this. He had either been in meetings, sleeping or patrolling around the camp. He couldn't complain about any of it, he had never complained about things like this. He knew how serious the situation was, so complaining would only make it worse.

'I've always been like that though, in a less serious situation I never complained...what was the point? I would just get things done to save anybody any hassle. Even when I lived with Misato and she unfairly allocated me the chores...I didn't complain when I had the right too...'

He smiled weakly, those memories from over thirteen years ago were still pretty vivid in his mind. At the time he had hated being there but now he wished he could go back, to a time before NERV, before Angels and SEELE, before his home had became nothing more than a desolate wasteland.

Shinji turned his head around as he became aware of a presence behind him, he saw Asuka looking down at him. She too was looking just as tired as the rest of them. Asuka, however was masking the look of worry that the rest of them wore. She handed Shinji a cup of coffee and sat down next to him, that was just what Shinji needed...more caffeine.

"Asuka you should be sleep-"

She cut him off quickly, not wanting to be lectured by him, "Yes I know, but my next shift isn't until sometime tomorrow so I thought I'd see how you're doing."

He sighed knowing better than to argue back with her, "I'm all right I guess. Just wondering how long we're going to have to keep this up before the tension in the camp goes back down. Keel can't get to us here...can he?"

She shook her head, "Your father explained that there's something here that serves as a repellent to the aliens. It's what they're using to create the virus, they just needed the instructions that we managed to pick up...but everyone is so tense that they expect an attack at any moment. Us keeping watch helps them calm down, I suppose."

Her voice was unusually calm, there was no 'matter of fact' tone like he had heard so many times before. Maybe the tiredness was affecting her more than she was letting on, or maybe she just didn't care any more.

"I have to admit, I keep on looking out all the time thinking I can hear or see something myself. What happened in Tokyo 3 has got us all on edge a bit I guess."

He hadn't spoke about what had happened in Tokyo 3 to anyone yet, only really choosing to think about it briefly and focus instead on matters such as their next move but the memory was still there. There was no hiding from it, what had happened dealt a serious blow to them and the rest of the movement. They had only lost a small number but it was still significant enough to cause serious panic and there was of course the matter of what had happened to Misato.

Asuka turned to look at him not really sure how to approach the subject, this had been what she wanted to come out here to talk to him about. What had happened in Tokyo 3 and more importantly what had happened to Misato. There had been some things she had noticed about his former guardian that she thought he should know but she knew how important she was too him. If she just blurted this out then she risked angering him which at this point she didn't want. She had only just come to terms with her feelings for him. Luckily for her it was Shinji who approached the subject first.

"Asuka...have you seen Misato today?"

She nodded, "I went to see her earlier today, I told her why you hadn't been able to visit her yet. How your father is keeping you busy with patrolling and meetings."

"I see, she isn't mad is she?"

"More so with herself for agreeing to accompany us to Tokyo 3, she blames herself for putting her baby at risk and for what happened."

"You told her she is being silly obviously?"

She laughed, "Of course, did you expect anything else from me?"

He joined in laughing, "No of course not."

"Actually Shinji...I wanted to talk to you about Misato and about what happened..."

She paused for a moment, waiting for his response. He didn't give any just yet, instead wondering what Asuka was about to say. He would be lying if he said he didn't have any concerns over what had happened with Misato and why Keel seemed to want her and her child. They were the same concerns that he had had when he first learnt that she was pregnant, the same concerns that had been amplified when she had been attacked by Carter.

He finally responded to her, "What was it you wanted to talk about?"

She didn't look at him, instead choosing to look straight ahead, for some reason she felt incredibly nervous approaching this subject. She had never really felt this way talking about anything but because of who she was talking to she felt almost sick with fear.

"It's just...I think there is something happening with her child that we don't know about. Something Keel wanted the other day, something that your father probably knows about."

"I see."

She continued speaking, "I mean you saw what happened, Keel wanted her and the child and when we refused to hand them over he attacked. Misato was attacked directly, her being shot was no accident I saw it happen...and when she was shot I saw..."

She trailed off wondering how Shinji would react to this, "I saw an A.T. Field Shinji, Misato projected an A.T. Field and her wound...she was shot...directly in the shoulder but you look at her now and there's no trace of it. She's made a full recovery, that's impossible."

He nodded taking all of this in, the news of her making a full recovery was certainly new to him and it was only confirming his fear that Misato was in danger. He tried to formulate a response but Asuka spoke again much to his relief.

"I know how much Misato means to you but there's something wrong Shinji, either with her or with her child. I know you don't want to hear this but she is at great risk and I think your father knows why. Keel already knows and has gone to great trouble to get her..."

Finally Shinji responded his throat somewhat dry, "So what do you suggest we do? Are we in danger because of her?"

She nodded, "I think so but I think we're in danger anyway purely because of who and what we are. As for what we should do, I think we need to speak to your father about this, but not just yet. In six days he's promised to take us back into Tokyo 3 there's another lab in there that we need to go to in order to get the final piece for the virus. Once there I think we should find out what we can about Misato...whatever is happening it poses a threat to all of us."

9th December 2015

Tokyo 3 Ruins

Derelict, devastated, destroyed...just three of the words that came to their minds as they looked towards Tokyo 3. It still looked as it had done a week and a half ago, it's tallest buildings damaged, abandoned vehicles littering the streets, collapsed buildings blocking roads. It was remarkable that all this destruction was brought about in only eight days. As they entered the city itself Shinji wondered if there were any people left within the city or was everybody driven out or taken just as they had been with old Tokyo.

It was incredibly weird walking through those empty streets, at this time of the day they would usually be full of people going back and forth. Tourists, businessmen, shoppers and school children and now it was home to rubble and parked cars. There we no signs of life at all, no sign that anybody had been here since the attacks.

Shinji spoke, making sure he kept his voice hushed, "Do you think there are any survivors inside the city?"

Up front Gendo stopped and shook his head, "Unlikely, Keel will most likely have sent around mop up teams to ensure any survivors were taken by force. They most likely know we're here now and will have sent people to search for us as we speak."

Shinji was surprise by how calm his father sounded, even in a situation like this the man showed no emotion. More so now that he knew they were being hunted down. As they moved a bit further Asuka finally spoke, directly addressing Gendo.

"Why did Keel want Misato?"

Gendo didn't stop moving but he did respond immediately, "Direct and to the point. Keel does not want Katsuragi, it is the child that she carries that he is more concerned with. Katsuragi surviving the impact was not an accident, it was planned. Much like I was the one who chose the candidates for the Evangelion Project it was also I who picked out the lone survivor of the impact. At first it was because they needed a survivor, they needed someone to manipulate to bend the truth. Luckily for them Katsuragi could not speak for two months after the incident, let alone remember it."

Gendo paused for a moment, as Shinji questioned him a bit further.

"So Misato coming into contact with me...that was no accident?"

"Correct, I needed you in a place where I could keep an eye on you but not have any direct contact with you. Katsuragi was an ideal candidate so I ensured you two would come into contact, Keel was intent on taking you away. Moving you to Germany where he could influence your development, fortunately they trusted me so I was able to keep you here away from them."

"She had only just found out she was unable to have children at that time...you knew she would see me and take me in because she felt sorry for me..."

Up ahead Shinji saw Gendo nodding, he replied, his voice as emotionless as ever, "That's right. It is a fact I am not proud of but I had to ensure my son was protected and at least able to grow up somewhat normally."

"So what about Misato, she was supposed to be unable to have children. Why is she suddenly pregnant and why is Keel after her child?"

Gendo paused up ahead at one of the intersections, he looked across at one of the small buildings and then turned back around to Shinji and Asuka. "We're here...that building over there, the basement level there is a laboratory. This key card will get you in. Once inside you will find a computer, activate the software on this disk."

It sounded easy, it sounded too easy. Shinji took the key card and disk from his father and looked across at the building. This couldn't have been it, the virus had been created and all they had to do was activate it.

"Is that it?"

Gendo nodded and began to walk out into the street, before he could get very far Shinji called across to him. "Wait...you didn't answer my question about Misato."

Gendo stopped in his tracks and turned back round, Shinji questioned him again. "Why is Keel after Misato's child, after all that has happened I think you owe me this."

Gendo smirked, "I guess I do...That is-"

He was immediately cut off by the sound of a single gunshot ringing through the air. The three of them quickly ducked into a nearby alleyway and looked around into the centre of the street at the person that had just appeared. It was a single man carrying a handgun and wearing a black suit, he had the same white hair that Kaworou had and Shinji could see the man's red eyes. Was this another Angel? That couldn't have been, all the Angels had been killed.

It looked like Shinji was about to get his answer as the man called across to the three of them, "That is a very good question Agent Ikari. I fear however that you will not be finding out the answer to that question just yet."

The three of them said nothing and remained hidden pressed up against the wall. Shinji looked around and observed the man putting the gun away and looking down at the floor. After a few more moments he spoke again.

"I want to make this simple, you step out of that place you're hiding and you hand over the virus, we then leave you and your people alone. You remain hidden there and we will come after you and take it from you by force. I will give you some time to think it over but please, for your people's sake, do not take too long over it."

Shinji slipped the disk into his inside jacket pocket and slowly stepped out, soon followed by Asuka and Gendo. The three of them stood facing the man who had appeared, they looked at the other three roads joining the intersection and saw more men standing facing inwards towards them. Nine in total, they were completely surrounded.

The man who had spoken previously looked at them and smiled, "I'm pleased you decided to end this peacefully, we do not want to spill any more blood than is necessary."

Shinji did not reply, instead he looked around him again, from Asuka and his father to the man standing in the middle of the intersection and the eight men which accompanied him. Slowly Shinji reached into his inside pocket and pulled out the disk.

"Good move Ikari, now move into the centre and place it down on the floor. Then turn around and go back to them."

Shinji complied, he walked forward not taking his eyes off of the man. He knelt down and placed the disk down and walked away. As he turned around and walked back he made brief eye contact with Asuka. She was glaring at him angrily for turning it over like that, Shinji shrugged and gave a slight smile as he walked back.

"Right, now I want you three to turn around and head in the opposite direction."

Shinji nodded and turned around, he slowly began to walk down the street making sure to not look behind him. Asuka and Gendo followed him both equally stunned as to how he had given the disk away that easily. They moved a bit further down before Asuka quickly moved around stopping Shinji in his tracks.

"What the hell was that Ikari? After all we've worked for, you just handed it over like that?"

Shinji could sense the anger in her voice despite her quietness. He shrugged and smiled much to Asuka's disgust.

"I did what had to be done Asuka, they were going to kill us where we stood if we didn't. What use would we have been if we were dead?"

"You idiot we still could have done something, you could have made a run for the lab. Now they have it, now we have nothing."

"No Asuka, you're wrong."

He turned around and looked at the nine men, they had moved in towards the disk and were facing away from them. Shinji smiled again and continued walking down the road quickly ducking into another alleyway. This time it was his father who questioned him.

"Sohryu is correct, that was our only chance."

"So what was I supposed to do? Make a run for it and risk the lives of everyone back at the camp? They were waiting for this opportunity, if we made one wrong move that would have been it, they would have sent a signal to Keel and they would have stormed the camp capturing everyone there. Keel is probably monitoring us now, that's why I did this."

Asuka glared at him replying, she couldn't get over what he had done. She never thought he would do something like this. Her voice was lowered but still venomous. "What if you're wrong? You just handed over our future."

"No Asuka, I don't mean that."

He paused for a few moments before moving back out into the street and staring straight ahead, the men were still visible but had moved down the road slightly. Shinji reached into his pocket and drew out a small remote.

"I mean this..."

He pressed the button on the remote and as soon as he did the area where the men were walking erupted in a ball of flame. The three of them looked on as the dust from the small explosion settled leaving on the men's dead bodies and debris scattered everywhere. Shinji quickly moved forward and turned to Asuka.

"We need to get there quickly, we really don't have much time if they definitely know we're here now."

A part of Shinji was shocked that it had worked, it has only been a last minute decision to have a fake disk made and fitted with an explosive but it had paid off. He knew Keel would have been watching them and he knew they'd want the virus from them. They moved forward back into the intersection but were stopped by another gun shot, Shinji expanded his A.T. Field and quickly turned towards the source raising his own gun and firing back. It was one of the men, he had... gotten up and regenerated somehow.

"Not a smart move Ikari, now we have to use force."

Each of the other nine men had now gotten up and had also regenerated themselves. It was just the same as with Zeruel except now there were nine of them to content with. Without thinking Shinji charged forward at the first man tackling him directly into the wall of the nearest building. Without giving the man a chance to fight back he aimed two shots right where the man's heart would be.

'That's one.'

Shinji looked around, the remaining eight were moving back onto the intersection as Asuka and his father took cover. Shinji quickly dived over and joined them, Asuka looked at him taking out her own gun.

"You've took down one, there's eight left. That's four each."

Shinji nodded and looked at his father, "Right, me and Asuka will go back out. Can you provide cover for us?"

Gendo smiled and removed his glasses, "Of course, be quick though, they will regenerate."

With those words Shinji and Asuka leapt up from there position and began to run towards the remaining eight. They each fired in front of them making sure their A.T. Fields were expanded, Asuka leapt at her first target, her knee connecting with his face. She leapt over him firing a shot into his chest and then quickly aiming another shot at another oncoming target.

'Two in one go, this will be easy.'

She felt someone swinging her round and was caught with a backhand from one of the other men. He connected with a well placed kick to the gut and then followed up with another hand across her face. She fell to the floor and quickly moved out of the way before he tried to drive his knee into her face. She wiped the blood she now felt trickling down her chin away and dived at the man, tackling him to the floor. Using her A.T. Field to keep him in place and she fired two shots into his chest, silencing him.

She looked across at Shinji to see how he was handling things, he had just taken down his fourth one. She looked around trying to find where her fourth target was and then found him, she froze up when she saw where he was. Shinji turned round too and saw it, he screamed out but it was too late. It was almost like it happened in slow motion. She looked on as Shinji dived forward towards the man before his father's body had even hit the ground.

Shinji was like a rabid animal, he tackled the man to the floor delivering blow after blow to the person's body. Face, stomach, anywhere was a target for him. Asuka screamed out to him to stop but it was to no avail, soon a pool of LCL had began to trickle from the man as Shinji continued pounding away at him. She ran over and dragged Shinji away from him and pinned a struggling Shinji to the ground.

Just a few feet away from them lay the dead body of Gendo, she gently allowed Shinji to get to his knees and looked in his tear stained eyes. He looked back at her for a moment before throwing himself at her, holding her tightly. She looked around at the scene, nine dead bodies and that of Shinji's father. So much for no bloodshed, so much for this being easy.

She whispered in Shinji's ear as he knelt sobbing into her shoulder, "Shinji...I'm sorry it happened like this..."

He withdrew his arms and looked around himself, he scrambled over towards Gendo and looked down at him. The man was gone already, no final words, no last ditch attempt to fight back. The man who had sacrificed so much to get to this point had been taken away so easily. Shinji understood his father's actions, he didn't condone them, he didn't like them but he understood. The man had been through so much and sacrificed so much. His wife had been taken from him, he had to give Shinji away so that he could not be in any danger. For each time he thought his father had abandoned him he had been there, at first it may have seemed like he was being manipulated but at the same time he was watching, ensuring nothing would happen.

Shinji didn't have much time to process these thoughts as Asuka put her hand on his shoulder and whispered into his ear again.

"Shinji...take the key card and the disk. Make a run for the lab, we have company again."

Shinji looked around wondering what she meant and he saw it immediately. The nine people who had just been taken down were getting up again. Their wounds not quite healed , but still, they were up and alive. Shinji stood and prepared himself only for Asuka to call to him again.

"Shinji...you need to go."

He shook his head, "No I can't leave you, you can't take on all nine of them!"

"I don't care, if we both die we lose...if one of us dies then we still have a chance."

She dived at the nearest person taking him down again and silencing him for the third time. She shouted across at Shinji.

"Go now! I'll cover you."

She expanded her A.T. Field again sending another of the attackers flying backwards and stopped to reload her gun. During this time she never took her eyes off of Shinji, his destination was only a couple of metres away and he knew he should but how could he leave Asuka out here like this?

"Asuka...I can't."

"Shinji this isn't the time, go now!"

She took out another attacker just as the others started to get up, he had to make his decision now. He took another brief glance at Asuka and then to the doorway leading to the lab. He could do this, she could handle herself until he returned. He looked back to his dead father and whispered quietly.

"Thank you...father."

Laboratories

He ducked into the building and shut the door behind him, leaving Asuka to deal with the nine attackers. Something inside of him was screaming to go back out there and help her, the other part of him knew what had to be done. That the only way he could help her was to proceed down to the laboratories and insert this disk. He quickly made his way down the corridor and into a stairwell leading down to the laboratories. There it was, the door he needed to go through to end this, it all seemed so simple.

He withdrew the key card and placed it through the scanner, the door opened granting him access to the laboratory. After taking only a matter of steps he stopped dead in his tracks at what he saw in front of him. A huge cylindrical tank with a computer terminal hooked up to it. Around it were several smaller tanks he could not see into. It was what was inside the main tank that scared him because he knew that it was...or that it should have been impossible.

He stepped up to the computer terminal and inserted the disk, waiting for it to load up and trying to keep his eyes from what was floating in the LCL contained in the tank. He couldn't help it though, every moment he found himself looking at what was there. There was no mistaking it, even with the mask obscuring it's face, even with the body obscured by a tangle assortment of wires...she was there.

Finally the program booted up and he could focus on something else other then what was floating in the tank. The program had a very basic text driven interface, it gave him two options, 'Yes' or 'No'. He typed Yes and then the program began to run, text rolled by on the screen as the machinery in the lab began to start up.

/----------------------------------------------

/Loading Program

/PROJECT-E

/INT LCL DRAINAGE

/TANK PRESSURE 100

/87

/64

/59

/42

/23

/16

/15

/8

/4

/0

/DRAINAGE COMPLETE

/BEGIN ARTIFICAL CORE INJECTION

/SUBJECT NAME: AYANAMI, REI

/SUBJECT OCCUPATION: NERV AGENT

/BEGIN ARTIFCIAL SOUL INSERTION

/----------------------------------------------

Shinji could only watch as the machinery sprang to life, there was a loud whirring noise as the LCL in the tank drained out, flooding the nearby tanks. Stumbling back he looked on as the wires surrounding Rei's body untangled themselves leaving only her naked form held in place by the mask she was wearing.

He looked down as more text filled the screen.

/----------------------------------------------

/CORE INJECTION: COMPLETE

/ARTIFICAL SOUL INSERTION: COMPLETE

/MEMORY RECOVERY: COMPLETE

/----------------------------------------------

Core Injection, Soul Insertion, Memory Recovery...the text stayed fixed on screen as more whirring was heard from the tank and the machine. Shinji observed as Rei's body twitched as each process completed. Was this what he father had wanted him to find? Was Rei the weapon they were supposed to use?

/----------------------------------------------

/DOWNLOADING OBJECTIVE

/INITIATIVE-S8472

/----------------------------------------------

There was another pause on the screen as Shinji continued looking on as Rei was being awakened in front of his eyes. This made no sense...she was supposed to have died hundreds of miles away from here. What was she doing in this laboratory?

/----------------------------------------------

/OBJECTIVE DOWNLOADED

/SUBJECT AWAKENING COMPLETE
/SEEK OUT INSTRUMENTALITY

/----------------------------------------------

Instrumentality? What was Instrumentality? Was this what was supposed to happen, was this supposed to help them? Rei waking up and then some process called Instrumentality? The mask covering Reis face lifted and the tank opened ,allowing her to step out. She looked across at Shinji either unaware or simply not concerned that she was not clothed. Shinji was barely able to speak as he addressed her. His only thoughts being what the hell was going on.

"Ayanami...you're...I thought you were dead...you..."

She did not respond instead she simply looked at him and then with one swift movement she expanded her A.T. Field knocking him off of his feet and sending him flying back. He quickly scrambled to his feet and went after her. She spun around and stopped him, sending him flying back again.

This time it was accompanied by a brilliant flash of light, Shinji got back up and looked at where she had stood. Ayanami had vanished, she had attacked him and then vanished in that flash of light. Just as he thought more about it he remembered Asuka up top. He had left her to deal with nine attackers and she hadn't followed him in yet.

Shinji sprinted back out of the building back to where he and Asuka had been attacked only to find the area completely deserted. He looked around but there was nothing there, none of the attackers, no Asuka...not even his father's body. Had they all vanished just like Ayanami had a minute ago?

"What took you so long?"

He span around at the sound of the voice and saw Asuka emerging from a nearby alleyway. She looked badly injured, her face was cut and her shirt was torn. Shinji could see a mixture of blood and LCL dripping from wounds on her Arms and near her eye. He ran over embracing her, not caring that she screamed out in pain when he wrapped his arms around her. She shoved him off and nursed her injuries muttering to herself.

"Well if they didn't hurt before they do now...what happened down there Shinji? They were attacking relentlessly, I kept on taking them down but they kept on getting back up and then...I don't know if it was the blood loss or what but...Ayanami appeared and expanded some sort of A.T. Field and then...they were gone in a flash of light."

Shinji nodded wiping his eyes, "I know...she attacked me, that was what was inside the lab Asuka...Ayanami was there in some sort of tank..."

"Are you sure?"

He looked at her, "Yes...of course I am, we need to get back Asuka. Whatever happened it can't be good."

He took a few steps forward before Asuka called after him, "Shinji...I'm sorry about what happened to your father..."

He paused and responded his voice emotionless, "I know."

10h December 2015

Command Centre

It was well past midnight when they finally arrived back at the camp. Asuka threw the bag she was carrying down on the floor and paused at the entrance. They had to ditch the car they were driving some time ago much to her annoyance. The rest of the journey back they had walked mostly in silence only really speaking to say when one needed to rest or to utter something else.

She didn't mind it being that way though, all she wanted to do was get back, confirm that they had completed their mission and then rest. She knew though that that would be impossible, they hadn't completed the mission. Shinji's father had been killed in the process, Ayanami had somehow been restored to life and for all she knew there were still nine people with advanced Evangelion serum flowing through them out there.

"Asuka, I..."

She turned around just in time to catch Shinji before he fell to the ground. She quickly hooked her arms under his shoulders and gently guided him to the floor laying him down. Exhaustion she told herself, he was just exhausted. Blood loss, a couple of miles walk and narrowly escaping nine genetically enhanced freaks...anyone would go down from all that.

If that was the case then why did she find herself trembling with fear that he might not wake up? Why was she on the verge of breaking down, fearing that he was gone? She took a few deep breaths and wiped the tears from her eyes, telling herself that he would wake up. That he had just collapsed from all the strain but something inside her wasn't letting her think that way. She turned and placed her hands on his shoulders and began shaking him.

"Don't do this...wake up damn it."

She shook him more violently as she felt tears streaming down her face. Every part of her just wanting him to wake back up. She didn't care if he was exhausted, she needed him there with her.

"Don't leave me like this, please...don't leave me..."

She stopped shaking him as she saw his eyes open slowly, he looked directly into her own eyes and smiled.

"Sorry."

She laid down next him and laid her head on his chest, "Idiot..."

"I know."

"I wish this could be over, that we could just have...semi normal lives again."

She thought about what she had said, what would she be doing if this wasn't happening? Would she be working with Shinji? Would they have even met?

Shinji was thinking about it too, "If this didn't happen we wouldn't have met though, I suppose that's one good thing to come out of it."

"Maybe but it isn't exactly convenient, either of us could die any time from now. We're pretty much the only free thinking humans left on Earth aside from those inside the camp."

She paused for a moment, thinking about it a bit more, "You know even if we had have met and still been assigned to each other what would we be doing? We'd probably be stuck investigating some random paranormal occurrence in a Tokyo 3 suburb. I'd think you were an idiot with your theories and you'd think I was the closed minded sceptic who isn't willing to listen. We'd solve the case and then both go home to our pathetic lives..."

Shinji chuckled, "Yeah that sounds about right..."

Immediately the chuckling stopped as the events of the day came back to him. "I just wish..."

He paused finding it difficult to get the words out, "I wish I could have gotten to know my father a bit more, I always thought I hated him because I didn't know why he abandoned me and why he placed all this on me."

She didn't respond yet, waiting to see if he would say anything else. When she wanted to respond she found that she couldn't. What could she say to him? He had only just that day saw his father shot dead in the middle of the street.

"He died for the cause he worked hard for Shinji. He was dedicated to it, I know its cold but he died so that you could get into that lab and insert that software."

"I suppose but...what did we achieve with that...Ayanami appearing to us and then vanishing. It doesn't feel like we have achieved anything."

"I know what you mean, I was at least expecting someone to greet us when we got back. What a disappointment that was."

For the first time the two of them sat up and looked into the camp. Every light in the camp except for those illuminating the entrance was off and there was complete silence. It was strange how none of them had even noticed it before. They had been so preoccupied they had never bothered to look inside. Shinji quickly got to his feet and took out his flashlight.

"Asuka, you check the western quarters I'll look at the eastern ones. Something isn't right here."

She nodded and also took out her flash light and headed off in the opposite direction to him. Shinji quickly made his way over to the quarters and peered inside aiming his flash light at the various bunks there. Just as he suspected everyone inside was gone, their belongings left scattered but the people themselves vanished.

He turned away and went back over towards the camp where Asuka was stood waiting for him, he called across to her. "They've all gone, no one has left it's like they were there then just...vanished."

"You don't think Keel could have-"

He cut her off, "No I don't, if Keel had been here I think we'd know about it. He'd use some of them as a bargaining chip or leave some sort of message. There's no sign of forced entry or anything though..."

"I noticed that, it looks like they just...disappeared."

Shinji got ready to respond but was promptly interrupted by a terrifying roar screaming across the sky accompanied by a white flash. He turned towards the source of the flash and saw it was coming from the direction of where SEELE's bunker was. It was a huge cross shaped explosion, he saw several more flaring up next to it before everything turned white around him. He felt his body being forced upwards but he didn't try to resist. Instead he allowed himself to be taken to wherever this force wanted him to be.

-------------

When Shinji opened his eyes again he found himself in a white room or, to be precise not so much a room, but a white space, stretching on into eternity. He took a few steps and his footsteps echoed loudly into the distance. What had just happened to him? This was so different to when he had been taken before. The force pulling him, the cross shaped explosion and this white space, was this what was supposed to happen when he loaded up that program?

"That is correct, Ikari."

Shinji spun around at the sound of the voice and then saw her, she was only a matter of metres away from him and was wearing the same black catsuit he had seen her in when they first met. The strange thing about her was that she was floating, only a matter of inches from the ground but she was.

Shinji questioned her, "What is this place? Did I die?"

Ayanami shook her head and moved towards him.

"You did not die Ikari...this is the Instrumentality that you started when you awakened me. This is what your father wanted you to achieve. The process in which every human soul is taken from the body and connected."

This didn't make any sense, she had just said that the soul had left the body but...he could still see his body. He could still move and use his body, it was still there and it was still a part of him. Besides which even if that was the case how could the soul survive without the body?

"Your body has been harvested and inserted into the collective, as has Sohryu's and every other living human. It is still alive and functioning, your soul has simply ascended for this moment in time."

He turned to her and shouted back angrily, "That wasn't meant to happen, we were supposed to avoid this. We were supposed to be freeing humanity! You mean my fathers plan was for this to happen anyway?"

"That is correct."

Shinji dashed forward and grabbed hold of Rei's shoulders shaking her violently, "He lied to me then, there was no virus was there?"

"Your father's scenario was carried out as planned, he did not lie to you."

Shinji shouted, "If he didn't lie then why am I here now? Why aren't I back at the camp? Why is every other human going through this process?"

"Because that was a requirement Ikari, you and Sohryu are the only two humans going through this process."

Shinji calmed himself down and released Rei from his grip shaking his head, "So is there some way to return, is there a way to go back?"

Rei did not answer his question directly instead she told him more about this strange process. "I cannot answer that, it is not for me to say. This process was designed to provide an idyllic environment for the souls of those harvested."

She paused before continuing, "While the bodies themselves are used as slaves the minds and souls are taken through this process where each one enters their own perfect world. All my race seeks is perfection for all species across the galaxy. While you may not agree with their methods, you cannot disagree with their goals."

Shinji was about to argue back when he noticed one thing in Rei's short speech, she had referred to them as 'my race'.

"Your race?"

"Allow me to correct myself, the being you see in front of you is the being you know as Rei Ayanami. Rei Ayanami was created shortly before what you came to know as the Impact, she was created as a vessel to hold the soul of the second angel. The Angel known as Lilith, I stand before you now as both Lilith and Rei Ayanami, we are both one and the same entity."

"Why? If you have the force and power you do have then why didn't you just take us by force? Why all the lies and secrets, why not a full on attack?"

"That was not a choice of mine, my race was split into two factions, each with similar goals. We came to your planet thousands of years ago. There was a war which lead to both myself and the representative of the other faction, the being known as Adam, being placed in stasis until we were discovered by SEELE. Adam struck a deal with SEELE to split power and colonize this planet by force."

She paused for a moment, "My side do not desire the same, we offer races a choice between ascending and not. If people desire they may return at any time. I was found by your father and was placed into this vessel. I lived as Rei Ayanami for a short time coming to terms with who I was and finding out about humanity. It was not an easy process as you can imagine, at many times I was unable to recall my identity as Lilith and often found myself longing for something more as a human."

"But Rei...you..."

"Died?"

She paused, "Yes I did, however the soul of what you know as an angel is transferable, I was simply transported into this body and awaited being awakened by your father. It was a pleasant surprise to see that it was you who had activated the clone."

"You attacked me though and then you disappeared."

"I know and for that I apologize, I was disorientated and I needed to..."

"You needed to harvest those remaining on Earth?"

She nodded and smiled, "That is correct."

Shinji walked forward but was blocked by her A.T. Field, almost immediately the scene around him began to shift. It was no longer the white space but instead what he recognised to be a small suburb in Tokyo 3. He tried to turn around but found he was no longer in his body but was instead just an observer.

"What is this?"

"This is what your heart desires Shinji Ikari, this is your perfect existence."

He watched on as he saw a group of people on the front lawn of a house, three women and an equal number of men. He recognised two of them immediately but the third one he couldn't quite figure out who she was just yet. He heard Ayanami's voice again as he tried to remember.

"Strange that you do not recognise the third one, she is the person for which Ayanami's body is based off of. She is the one who guided you into trusting your father."

"My mother...why is she alive?"

"This is what your heart created, a perfect world where your mother never died, your world where you cannot be hurt...where you do not feel that pain you do every day...where you were never abandoned and never had the fate of the world placed on you."

Shinji watched a bit more as the other version of himself stood with his arms around Asuka. It looked peaceful, Misato was there alongside Kaji, his father was there along with his mother. It was as had been described his ideal world, a world where he could not be hurt but why was she showing him this? Did she want him to just accept this? It was tempting but at the same time it wasn't real.

"This is wrong..."

"You do not like this?"

He watched a few moments longer, trying to decide if he really thought it was wrong. He was tempted, and it most certainly seemed real. He could feel the breeze against him, he could smell the air and the faint smell of barbecued food drifted over to him. The voices and the laughter from the people gathered, from the family...his family, rang in his ears.

"I...don't know what to think."

"It is what is inside your heart which created this world Ikari.. your dreams and desires helped to shape this. Everything you wanted is here, family, friends, a proper life..."

A car pulled up to the front of the house, Shinji felt tears well up in his eyes when he saw the person who stepped out.

"Touji..."

"Yes...in this world there was no Evangelion project...NERV still exists and you still work for NERV but there was no colonization project, no SEELE, which means Touji never died."

It was becoming more real for him, the idea of leaving it all behind and accepting this. Shinji thought about his life so far, lies...manipulation...abandonment...loss...he had never had nor was likely to have a good or a happy life. The people who he cared for were dead or likely to die, if he went back then what would happen? They'd just spend time running away, here...well it wasn't real but...it was as good as.

He was about to take a few more steps across when he caught this worlds version of Asuka looking over at where he was. She was staring through him, Shinji knew she couldn't see him but for a moment he could have sworn he saw her expression change. Disgust...was that it? He thought about Asuka, the real Asuka...not this fantasy Asuka. What would Asuka tell him right now? If she knew he was considering this? Considering accepting a false reality? She'd hate him for it, and in the end he'd only end up hating himself even more.

"You are still having doubts?"

"I like it but...it isn't real, even though I desire this, even though I want it...it isn't real. It's just a facsimile, it's fake. I'd just be running away if I accepted this and I've done too much of that. The Asuka there...she might accept me but the real Asuka she would never accept me if I did something like that."

"You would rather live where you can be hurt than where you cannot?"

"I guess that's correct...because at least then I know what's real and what isn't. Knowing that it wasn't real would just cause me more pain because no one there would be the real people."

The scene shifted again and Shinji found himself back in the white space he had been in earlier, Ayanami was stood in front of him again.

"It was just as your father said. You would be strong enough to reject it."

Shinji looked around, confused as to her meaning.

"There was no virus Shinji, the virus was me. I am the one with the power to end this, I can send you back to where you want to be. I can end this process of instrumentality for everyone if you desire it."

"I do."

She smiled, "You must understand though that not everyone will feel the same way you do. The majority will wish to remain in their perfect worlds. These people will over time become your enemies as my enemies use them to fight against you. You must be prepared to make choices you may not like."

"I understand."

"People will only return to you if they desire it, and even then the rebuilding process will be slow. I will have my people assist you as there will be a backlash. Thanks to the serum that was developed this process will happen across my enemies' ships as well. You must be sure you want this."

He nodded understanding her completely, there was no turning back now.

"I do want this."

As soon as he finished speaking the scene shifted again, cross shaped light flared up around him as he felt his body being forced away again. Pain shot through each part of his body as if he was being torn apart and slowly stitched back together.

'What...what is this?'

The pain was too much, he felt his body lifted but he wasn't able to find out where too. Closing his eyes he allowed himself to pass out.

-------------

Asuka blinked and found herself looking into an eternal white space. A room what appeared to be completely white and stretched on forever. She reached into her jacket for her hand gun but found her pockets completely empty. She turned around at the sound of a familiar voice.

"Sohryu I do not wish to hurt you, I wish to speak with you."

The voice sent a chill down Asuka's spine because it belonged to a person that Asuka had up until now thought was dead. Even with the sighting earlier it still scared her, the fact that she could hear Ayanami and could now see her. Asuka stumbled backwards with fear.

"Ayanami you…you're...how?"

"There is much I need to explain to you Sohryu, this is the process of Instrumentality which yourself and Ikari started. The process in which every human soul has ascended from their bodies and connected in one collective entity. Each soul living peacefully in their desired world, yourself and Ikari have been disconnected from this process. Shinji because he is the one who began the process...yourself however...your heart rejected it from the beginning."

"My...my heart rejected it?" Asuka stammered out.

"That is correct, your only desire is to go back and not to live within a perfect world. You desire immediately to go back to a world where there is pain and suffering."

She thought about what she had just been told, it was true. Given the choice she would reject it immediately, she wouldn't run away like that. The thought of it made her sick even though she knew she had in the past tried to convince herself that her problems did not exist.

"If my desire is to go back then why am I here?"

"Because you are only one half, both you and Shinji must agree to allow humanity to return for you to successfully return."

"So why are you here Ayanami?"

"I am here because I am the centre, I am the gateway through with all souls pass. What you see in front of you is the human vessel designated Rei Ayanami but this vessel contains the soul of the second Angel, Lillith."

"You...you're an Angel?"

"That is correct, my designation by your standards would be the second but I was born at the same time as the one known as Adam. I am the leader of another faction working against the ones you have seen. We arrived on this planet thousands of years ago but a war forced both me and Adam into stasis until we were discovered by SEELE."

She stopped speaking for a moment as the scene shifted to an unfamiliar setting. From what she could see it appeared to be a tomb of sorts, from the markings and ornaments she would guess Egyptian but there were many other markings there unfamiliar to her.

"What is this place?"

"This is where they held me for thousands of years until I was discovered by Gendo Ikari and awoken. This is a recreation of the tomb from my own memories."

"Egyptian?"

"No, but many of the things here did find their way into the Egyptian empire. No, this is a place that sank before the Egyptian empire. A place spoke of only in your legends..."

Asuka turned and looked at her sceptically, "You can't be serious?"

"I do not understand why you have trouble believing this, considering all that you have seen."

Asuka laughed, "I guess the idea of a sunken continent is still a bit hard for me to believe especially considering that you're telling me that your people have been here since before that time."

"Understandable but my origin is not important, I needed to show you this so that you could see that I am on your side."

"If you were on our side you would have prevented this and not brought us here. Instead you..."

"Took the rest of the survivors and did the same to them as our enemies did? I know Sohryu, but we had no choice, for this to occur every human had to undergo this process. It was the only way, I promise you will return. Shinji is currently making the decision. I regret I have to offer him the choice but I am sure he will make the right decision."

She paused again but before Asuka could speak she started speaking again, "There is one thing I would like to mention to you. One thing that has not been cleared up, the subject of Katsuragi and her child."

"Why did Keel want her child?"

"He saw the child as a threat, that child is the first of a new line of humans. Genetically engineered to be resistant to disease, to be resistant to us and to be very much like yourself and Ikari. It was a desperation manoeuvre by Gendo which may have placed you all in unnecessary danger but it was one that he deemed necessary."

Asuka could barely hide her anger, she had begun to actually trust Gendo but now hearing this she didn't know any more. Her thoughts wandered across to Shinji, did he know about this too now? If their minds were connected there was the chance he might know about it. She turned to Ayanami and questioned her further.

"Why a child though, why not more people like me and Shinji who were already grown? Surely Keel would have known a baby would be unable to fight."

"That is correct but Keel was paranoid, the child was a potential threat so he wanted it. That child though is not alone, there are more in the world that will be like it. A new race of humanity, however unfair it may seem you and Shinji must ensure that they survive. When you return Keel and the others will hunt you down, they will use the bodies of those humans that did not return against you and when they do you must be ready to fight back."

It sounded so strange, so bizarre that this person...that Rei was talking to her like this. This was not the Rei that Asuka had known but at the same time she could see it was. She was still there but something else had taken hold. Asuka nodded.

"We'll fight back, we've came too far to give up now."

-------------

Shoreline

Shinji opened his eyes and looked out across the sea, it was still night time but he could see huge white flashes in the sky. In the distance he thought he could make out the faint image of Rei Ayanami but when he blinked it was gone.

'Must have been my imagination...'

He slowly turned his head to the right and saw, in the distance, another figure lying down. Her red hair scattered around her head. Shinji scrambled to his feet but found himself unable to carry his own weight. He resorted to crawling over towards her and knelt beside her.

'Asuka...is this really her? Is this real, am I actually back?'

He reached out with his hand and gently stroked the woman's forehead, it was warm and it was definitely real. She didn't stir though, he decided for a moment just to leave her and let her rest. He looked out across the shore and into the distance. Everything was silent, it didn't seem like there was a living thing for miles around but he was fine with that. They would return in time and when they did he would be ready. They would rebuild and they would continue to fight back.

He took a brief look at Asuka again and smiled before laying himself down next to her, he put his arm round her and held her close to him. He didn't know how she would take it when she did wake up but at the moment he didn't care. She was all he wanted right now, to be close to him and to be next to him.

Ayanami's words were still etched into his mind though, 'You must understand though that not everyone will feel the same way you do. The majority will wish to remain in their perfect worlds. These people will over time become your enemies as my enemies use them to fight against you. You must be prepared to make choices you may not like.'

He thought about it, would he be able to fight against people he once knew if it came down to it? Would he be able to defend himself, he had already seen situations in the past where he hadn't been able to and it has cost people their lives. Would he be faced with decisions like that again?

"You know Shinji...if you keep thinking like that then you won't be ready."

He jumped a little when he heard Asuka's words, he must not have been aware that he was thinking out loud nor must he have been aware that she had woken up.

"How long have you been awake?"

She grinned, "Since you put your arm around me...I would have said something but I knew you weren't going to rape me so I didn't mind. We're the only two here...we're the last two people on Earth for this moment in time."

"I know...it's unusual. They'll return though...I made sure they would...in time they'll all return to us."

She reached up and kissed him, taking him by surprise, he returned the kiss wrapping his arms around her and gently stroking her body. She pulled away and whispered too him "Congratulations Shinji."

A/N: Wow thirty chapters and it's finally over. Not to mention this is my longest chapter ever so that's pretty good. This has taken up a good portion of my time over the past year or so but it's been worth it. I loved writing this, making improvement with every chapter I wrote and seeing people's reactions to it. The ending was difficult to write as you would imagine, I'd like to think I did a good job with it and that the people reading it will enjoy it.

Before I go on there are two people I'd really really like to thank for this. The first of which would be my girlfriend Charly. Not really much to say really, she had supported the fic and read a good chunk of it. She is also responsible for drawing the fic's version of Asuka and Shinji. If you would like to see it then it is available for viewing on her DeviantArt page, her username there is LadyMyrina and the picture is simply titled conspiracy. This is something she didn't have to do but did for me, and I really appreciate it. For being so awesome and supportive, I'm dedicating this chapter specifically to her.

The second of which would be my pre reader Ste, the same guy who pre read my previous fic Strange New Worlds. Ste is an awesome guy who has had to put up with my endless number of grammatical mistakes and confusion over the then/than. He had taken time out of his life to read this when he could be doing something better. I really appreciate that and I'm glad to have a friend like that.

Third of which is the cheesy one, all the people who had read this fic and reviewed and everything. J.G, Dartz, Himonky, Hououza and anyone else who has commented on it. Thank you so much, your words and comments mean a lot to me and any advice and criticism that was given was taken on board and employed.

Anyway like I said I hope you enjoyed this fic, please don't hesitate to leave a review or contact me.