Disclaimer: I don't own NGE

Chapter 3: Wake-up call

- NERV, hospital -

Rei was intrigued. No one had ordered her to be here, yet here she was; Sitting on a chair to watch over the third child while he laid unmoving in his hospital bed.

Twenty-six hours ago the battle with the third angel took place. And for those twenty-six hours she had been at his side for a total of eighteen. She had not slept, had hardly eaten and only left his side when ordered to.

Why was she doing this? Rei didn't understand.

Love.

She knew its definition. And at first glance it seemed to fit, as she was drawn to the boy for reasons she couldn't quiet describe. However love suggested some emotional connection between the two, which was decidedly missing.

The concept was not applicable here.

Friendship.

Friends often wish to be there for each other. Especially if one of them is in a state of distress. However Friendship requires past experiences made together. A friendship is a construct that requires all parties involved to invest into it to keep it alive. Rei had no prior experiences with the third child and neither did the two of them ever build a friendship.

The concept was not applicable here.

Camaraderie.

Both Rei and the third child were EVA pilots. That made them comrades in the war against the angels. However camaraderie also implied them to have sortied together in the past, to, again, have an emotional connection forged in battle. As it stood she and the third child were more like coworkers than true brothers-in-arms.

The concept was not applicable here.

The reason for her attraction to him eluded Rei. She felt no sexual or emotional desire to be near him, yet she was drawn to him.

His pale skin mirrored that of her own and his eyes and hair were of no natural color either.

Rei had read the third child's file while she watched over him. From what little stood in it, she had gathered that he was lonely, fearful and overall avoiding other human beings.

He was abnormal, ever frightened, ever isolated from contact with others. He would not engage with others unless forced to.

She was abnormal, ever present, ever unresponsive. She would not engage with others unless ordered to.

Both of them failed to meet the expectations one might have for a child their age. Both had no one. He because he fled from any social interactions and she because she simply did not participate in them.

Rei, moving for the first time in hours, shifted her seat closer to the third child.

The two of them were... similar. Similar in both mind and body. The only difference between the two was seemingly that unlike the third, Rei had her orders.

Orders to live by. Orders that dictated her every move, her every action, her every thought. Orders to fulfill, even if at the cost of her own life. A purpose.

Would she become like the third if her orders were to disappear? If she was left without guidance? Would she begin to wander the earth unsure of what to do? Afraid of what needed to be done?

Would he become like her if given orders to live by? If he was given guidance? Would his fears fade into quiet endurance if he did not have to think for himself?

Empathy. Sympathy.

Rei saw herself in the third child. An alternate version of herself. An alternate way she could have turned out. But at their cores, they were the same. He was the only other person she could understand, not only from a purely logical point of view, but also on a deeper level. And she would likely be the only other person that he could understand...

These concepts were applicable here.

She was at his side because he was the only one she could relate to.

It was a satisfactory answer for Rei.

- NERV, bar -

They were throwing a party.

She almost send a kid to his death and they were throwing a party.

A. FUCKING. PARTY.

Misato's mood was taking a nosedive as the music behind her started again. Colorful neon lights danced about.

To her that meant that she needed more alcohol. One or two, or maybe five more shots and she wouldn't need to remember this "victory" party.

They were celebrating a pyrrhic victory. Half the city was trashed, Unit 01 was in need of extensive repairs, the likes of which were hard to afford, even for the UN and they almost had their first casualty in this war.

Misato looked out of the bar's window in hopes to to take her mind of things. Outside the geofront was dimly lit, only illuminated by a few artificial lights on its ceiling. It was around midnight, after all.

The music began to pick up speed, people were talking loudly all around her. Laughing, dancing, joking around. Misato tightened her grip on the glass before her. It was nearly empty. 'Gonna need to get this refilled soon'.

"Some whiskey, for the two of us, please" a distinctly male voice said as an empty seat next to her was seized. She turned her head to take a look at the guy who just bought her alcohol.

"Who..." Misato slurred out. Next to her sat a rather good looking man. He was dressed in a black business suit, with his hair a matching color. His eyes were green and he did have a nicely pronounced jawline. And unlike someone this new man knew how to shave. Looking at his body, he seemed to hit the gym at a regular basis. She was certain she also smelled something. Probably deodorant, though it could be something more fancy.

"I'm Virgil" he gave her a warm smile.

"Do I know you?" Misato narrowed her eyes. Her speech was barely intelligible.

"I doubt that. Though even if we are strangers, I can't just sit by and watch such a beautiful woman as yourself sit around and sulk" he gestured to the dancing people around them "especially on such a festive occasion"

"It is hardly festive" Misato averted her gaze back to the window. "We almost had our first death in this war". The anger and dread the thought carried with it seemed to be purging the alcohol out of her bloodstream.

"Ah, I see" Virgil too began to look out of the window. "And you blame yourself for it?"

"They are just children!" Misato was eyeing the remainder of her drink "they shouldn't have to shoulder this responsibility. To save mankind. To possibly get killed"

"As it stands we have no other choice. And this is a war, casualties are not only possible but expected" Misato was beginning to glare at him, daring him to keep talking, but he continued nonetheless "And when someone finally dies,... there just isn't a way to prepare for it"

"And, pray tell, how would you know that" Misato was nearly fully sobered up. 'the audacity! Like he knows what I'm going through!'

"From experience" He took a deep breath and closed his eyes for a moment as he prepared himself to tell his story. "I was not always some UN bureaucrat. Up until eight years ago I was part of a UN peacekeeping force in Africa. I know what it feels like to loose others... to loose those close to me"

Misato's anger was gone as quickly as it came. Perhaps she was too quick to judge. "A veteran from those days... ". A new thought entered he mind "your stories must make all this look like a mild inconvenience", she sneered, "here I sit complaining about the near-death of one child to the man who helped clean up Africa after the second impact."

"Please..." He carefully placed his hand on her shoulder, she didn't pull away. "I would never dare to compare my traumas to those of others. Yes I have seen and done horrible things, but that doesn't make what you are going through any easier for you"

Misato turned to look at him and he smile once more. "It is okay to be scared of loosing those under your command. It shows that you still have some humanity left within you"

"We had a visual connection to him for most of the fight... the look on his face when he was grabbed..." Misato felt like she was being drained of all her energy as she recalled those moments.

"The look of utter despair? Of staring death in the eyes? I know that look all to well"

"Even on a child's face?" She wasn't angry anymore, or even annoyed. She just felt dead inside.

"I'm afraid so" Virgil took an other deep breath "When we were clearing small towns and villages they would often send children at us. They would be told to beg for food, water or money. All the while they would be loaded with explosives. And when they got close enough to us..." He needed a moment to calm himself. "Standing orders, for a while, were to shoot anyone who tried to approach us. I had to carry them out on more than a few occasions. The looks on their faces, when I raised my weapon,... were always the same"

Their drinks had arrived and Virgil gulped his down in a single swing.

"Those kids often had nothing. Even their bodies would already owned by someone else. Their life was the last thing to their name and I would take even that from them. In the fraction of a second before I fired, I would always get a good look at them... The children who had just lost truly everything"

"I'm... sorry" Misato wasn't sure how to react to such information.

"Don't be" A stern look returned to him "I leaned to accept my actions"

She was still at a loss for what to do. This man had just poured out his deepest trauma to her. Trauma that he had apparently dealt with. And seeing how she was struggling with her own... 'Perhaps... he could teach me'

"How did you do it? Get over it, I mean"

"I didn't. Those memories are still as fresh as the day they were forged" He smiled weakly "but I did learn how to live with them and how to not be guided and defined by them". His smile cracked a bit. "The thing I found helped me the most was to not be alone. To have someone else around, even if they are a complete stranger. I tried to shut myself off from the world for a while, but then those memories would be my only companions"

"..."

Misato felt like he had helped her. How exactly she didn't know yet, but she felt better. It was as if some secret, some long thought lost wisdom had just been shared with her.

She looked around for a clock and it only took a few moments for her to spot one. It was late. "I have to get going. There is a lot of work waiting for me tomorrow", she said as she got up from her seat. The whiskey Virgil had bought her was still untouched. "But... thank you"

"Please, allow me to accompany you. You are hardly in any state to return home alone". Virgil got up as well.

And before long, he helped a drunken Misato move through the crowd around them.

- NERV, laboratories -

"Sempai" Maya began as she stepped into the large sterile room Ritsuko was currently residing in. It was filled by long rows of tables which held laboratory equipment. The walls were lined with cabinets, all of which were fully loaded with various chemicals and concoctions. "I finished Shinji's blood work"

Ritsuko herself was busy working on consoles, microscopes, centrifuges and a host of other machines, seemingly all at the same time. It had been a long while since she had last slept and it showed. Nevertheless, she had work to do. Lots of it. When she mused that she'd run every test under the sun on the third child if they survived the battle, she meant it.

To any outsider it would still look like as if Ritsuko was desperately trying to meet some quickly closing in deadline. But those that worked closer to her, like Maya, knew that what Ritsuko was displaying was just her regular speed at work.

"And?" the faux blonde asked, not taking her eyes off her work.

"I... I ran the tests four times... on separate equipment" Maya simply handed her the stack of papers that were her findings. It would be quicker for Ritsuko to read them herself.

Taking a quick look at some of the results, Ritsuko stopped dead in her tracks. 'Christ...'. Simply looking at the boy, she had expected the results of all these tests to be similar to those of Rei. But this...

She began flicking through the various pages. Taking into account her own work on the tissue samples they had collected from the third...

It was painfully obvious that someone had meddled with him, down to the genetic level. But what truly worried Ritsuko was the extend to which things would have to be changed for these results to be possible...

She couldn't make heads or tails of what she was looking at.

Ritsuko sighed. "You can go and sleep, I will finish this up". Maya was truly an exemplary aide so she didn't want to work her into the ground if it could be somehow avoided.

Maya nodded and said her farewells for the day before leaving. As for Ritsuko, when she comes back tomorrow, she would begin to try to understand the changes that had been made to the third's genes, even if that meant that that she will have to take his DNA apart atom by atom.

One thing was certain however: her report to Gendo wasn't going to be a fun one.

- NERV, hospital -

'Ow', it was the first thing that came to his mind after he woke up. Everything felt sore and even after sleeping for god knows how long he still felt tired and exhausted.

'Where am I?' Shinji open his eyes only to be immediately blinded by the sterile white light around him.

Shifting slightly in his hospital bed, he lifted a hand to cover his eyes. It wasn't easy, but he managed to do it, albeit barely.

"You have sustained moderate injuries in your battle with the third angel" He didn't recognize the voice. It was faint, almost delicate in nature. "Doctor Akagi has ordered you to rest until she clears you for active duty again"

'active duty', Shinji didn't like the sound of that at all. Also, his battle with the third angel? 'When did that happen?'. Also also, what's an angel?

His head was beginning to hurt, but at least his eyes slowly adjusted to the light.

Again rallying a lot of his strength, he turned to look at whoever was talking to him.

Before him, on a simple chair, sat a girl. She was no older than him. Her hair was blue and she had red eyes. Shinji felt that he had seen her before, but his memories were all messed up. She wore a hospital gown. And where it wasn't covered by bandages or casts, her skin... it was pale, almost to the point of being white. Like his own skin.

"Who..." his voice was ragged.

"Your vocal cords have sustained damage due to excessive screaming during the battle. It is advised that you do not speak until they have healed" Rei was quick to interject before he pushed his already strained voice any further.

"..." And so they remained in silence. Rei was seemingly content to simply overlook the hospital room they were in. Shinji, however, though he laid still, was anything but relaxed.

'She is like me...' he took an other look at her pale skin and then at his own. They were almost the same shade.

His skin... an eternal testament to his past. A daily reminder of days best forgotten.

A chill ran down his spine.

He knew he wasn't the only one who was taken by them, but so far he had been under the impression that he was the only one to live to tell the tale. Was it possible? 'A second survivor?'

More silence.

The door to the room opened and through it a blond woman wearing a labcoat entered. She had considerable bags under her eyes. Shinji knew that he knew her, but her name eluded him.

"Rei, Shinji" the woman greeted them.

"Doctor Akagi" Rei greeted her in return.

Ritsuko found it odd that Rei had decided to be at the third child's side ever since the battle, but she did not object. It was good to have someone look over him in case anything happened. "is everything alright here?"

"The third child has shown no abnormal behavior, considering his current condition" Rei answered.

The faux blonde woman looked at Shinji for a few moments, narrowing her eyes as if the answers to her question could be gained by staring at the boy. Before long, she gave up and turned to leave.

"Good, then I'll be leaving for the night"

And with that the NERV's lead scientist was gone again.

And Shinji was once again left with his own thoughts. 'Third child... what is that supposed to mean?'

Though he was tired, he would not sleep this night.

- NERV, commander's office -

"They say it was miscommunication. No more than an accident" Fuyutsuki handed Gendo a report from the UN.

The commander of NERV sat behind his desk, hands before his mouth. Though he looked as he always does, he was angry. Mistakes happened, of course, however lately more and more people have been found wanting. Far more than he was comfortable with. And worst of all, it was starting to affect the scenario.

Firstly there would be his dead wive's estranged brother. Gendo had dumped his son at the man's door some ten years ago.

And about four days ago he had sent a letter to the mans residence. A letter addressed to his son; telling him to come to Tokyo-3.

So imagine his surprise when instead of the third child, he received a letter from the man directed back at him, telling him that his son had ran away to be never seen again only a few months after Gendo had left him. That and a complementary "fuck you" to the commander of NERV, as if loosing his kid was somehow part of a plan to get back at him.

And thus, Gendo was left with only hours before the third angel would make landfall to find and get the third child. Luckily the search for his son didn't take too long as the Magi found him almost instantly; in NERV's employee databases of all places.

A fax addressed to the kid was quickly sent, telling him to come. It was worded much like the original letter.

As for the fool who couldn't look after a damn child and thus almost cost Gendo his scenario, he had severely underestimated the power Gendo held and the lengths to which the commander of NERV would go to to get back at those who had betrayed his trust.

That is to say that the man no longer existed and had never existed. He could no longer be found in any official records and his friends were currently being informed that they never knew anyone of his name.

And now, as if his child's incompetent guardian hadn't caused enough problems, the UN began interfering in things they had no business to. Things such as the transport of the third child to NERV-HQ. But then again, as NERV's commander, Gendo had worked with the UN before. They as an organization as well as their high-command, from whom those "accidental" orders stemmed, were hardly ones to make such mistakes. Especially since the UN was a direct extension of Seele.

"The UN is many things. Foolish. Ignorant. But they are not incompetent" Gendo muttered to himself but loud enough for his right hand to hear. And he would have meant it, if the third child was at least flown to him directly. But no, someone along the way decided that the VTOL carrying him was better of fighting the third angel.

Another failure that would have to be dealt with.

"You believe there is more to this?" it was a rhetorical question. Of course Gendo did. Fuyutsuki knew his former student well enough for that matter.

"The timing of this supposed miscommunication was extremely convenient. Had this accident not occurred the third child wouldn't have arrived in time" NERV's commander didn't turn to look at the vice-commander while they were conversing.

"Then perhaps the orders came from the council?" Fuyutsuki couldn't think of any other explanation right now. "Or it really was just an extremely lucky twist of fate"

"If it was the council then why would they have tried to disguise their orders as accidentally given? And if it was just an accident then the UN will have some internal restructuring to do to ensure it will not repeat itself". Gendo stopped to think.

As for Kozo, a new possibility came to mind. One which his former student had likely already considered and disregarded, but he would state it nonetheless. "What if we are dealing with an unknown third party?"

"Not impossible, however the old men were extremely careful to stomp out any competition for their position of power". Gendo came to a conclusion "as it stands, we do not have enough information to go by. For now we will simply monitor the situation. If it was an accident, we can count ourselves lucky. If it was the council who gave those orders, it would mean that they are keeping a closer eye on us than I'd like. And if it was someone else,... then we cannot form any plan of action right now. There would be to many unknown variables"

And with that, the matter was sealed... For now.

As for an other matter...

"What about your son?" Fuyutsuki began again.

"He is obedient to me and can pilot Unit-01"

"Aren't you worried about what happened to him? From when he went missing to when he was found again, two years later in Africa by a UN peacekeeping force, I might add, we have no record of his whereabouts."

"Doctor Akagi is currently tasked with uncovering the exact nature of the changes that have occurred to him. And I take it that you have already dispatched our own men to find out where he went in those years", though the sentence was worded like a question, Gendo said each part of it as if it were a fact. Of course his former teacher had already taken the initiative to look into the matter.

"I have. Still, we should be prepared for anything"

"Do you believe that the third child's disappearance ten years ago is connected to the UN's erratic behavior during the battle yesterday?"

Fuyutsuki sighed mentally. Was he truly this easy to read? It didn't matter right now. "Call it an old man's intuition, but yes"

Out of all his minions and pawns, there were two people whose concerns and ideas he would actually listen to and consider. His former teacher and his current faux blond love interest. And even though Gendo was NERV's commander and as such had the final say in all decisions made, one of these two people had a hunch. One that may not be completely unfounded either.

"Very well. I will tighten security around NERV and allocate more resources to Section two for them to find out the nature of the third child's disappearance"

- ? -

He stood on the roof of a two story building. Though to call it a mere building would have been an understatement. It, like all others around him, were more akin to massive bunkers, their roofs, walls and foundations reinforced to weather even the heaviest of bombardments. One of the many preparations they had made for the future. Sand and dust clung to everything, including his black labcoat, which he wore even now in the blazing heat. They permeated the air and made it hard to see very far. Nevertheless one could make out the orange tinted silhouettes of more bunkers, radio towers, defensive positions and even more exotic buildings all around him. Between them ran concrete roads, buzzing with activity, though instead of carrying cars, armored vehicles and flatbed trucks were moving about.

Behind him, like on other roofs, was an anti aircraft battery. Two 40mm autocannons staring skyward, waiting silently for the dreaded day to come. On the ground below him, even heavier weapons were emplaced. The question wasn't if, but when they would be attacked. When the final, deadly dance for the future of mankind would begin in earnest.

He, however, was not here to contemplate the future, the past or the present. That had its time and place, namely his meeting in the command center with the other three. No, he was here to oversee the reactivation of old weapon systems.

Before the reinforced building he was on lied a large intersection, in the center of which an armored hatch was situated, not to dissimilar to those in the streets of Tokyo-3.

below the hatch a large elevator shaft extended down into the deepest levels of the facility below. Indeed, all the constructs around him were not only connected by streets but also by an endless network of tunnels. Simple streets could be easily torn apart by bombings and artillery fire, after all.

Though unlike Tokyo-3, the shaft did not end in EVA cages. Instead it provided a direct access to a far colder place.

Trucks began assembling around the hatch as it slowly opened.

"Pierce"

The scientist turned around. "Sir?". It appeared the formal leader of the four had finished his meeting with the other two.

07. It was the number that had replaced the old man's name. It was done out of his own volition as well; and though the reasons for doing so were known to Pierce and the others, he suspected that their leader had chosen this as a form of penance in addition to what he told them.

07 was, as always, dressed in his black business suit. It was a fine piece of clothing, high quality without screaming opulence. He was in his late eighties, his hair fully white though his skin carried few wrinkles. Overall he was in good shape for someone this old. His personal guard followed behind him. Four men clad in armor and tactical gear. The armor was comprised of many metallic plates that allowed for a full range of motion while also offering protection from all sides. They ranged from a thickness of a centimeter around vital organs to only one or two millimeters around their fingers. As for color, the armor was a matte silver, indicating that these for individuals belonged to the taskforces Alpha-2, 3, 4 or 5.

Pierce, on the other hand, was dressed in his black labcoat. Next to his signature scientific mantle, he also wore black pants, shoes and even gloves. He was maybe in his mid fifties, the hair atop his head was still black, thought he first gray strands were making themselves known. Other than that, he was well build and healthy looking. As for his own entourage, he had dismissed them, seeing no reason to occupy members of their most potent and capable taskforces while in the safety of their headquarters.

"The weapons?" the elder of the two began.

"Their cores are fully thawed up and moved out of their cryogenic vaults. They will be kept in suspended animation until they are deployed"

"good"

The hatch was now fully open and from it a platform rose to the top. On it were dozens of cylinders, each no more than a meter tall and half a meter in diameter. Cables and tubes came from each of them, intermingled on the platform floor and ran to machinery strewn between the cylinders. A thin layer of ice had formed on the various contraptions on the platform, even in the hot, dry air and caused them to reflect the sun's intense light into the eyes of anyone who tried to look at them. As soon as the platform came to a halt workers began disconnecting the cylinders and moving them onto the waiting trucks.

"we have decided that we will station our forces to be used against the angels in Malaysia" 07 informed his lead researcher.

"I was under the impression that the country was too unstable for us to move any valuable assets there"

"It is and we will change that"

The first trucks were loaded and began to leave as the two men stood in silence.

Pierce was the first to speak up again. "Such information would have been included in the weekly reports we all make for the others, due tomorrow, so I take it you had an other reason for seeking me out"

"I did" 07 considered his words for a moment "During the meeting the matter of the third child came up. He poses a potential security risk due to his unique past with us"

"If you believe that he may leak information to Nerv, we can have Delta-2 go after him. We could even send out Iota"

"That is why I wanted to talk to you" the old man's voice carried none of the authority that might have been expected in such a moment. He was talking not as the commander of their operation speaking to his subordinate, but as a human being seeking advice. "To ask you if you believe that he will talk. You spend a lot of time with him, after all" 07 paused and gathered his thoughts. "Sending out Iota had been considered during the meeting as well, however neither I nor the others felt that it was right to do so"

The scientist's thoughts stopped dead in their tracks for but a moment. They were still lying to themselves...

Taskforce Iota was amongst the more unique ones out there. Where as Beta specialized in infiltration, aka being spies or Delta in sabotage, aka being spies that break stuff, Iota's main purpose was to act as counterintelligence; to find information leaks and kill them. Something further underlined by their affinity to use psychological warfare to keep mouths shut and lips tight. And in their work, they were ruthless. They needed to be, for if they were they not, the UN and with it the council would have already discovered them.

Pierce though about the matter for a scant few seconds before forming a conclusion. " I cannot say with certainty, however when I worked with him, I found his mind and will to be weak, or more accurately, broken. It will be hard for him to face his past and talk about it on his own volition, but it will also be hard for him to resist anyone forcing him to remember"

"So, if Nerv starts pressing, he will talk?"

"presumably"

07 didn't like the answer. Still it didn't mean that they would have to sign an other child's death warrant. "But you took appropriate measures before letting him go?". Of course his lead scientist, the man who had even allowed this organization to become what is it today, had taken measures to ensure no valuable information would be leaked. Still 07 wanted to hear it again, even if only to soothe his worried mind.

"That I did. His memories of his childhood will be fragmented at best. Furthermore memory deterioration is a known side effect of the reconstruction process, as we have come to learn. Even if he wanted to talk, he'd be unable to give Nerv anything cohesive"

And at that, 07 nodded once. "We will keep an eye on him to intervene in case he spills anything substantial, but otherwise let him be. After all, we still need him to defeat the angels until we can bring our full force to bear"

By now all vehicles had left the platform as it was lowered back down.

A lot of work had already been done, yet there was so much still left to do.

End chapter 3

Le authors note:

Well, I feel like this chapter turned out WAY better than the other two, in terms of structure and cohesion. So I think I'll set this chapter as my writings quality standard for the future.

Also holy shit writing this took nearly twice or thrice as long as the other two chapters, which is mostly due to the last part of it. Originally the chapter was supposed to end with the new organization's leaders in a meeting, discussing the third angels' attack on Tokyo-3. And I spend like a week trying to make it work.

And when it finally was in a semi-readable state, I found that it would just be shoving exposition down everyone's throats, so I scrapped it and rewrote the ending to what it is now.

That in addition to a week of writing everything else and the time needed for polishing and yeah, you got a pretty long time spent on this.

Also I noticed while writing this that I set up some major Shinji – Rei interactions. That wasn't planned from the get go, but hey, now there is the possibility of the two interacting in a way that isn't completely superficial ( And NO, there will NOTbe lemons, before you ask).

And with that, I think I'm out of things to say for now.

Christ, I'm just happy to be finally done with this chapter.