Beginnings and Endings – A Neon Genesis Evangelion Fanfiction

Disclaimer: I do not own Neon Genesis Evangelion, and I have no intention of making a profit of this story.

Author's Note: This story is AU, but instead of something strangely and bizzarely different, what happened if, after the events of the 3rd Angel, Misato was a little bit late to a very important meeting…

Chapter 1: Introjection

It wasn't fair, thought Misato Katsuragi, hair still wet from her quick shower, as she finally walked into NERV's central medical ward. It irritated her that even in death, the angel continued to cause her problems. Clean up had always been considered when dealing with the angels, but no one, she believed, had realized exactly what a monumental project it would turn out to be. If they had realized, there certainly would have been a far larger budget allocated to Section 6, the group assigned to the maintenance and repair of the Geofront and Tokyo-3. The repairs would take months to complete, and the crews weren't sure if they'd ever be able to restore the block where the angel had self-destructed to anywhere near operational condition. Which meant the residents of that area had to be accommodated somewhere. It was an organizational nightmare for all those who were involved, from the NERV technical and repair crews to the civilian city planners that had to deal with all the displaced civilians. She didn't envy any of them their jobs.

Well, at least the PR people of Section 5 were happy. They'd been chomping at the bit for over a year, Ritsuko had said, with nothing to do save for small community impact events and banquets for NERV grants to various academic institutions around the world. Now that things were moving, they had a chance to stretch their muscles and get down to work. They had a disaster to cover up, the start of a world crisis to deal with, and a new poster boy to promote; assuming they received permission from the Commander to even let the public knew he existed. They'd failed for years in getting permission to reveal things about Rei. Hell, they had had a hard enough time getting permission to reveal that Rei even existed. The fact they had worn the Commander down enough, even for just that, was a testament to Section 5's persistence.

Speaking of the new poster boy, Misato had left the clean-up efforts to debrief the boy and escort him to his new living assignment, something she wasn't entirely pleased about. It wasn't that she minded doing it, but she certainly had better things to do with her time. Shinji Ikari was a strange boy. Nothing like his father, it seemed, and came across as something of a coward to boot, though admittedly Misato couldn't really fault him for that. She doubted her response to being suddenly approached and asked to pilot a giant robot to save the world would have been much better. It was, after all, a lot of responsibility to drop on child unexpectedly. Hell, that was the understatement of the century. So perhaps, he wasn't such a coward at all, just a young boy confronted with a situation fully beyond his control and understanding. Though it might be better if he was a coward, she thought cynically. After all, it would make him easier to control.

Walking to the reception desk, Misato politely asked for the boy's room number and checkout information. She was supposed to have been there to pick him up and sign him out an hour and a half ago, but the site inspection had ended up taking far longer than she had expected. And when she had finished that, it had turned out the personnel decontamination unit hadn't arrived, and she had had to wait another half-hour. By that time, she had figured if she was going to be late, it wouldn't hurt to be a little more late. She had quickly run home and showered and changed into something a little more…formal, not to mention a little more revealing. After all, it wouldn't hurt to reward the poor boy with a little service for dealing with the wait, would it?

Misato was utterly flabbergasted when the receptionist gave her a sour look, and informed her that when the Chief of Operations had failed to arrive an hour after the appointed time, Section 2 had taken the initiative and had chosen to escort the boy to his new residence. Which meant that technically, the boy had left the hospital without having his release paperwork filled out. Such a thing was contrary to NERV policy, and Misato found herself, to her great anger, facing a pile of paperwork, explaining in detail exactly why she had been late, and why that had warranted Section 2's action.

The pile was large. It seemed it would be a while before she could deal with the Third Child.


Shinji Ikari was, by now, used to other people running his life. It wasn't as if he had given up on being his own person, at least not in the beginning, but he had found that despite everything he did, things always seemed to move beyond his control. If his opinions never mattered and his actions never accomplished anything, what was the point in even trying? Case in point, he had been instructed by a friendly nurse to wait for the Chief of Operations, whoever that was, to come sign him out of the hospital ward and take him to wherever he was staying. The Chief of whatever had apparently been running late, and a suited man that had been following him since he had left the room (whom Shinji had assumed to be a guard of some sort, despite the lack of obvious weapons, he had just had that sort of look), had called someone on a cell phone. Ten minutes later, three other men had arrived, consulted quietly with the receptionist, and had escorted him out of the building with as few words as possible. He had thought about protesting, but in the end, decided it wasn't worth the effort. After all, what would it accomplish?

He hoped he hadn't been kidnapped. He didn't honestly think he had been, but after the thing with the giant robot, he found himself having to revise his opinion on what was impossible and what was not. The men who had taken him from the medical building certainly looked like stereotypical kidnappers, but the NERV lapel pins on their collars reassured him that they were not. Well, at least not the illegal sort. He had no problem imagining his father having his personal security kidnap him and 'deal' with him out of sight from the rest of the world. It wasn't a pleasant thought, but he was sure if it came down to that, at least it would be quick. His father owed him that much, at least. He'd saved the world, hadn't he?

Still, other than to be vastly uncommunicative, the men had been polite. The four of them had surrounded him almost protectively as they had left the ward and they had moved to a nearby parking garage where they had gotten into an unmarked, but obviously, even from the outside and to Shinji, heavily armored van. Now they were heading…somewhere. He could tell from the sounds that filtered through the wall of the van that they were still in the city, which was somewhat reassuring. If they were going to shoot him, they'd probably do it in the country or at least a park in the suburbs. Though, that may have just been optimism and too many yakuza movies on his part.

With no windows, to stare out of, Shinji was left with nothing to do but observe his…captors? Escorts? Whatever they were, they were the only thing to look at in the van other than the floor or the ceiling. The van they were in had three rows of seating, and Shinji was positioned in the middle row beside one of the men. Another was seated in the row behind him, and the remaining two sat in the front, one driving, and the other quietly reading off what sounded like driving directions.

The man behind him looked European, or maybe American, with his blond hair done in a short, military-style haircut. Shinji couldn't see his eyes, but he could see the long scar that ran from above his forehead, behind the sunglasses all the men wore and presumably over the left eye, down his face, and below the man's short collar. He looked…young, Shinji supposed, though he knew wasn't the best at judging those things.

The man next to him was an older and of Japanese descent, who could have passed for a normal salaryman heading home on the train. He really had no notable features. No scars, moles, or any sort of identifying feature, just black hair and an average, even kind of dopey looking face. Shinji wouldn't have really been surprised to see the man disappear in a crowd a few seconds after entering it. The lack of scars was a surprising thing, though. Shinji was no expert on bodyguards or security people, but he knew that it wasn't a job one walked away from without injuries. The blond-haired man behind was proof of that, and he'd seen facial scars on the other two men in the few glances he had got of them. The man next to him was either very new, or possibly very good. Shinji was pretty sure both of those things were supposed to be frightening in this business. Whatever this business was.

Shinji really hadn't gotten a decent look at the two men in the front, due to the sheet of what he assumed to be tinted bulletproof glass that separated the driver's compartment from the rear. He could, however see that the driver at least looked Japanese, and the other man had very dark skin, possibly of Indian or African descent. Or he could have had a really good tan. Shinji really couldn't tell.

All of the men were large, imposing, physically fit, and wore sunglasses that prevented people from seeing their eyes. Maybe they were just crazily tinted, because there really wasn't much light in the van. What little there was came in from the front windshield and the driver's and passenger's front windows, and those windows were tinted, too, so even they did not give much light. The two in the back must have had the hardest time seeing. Or maybe they were used to it. Maybe working blind was considered a challenge?

Shinji fidgeted and tried to keep himself distracted by rummaging through his backpack. He had his S-DAT player, a few extra tapes for it, a change of clothes, a book he had brought to read on the train, and toiletries. And the letter from his father. He took it out, a stared at it. When he had first gotten the letter, he had ripped it up without even looking at it. He didn't want to hear from his father. He didn't want to see his father. They were done, through, end of story. And he had left the pieces in the garbage can. Of course, that hadn't prevented his guardian from fishing the pieces out of the garbage and putting them back together. It had been his guardian who had bought the ticket, and his guardian who had pushed him reluctantly into the train.

Shinji realized the hand holding the letter was clenching and unclenching by itself, and the letter was getting torn, again. He stopped his hand, and looked at the letter again, considering just ripping the letter into pieces once, again. He didn't, though, and instead tried to smooth the new creases the best he could, and reattach the tape that had come lose. It still looked worse off than it had before, but Shinji couldn't find it in himself to care. He folded up the letter, and placed it back in his bag.

"Got quite a chip on your shoulder, there, Pilot Ikari?" said a calm, deep voice to his left.

Shinji turned to face the older Japanese guard, for it was he who had spoken. "Well, I wouldn't say that…" He murmured quietly, and looked at the floor.

The man considered him for a moment, and then gave a small shrug. "As long as it doesn't mess with our business, it's your business, Pilot. Let me introduce my squad and myself. I am 1st Lieutenant. Shiro Yamada, and I'm the man in charge of protecting you. Behind you is your other primary, Sergeant Scott Hansen, and Sgts. Yuuichi Kawasumi and Mashudu Thilivhali up front, work night shift. I'm going to spell out how our relationship is going to work."

"Huh? Wait…what? Protect me?" Shinji sputtered out, looking the man in the face. The man wasn't making sense. He was going to be protected? Why? He had served his purpose and killed the monster, hadn't he? What was going on?

Lt. Yamada raised an eyebrow and frowned. "Haven't you received your briefing?"

Shinji frowned and looked at the lieutenant, more confused than before, "My what?"

Yamada's eyes went wide, and he turned to the man behind him, "Looks like Section One is playing games, again, Switch." The man rolled his eyes, but did not speak, and Yamada turned to face Shinji again. "Alright, we'll start from the beginning, then. You received a couple things from whoever brought you in, didn't you?"

Shinji thought for a moment, then nodded, and opened his bag. He rummaged around for a moment, before pulling out a small notebook with "Welcome to NERV!" on the cover. "Is this what you are talking about?"

The man blinked, picked up the book, and flipped through a few of the pages, before tossing it back to Shinji with a puzzled look on his face. "Was that it? Nothing else?"

"That was all Misato gave me. Was there supposed to be something else?" Shinji asked curiously, and picked up the book, and flipped through a few of the pages "This book is pretty useless. It just went on and on about how NERV was helping the world and saving humanity without saying how. It was pretty make a hundred pages of nothing."

The man brought his hands up to his face and massaged the top of his nose for a moment, before letting out a sigh. When he spoke, Shinji had the feeling the lieutenant was straining to control himself. From what, or who, Shinji didn't have the foggiest. "I don't know what happened, Pilot, but someone in Section One has screwed up, big time. When we're done here, I'll give them a call, and try to straighten this out. I'll try to cover the basics, but I'll probably miss some things. I've only got what my orders tell me, so I'll do my best, and we'll all just have to go from there. Got it, Pilot?"

Shinji nodded. He didn't know what was going on, but it seemed he wasn't being kidnapped or executed, or whatever other horrors his father was possibly capable. There was even going to be someone trying to explain what was going on. That in itself, was perhaps the best news he had gotten all day. Now if only these men had a train ticket home for him, everything would be set. Unfortunately, he didn't think that was where this conversation was going.

"Alright, first things first, who you are, and who we are. You are Shinji Ikari. Designated Third Children and Pilot of Evangelion Unit 01. You are, as of yesterday, a member of the UN military, attached to NERV-01 and in a short period of time will receive identification proving such. Your title within the NERV organization is 'Pilot', but you are formally ranked as a 2nd Lieutenant within the larger UN military structure. You are a member of Section 1 of NERV, classified as command and essential personnel, and are entitled to receive all such duties, benefits, and pay warranted one. Got all that, Pilot?" said Yamada, in the tone of one quoting regulation learned by rote.

"Not…really…" said Shinji, feeling a bit dazed. "Wait…what does all that mean? Didn't I kill the thing? Isn't it all over? I thought I was supposed to go home. Father doesn't have any more use for me, does he? The monster's dead, right?"

The lieutenant's eyes went wide, and he traded another look with the man in the back seat. They seemed to share something between the two of them, before the man turned back to face Shinji again. "I really can't answer that question, because I really don't know the answer myself. The word from up above says, that yes, there will be more. And that they should be following this one fairly quickly, though what exactly 'quickly' means, I can't tell you. A day, a month, a year, it could be any of those, Pilot Ikari."

Shinji closed his eyes and took a deep breath. He wanted to scream, he wanted to cry, and he wanted to hide in a corner. No one had told him anything, and if this man's reaction was anything, someone should have. Maybe it was the Director of Operation's job to do so, or maybe he'd just been accidentally skipped over. He didn't think so, though. His father just hadn't cared. Or had figured that he would stay even if he didn't.

Though, Shinji realized painfully as he thought it over, his father would be right in that assumption. He wanted to be here were his father was. As much as he hated him, despised him, and wanted nothing to do with him, he loved him to. He wanted to do something for his father, even if he was only a tool. Maybe this was the only thing he could do for him. How can a son not love his father? That was something Shinji longed to know. Or at least how to stop.

"The four of us, however, are from Section 2," Yamada continued. "Section 2 is assigned, among other things, with the protection of the Pilots. We are, for a lack of a more elegant term, your bodyguards. I'm sure you won't appreciate it, because inevitably we'll screw with your life somehow, intentionally or not, but I'd like you to remember that we are here to keep you safe, Pilot Ikari." The man fixed him with a stern eye, which felt strange coming from the man's slightly dopey-looking face.

Shinji found himself unable to meet that eye and brought his eyes to the floor again. The man seemed quite serious, which made Shinji worried. Was there something to worry about? "Is all of this…necessary?" He mumbled quietly, not quite expecting an answer, but hoping for one all the same, even if he knew he would probably not be pleased by it.

"Yes, it is, Ikari." The man said, dropping the title for the first time in the entire conversation, and Shinji couldn't help but bring himself to meet the man's eyes. He was surprised to see compassion in the man's eyes, though it felt very distant, "From the day you walked into NERV and got into the Eva, your life was in danger. There are cults, crazies, and conspiracy theorists, not to mention possible government agents that would love to either kill or get a hold of a Pilot. As much as this city is a fortress, even NERV," the man seemed to grimace, "can't always keep track of its personnel with any reliability without active manpower on the scene. How many attempts on the First's life have been foiled this year, Switch?"

The man in the back blinked, then spoke in a monotone, "5. Crazy outside NERV main entrance. Door security took him out. Assassin while attending the UN-NERV summit with the commander. Stopped by the commander's bodyguard. Attempted poisoning of the water supply of the First's apartment complex. Stopped by city water employees. Sniper while at NERV-5 base at Matsushiro. Stopped by base security. Crazy on the way to school. Hit by a bus." The last one seemed to make both of the men smile, but Shinji just shuddered.

"With the Third Angel's appearance," the lieutenant continued, "it's likely that the activity will increase even more. Attacks have been slacking for the past year or two, but we expect them to double, triple or even quadruple in frequency. Sorry, Pilot, but you might have been marked the moment your father sent for you."

With that, the man lapsed into silence, and Shinji was left to grapple with these revelations. He didn't know what to make of the situation. He could almost deal with being in danger trying to kill the…Angels, he guessed they were called, but he would be in danger from other…normal people as well. People that might very well kill him if they got a chance. He should feel angry with his father for dragging him into this without warning, but he couldn't bring himself to do it. After all, what point would it serve? It was already said and done. Not that his father would take it back even if he could.

"This is going to follow me for the rest of my life, isn't it?" Shinji said, giving Yamada a weary smile, and then looked at the floor once again, bringing his hands to cover his face.

The man paused before replying. "…In all likelihood…yes. You'll be dealing with people like us and like them for the rest of you life, however long it may be. While you are in our care, however, I promise, we will do our best to let you live as normal a life as possible. That brings me back to my original topic. How you and us will work together to keep you safe, Pilot Ikari."

Shinji nodded wearily, and brought his head up to pay attention. However much he hated his life at the moment, he had no wish for it to end. If cooperating with these people helped him live longer, he would do so. The longer he lived, the larger the chance that he had to get out of here…Not that it was guaranteed that he'd take the opportunity if it was presented. If he could bring himself to leave his father again, now that they were so close…in distance of course, not anything that actually counted for anything.

"First thing to remember is that two of us will be near you, if not in sight, at all times. As I said beforehand, Sgt Hansen and I will follow you during the day and Sgts. Kawasumi and Thilvhali will guard you at night. We will do our best to be unobtrusive and invisible in order so that you can live your life as freely as possible, but to do that, you must be ready to cooperate with us." He gave Shinji a considering look, "That largely means using your brain. Don't do stupid things, Pilot. Don't go places that invite trouble. Try to stick with large groups of people. Never walk home alone at night. That sort of thing. It'll go a long way to making our job easier, and will also make you feel safer."

"…I think I can do that." Shinji said weakly. He wasn't the type to do stupidly dangerous things or visit shady places, anyway. In fact, those were things he actively tried to avoid.

"Secondly," Yamada reached into his pocket and pulled out an object, which he handed to Shinji, "Keep this cell phone on you at all times. It will allow you to be contacted in the case of Angel attacks, as well as security concerns. There is a number in there that calls whoever is charge of watching you for moment. Also my personal home phone number is on there, " he fixed Shinji with a stern eye, "I expect you to use them only when it is absolutely necessary."

Shinji nodded in easy agreement. That made sense. Especially for the home number. Even the people of NERV wanted to keep their jobs out of whatever personal lives they had. Unless they were like him, he supposed, and the job couldn't help but interfere with the rest of their lives.

"Feel free to use it as a personal phone as well. The bill goes to NERV. In the memory, in addition to the first two numbers, are the local medical and police dispatches, as well as the NERV Section 4 emergency medical ward. And Switch here had the foresight of adding a few decent take-out places, just in case it takes you a couple days to get settled in and get food for yourself."

Shinji turned and nodded thanks at the sergeant in the back seat, who returned it after a moment's pause. He hadn't even thought of food, though that wasn't terribly surprising, as he had expected a short stay here and then a quick train ride back home. Except it wasn't home anymore, he supposed. Some house or apartment in Tokyo-3 would be, he guessed. He started building a list of things he'd need for himself, and listened with half an ear while Lt. Yamada continued.

"The third and final thing, Pilot, is fairly simple. While you are not in the Evangelion, your first and only job is to survive." If the looks the man had been sending him had been hard before, this one pierced through him and nailed him to the van's door, and Shinji abruptly forgot the grocery list he had been building, "Your life is not entirely your own, anymore, Pilot Ikari. Billons of people are relying on you to kill the Angels. If some crazy kills you in a back alley, or you accidentally slip and fall off a bridge, then there is one less pilot protecting the world. You are 1 of 3 people currently capable of performing your job. Do not hesitate to put your life ahead of others. In the long run, your life is more important. Look out for yourself, and we'll do our best to stop the things that you can't prevent."

Shinji was shaken by the man's words. Put his life ahead of others? What did he mean by that? Didn't Yamada know how worthless he was? Hadn't the man seen or at least heard about what his father thought of him? How could he justify sacrificing others just to continue his own pitiful existence, even if he was a pilot of giant robot that was supposed to save the world? Surely there were other people just as qualified as he was to pilot the monstrosity.

But Shinji looked into the lieutenant's eyes, and saw sincerity, and even a touch of the distant compassion that had graced the man's eyes before. The man was entirely serious about what he had said. He believed it, and more importantly he wanted Shinji to believe it as well. Yamada truly believed that he, Shinji Ikari, unwanted and abandoned son of Gendo Ikari, was worth all that consideration. And even if the man believed it for selfish reasons, like wanting to survive, Shinji felt a strange warmth. It made him feel uncomfortable, but when the man spoke again, asking if he would follow all the three rules, he couldn't help but give a quiet, but confident, "Yes, I will, Lieutenant. Thank you."


From: Section One, Office of the Director of Operations, Capt. Misato Katsuragi

To: Section Two, Security Division, Capt. Koizumi Arima

Message: Just what the hell were your men doing today, Capt. Arima? Debriefing and escorting the pilot was clearly my job. Your men overstepped the bounds of their authority! I'm submitting a complaint to the Commander! If you and your men are lucky, you'll be on night watch at NERV-Siberia for the next five years!

Do you know how much paperwork I had to fill out to straighten all of this out?!

Capt. Misato Katsuragi

Opeartions Director


From: Section Two, Security Division, Capt. Koizumi Arima

To: Section One, Office of the Director of Operations, Capt. Misato Katsuragi

Message: Send all the complaints you want, Capt. Katsuragi. My men were well within their bounds of their authority. If you had shown up on time, maybe they wouldn't have had to act. If you had simply called ahead to inform the hospital staff and Section Two that you were going to be late, this could all have been avoided. Your irresponsibility caused what happened. I had to shift two squads from guarding the clean-up operation to look for you, because you didn't show up, and we thought you had possibly been killed.

And I have a complaint of my own. Why the hell hadn't the kid received a briefing on what's going on? He's been in the hospital for two days, for God's sake! Couldn't someone have wandered in and, I don't know, given him the basics? My officer to explain everything to the kid on the scene, Captain! The kid didn't even know that he was being taken to his new apartment! He thought he was going to the train station to go home! Who screwed up that one, Captain?

Capt. Koizumi Arima

Section Two, Security Division Commander


From: Section One, Office of the Director of Operations, Capt. Misato Katsuragi

To: Section Two, Security Division, Capt. Koizumi Arima

Message: Damn you, Arima!

Misato Katsuragi

Director of Operations

I have to admit this idea has been in my brain for a good bit. I really am not a huge fan of stories that take an enourmously different approach to a story, at least at the beginning. I prefer small changes, like this one, which open slightly new possibilities for the reader. Also this stories allows me to indulge myself a bit in some of my personal interests, one of which includes how NERV works and is structured. I know, kind of random, but I've always wondered how it functioned, and now I have an excuse to write up how it does. So, if every now and then, I seem to get sidetracked on a little bit of organizational structure or something, please be forgiving.

I really don't know when the next chapter of this will be out. Possibly never (though I hope not), maybe in a month or less, but probably more. I'm a college student and finals are coming up.

I hope you enjoyed reading this as much I did writing it (Even if Shinji angst gets irritating to write after a while)!