Evangelion Fan Fiction

Evangelion Misfile

By Kraven Ergeist

A/N: Fans of Chris Hazelton's web comic "Misfile" will recognize the name and concept this fan fic. Those of you who haven't, check out the comic at .com.

Chapter One

Shinji yawned as he rolled out of bed. It was early in the morning, and there was already shouting going on in the kitchen. He had been living with Misato and Asuka for almost a year now, but sometimes it was just difficult. It was bad enough that he was the unwanted child of a megalomaniac in charge of a multi-billion dollar paramilitary organization in charge of skyscraper sized biomechanical robots that fought against equally sized monsters bent on destroying the world. It was bad enough that he was forced to pilot one of these giant robots to fight said monsters to protect the world. Adding hormonal roommates on top of it all, however, was just putting salt on the wound.

Groaning, he meandered to the bathroom, seeing Pen-pen cowering in the corner. Shinji sighed in amusement reaching for his toothbrush.

"You and me both, buddy…" his voice trailed off as he cleared his throat. His voice sounded weird for some reason. A cold? Laryngitis? Whatever, he was too tired to deal with it at this point.

He finished brushing his teeth and gargled some mouthwash to try to clear out his throat. He spit into the sink. A loud thud sounded outside in the living room, and there was the sound of the table feet groaning as they were drawn against the hardwood floor. Then there was the sound of breaking glass.

"What is going on out there?" Shinji muttered, forgetting about the way his voice sounded. "Asuka's never been this bad…"

He stepped out of the bathroom just in time to see the table tumble over.

"Let go of me!" came a young girl's voice. But it wasn't Asuka's.

Shinji stumbled around the overturned table and saw Misato…no…Ritsuko? What was she doing here? And she was wrestling with…not Asuka, but…who…?

"Shinji!" the girl shouted, breaking free of Ritsuko's grip. She got to her feet and grabbed Shinji by the shoulders. "Thank god! Please! You've got to listen to me!"

Shinji just stood there, stunned. The girl had raven hair, shoulder length. She had dark eyes and was wearing a pair of blue pajamas. Her hair was a mess, like she had just woken up. Whoever she was, it was apparent she had spent the night here.

"Uh…who…" Shinji managed to get out, his face growing red from the proximity.

"Shinji!" the girl blurted, sounding helpless. "Don't you recognize me!"

The boy could only let his jaw hang open helplessly, no words coming to his mind.

"Misato!" Ritsuko grabbed the girl by the shoulder. "Would you calm down already! I don't know what's gotten into you, young lady, but if you don't settle down, I'm calling Section Two!"

Time stopped. Shinji blinked his eyes, staring at the girl in front of him with something akin to shock.


The girl's eyes seemed to soften slightly. As she did, her features suddenly became recognizable. Her black hair, with a subtle violet sheen, her dark round eyes, and out of the blue, she was the same woman who had been his guardian since he'd arrived in Tokyo-3, since the day his life had changed.

And she looked like she was no older than he was.

"Wh…what…?" Shinji breathed incredulously.

Ritsuko looked at her watch and cursed. "Damnit, I don't have time for this – Shina, can you make sure she gets to school on time? I have to get to work – I'm late as it is…"

Shinji barely registered the comment. His eyes were still on Misato's, who was looking at him with a similar incredulity. Ritsuko fled to her room, leaving the living room an utter mess, with broken dishes and overturned furniture littering the floor. Pen-pen's head peeked out of the bathroom to see if the coast was clear.

And all the while, Misato was holding onto Shinji with a face of utter stupor, and he was looking back at her with the same expression.

"Misato…?" he breathed, blinking in disbelief. "Is that…really…?"

"Shinji…" Misato's eyes fell bellow with neckline, her eyebrows narrowing. "How long have you had those…?"

Shinji blinked, before turning his head to down to see what Misato was staring at. His chest was…different…oddly shaped…

Shinji let out a shrill sound as Misato brought her hand up to poke one of the peculiar growths protruding from his shirt. Shinji recoiled, clutching his chest in embarrassment. "Misato!" he hollered, his voice hitting a high note, even for him.

The younger Misato was blinking in astonishment. "This is…some kind of dream, right? I mean, I feel like I'm a teenager again, Ritsuko's my mom, and Shinji's a girl? I'm just gonna go back to bed and wait until I wake up…"

Shinji was too busy trying to figure out what was going on with his body, his face growing redder and redder as his mind grew nearer and nearer to the only viable conclusion, until finally he made a mad dash to the bathroom and yanked off his shirt in front of the mirror.

For miles around, people thought they heard the wail of a klaxon, but it turned out to be a false alarm.

God's in his heaven, all's right with the world, but in one little corner of the universe, there is nothing more irritating than a misfile…

Shortly after noon, there was a knock on Shinji's door. Shinji was lying facedown on his…her…pillow, eyes red and sobbing.


Shinji didn't answer. She wasn't asleep, but she wasn't sure she was awake either. She wasn't sure she wanted to acknowledge anything about the reality she found herself in.

Misato let herself into Shinji's room. She was showered and dressed in a school uniform she had found in her closet. About an hour of lying faceup in her bed, she had gotten up and paced her room. She had stared at herself in the mirror, slapped her face enough times for it to sting, and finally convinced herself that this may not be a dream after all. This wasn't even her room – it was Asuka's! She had never had a room like this! Even when she was a teenager, her bedroom was a pale white hospital room – it had never looked like this. She hadn't exactly grown up like a normal teenager.

And why was Ritsuko her guardian? She had never seen Ritsuko as a mother figure, and even if she had, why was Shinji suddenly a girl? This was a tad shy of a Freudian dream, and even if it was a dream, this was far too clear, and was lasting far too long.

She had gotten into the shower, and while it was unfamiliar, there was nothing strange about it at all. The water felt refreshing, the smell of her shampoo was overpowering, and Pen-pen was even squawking at her outside her shower for his neglected breakfast. She had hurried out of the shower and fed him his breakfast, pondering her situation. The apartment was the same, insofar as it was the same building and same room. The furniture was different, the fridge containing real food instead of her usual fare of beer and instant dinners, but apart from minor differences, the place was pretty much the same.

Except…it looked a lot like Ritsuko's house, she realized. The organization, the style of the furniture, the telltale signs of pet cats – the place looked almost identical in style to Ritsuko's apartment. So…Ritsuko was her and Shinji's guardian, she reasoned. This dream of hers, for she still wasn't convinced it wasn't a very elaborate dream, wasn't going anywhere soon, so she might as well learn the rules, she reasoned. But why was Pen-pen here? Penguins and cats didn't seem to her like compatible house pets.

She went back to her room and began rummaging through her closet and drawers. Everything fit, and despite the unfamiliarity of it all, all of the clothes, the accessories, the makeup and jewelry, everything in her room seemed like it suited her tastes. As she slipped into the school uniform that lay on her desk chair looking like it had been worn before, a funny idea came to her.

A part of her was really curious about this strange world. She had never really known a normal childhood. A part of her kind of liked the idea of being a normal teenager, of going to an actual high school, having friends that she could goof off with, maybe meeting some cute boy…

Then she remembered.


He had recognized her! And he…she…hadn't left the apartment as far as she knew. Knocking on her door, she was dissuaded when no response came. Curiosity got the better of her and she pushed the door open.

"Shinji?" she repeated, seeing him…her…still in her pajamas, lying facedown on the pillow.

The figure on the bed lay inert. Misato approached her, warily touching her shoulder with her hand. Shinji's head came up and she could tell she had been crying.

"Misato?" Shinji's voice was high pitched and squeaky. "What's going on?"

Misato kneeled down next to her bed, looking sadly down at the girl. "I don't know Shinji…what do you remember?"

The girl shook her head. "I don't know…I don't remember anything in particular…last night I went to bed like I usually do. This morning, I just woke up…like this…"

Shinji buried his…her…head back into the pillow, and Misato could tell she was crying.

"Shinji…" she breathed. It was oddly relieving to help Shinji deal with this predicament, because it distracted her from having to deal with her own.

But right now, she needed some answers.

"Shinji…" she touched the girl's shoulder again. "You remember me, right? You remember…that I'm not a kid? That I'm an adult? That I'm your guardian, and not Ritsuko?"

Shinji nodded, and Misato sighed in relief. At least she wasn't alone.

"Well…Ritsuko seems to think somehow this is normal…" Misato said, as if that one simple fact explained all the commotion caused earlier that morning. "I tried to tell her that something was wrong, but she's in full guardian mode – all she cared about was that I got up and got ready for school. She must have thought I was going through a mood swing or something."

Shinji's eyes began to dry as Misato sat back against the wall by her bed.

"But for some reason, you and I remember each other the way we used to be…but something tells me everyone else is going to be like Ritsuko, and think that this is normal for us…"

Shinji watched as Misato tried to figure out their predicament. For some reason, having Misato as a fellow victim made it all somehow easier to deal with. But as soon as his…her…mind managed to overcome the sheer shock of the situation, a slew of questions came to her.

"Where's…where's Asuka?"

She still hadn't gotten used to her voice – hell, she still wasn't used to being able to comfortably close her legs! But she hadn't seen Asuka this whole morning, and as abrasive as she was, Shinji trusted and depended on her, and more importantly, was worried that she might be dealing with something equally as weird and otherworldly.

"I haven't seen her, Shinji," Misato admitted, shaking her head. "I've been all over the apartment, but I must admit I haven't had the nerve to go outside yet. I…wanted to talk to you first."

Shinji's eyes began to water again. Her pajama top hung awkward over her feminine frame, still unused to the added mass in her chest.

"Misato…" Shinji began to tear up again, his…her lower lip quivering. "I'm scared…I don't understand this at all…"

Misato took a deep breath and shook her head. "I don't either, Shinji…"

"Perhaps I could offer an explanation…"

Both girls started as a figure climbed in through Shinji's window, sitting on the windowsill. He was young, about their age, with gray hair and red eyes, wearing a school uniform like Shinji's. He had a cheerful smile, an expression that hinted at something hidden underneath.

"Who are you!" Misato yelped more than asked, suddenly looking and feeling very vulnerable. She wasn't sure if her teenage body had the same fighting capacity as her normal body, and she wasn't ready to face anyone else she knew, let alone a stranger.

Shinji just stared at the boy, too bewildered to register any kind of fear that might've come naturally as a girl. Having grown up a male, he could not appreciate the kind of fear Misato felt in this instance. But the strange boy did not seem to exude any kind of threatening aura.

"You can call me Kaworu," the boy said in a friendly manner. "I'm afraid I'm the one responsible for this unfortunate predicament of yours."

That took a few seconds to sink in.

Then… "WHAT!

That had been Misato's shrill appraisal of Kaworu's revelation. Shinji, who might've given voice to his opinion, suddenly clutched her ears. Kaworu, for his part, didn't visibly react to the auditory bombardment.

"Let me explain…" he began, before Misato completely forgot about her earlier fear and marched straight up to his face and picked him up by the collar.

"You're telling me YOU did this!" She demanded, nearly shoving him back out the window. "Fuck the explanation! Fix it first! Explain it later!"

At that point, Kaworu was wincing at Misato's grip on his shirt. "Peace, child!"

"I'm not a fucking child!" Misato shouted. "I'm twenty-nine years old!"

"Actually, you're fourteen," Kaworu corrected. "And Shinji here is now Shina Ikari. You're both the same in every way, except Misato is fourteen years younger, and Shinji is a girl."

"Well, fix it!" Misato screeched.

"Can't. At least, not right now," Kaworu shrugged helplessly. "Maybe it would help if I started from the beginning."

"Well, maybe you should get started on that!" Misato barked, crossing her arms.

"Alright…" Kaworu said, sliding into the bedroom. Shinji curled her knees up protectively, and Misato sat next to her, also protectively.

"I am an angel," Kaworu announced, standing in the center of the room. He held his hands out as the two girls tensed. "Yes, the same type of angels you war with every day, but rest assured, I mean you no harm…much as the circumstances might show otherwise, this was entirely accidental."

Shinji curled up, instinctively backing away. Misato was skeptical.

"An Angel? You look pretty human to me. Can you prove it?"

Kaworu shrugged. "If I did, then NERV would pick up my AT field, and probably lock down, tear apart, or bomb the entire city block. That hardly seems an acceptable result for a mere display. No, you're just going to have to take my word for it. Frankly, my mere presence and knowledge of you two should be evidence enough."

Shinji was simply sitting still, taking all this in. She could hardly think straight.

Misato crossed her arms, still unconvinced.

"So you're some kind of Angel, and you managed to mess up our lives how?"

"I'm getting to that," Kaworu assured. "So my most recent position was in the astral wing of the fifth branch of the celestial filing depository."

Misato raised an eyebrow.

"Essentially, I was a cosmic records keeper," Kaworu smiled. "You see, in heaven, we keep files on every little piece of information in the universe, which is a considerably big job. There are files for people, files for plants, files for partially hydrogenated soybean oil, and so on and so forth. You with me so far?"

Now Misato's blank stared matched that of Shinji's. But she nodded.

"So each file is essentially a block of code, sort of like on a computer. Put the file in its proper place, and a person's file will make them that person. But put that file in, say, the vegetable cabinet, and suddenly that person could become a green onion. So it's important that each file is kept in its proper place at all times. And since there's an infinite amount of data and an infinite amount of file space, the job is, shall we say, taxing."

Shinji was following along diligently, if a little faraway. Misato was about ready to have the guy committed.

"Humoring you for no explainable reason – go on."

"So, I was running behind on my shift, when all of the sudden, my boss, Rumisiel, comes marching for an inspection. I sort of panicked, and put away everything I had been working on just in time, when I notice some papers on the floor – which is something the boss doesn't take kindly to, so I managed to kick them under the desk before Rumisiel could see. I would have put them back later, but Rumisiel and I got into an argument, and…long story short, I'm on leave without pay."

Shinji swallowed. "And those papers?"

Kaworu sighed. "They belonged to Misato. And Shinji, I placed your papers in the wrong file when I put them away. I would have corrected it all when my boss left, but I hadn't counted on him firing me and sending me to Earth."

"And assuming we believe this story…" Misato crossed her arms. "Which I don't, by the way…why, pray tell, did they send you to Earth?"

"And…why were Misato's and my files out to begin with?" Shinji piped in. "What exactly were you doing with us?"

"Well, we were getting things ready for the rapture."

"You mean Third Impact?" Misato quipped.

"Potato, potahto," Kaworu shrugged. "Anyway, the boss and his staff have got me here on a sort of trial period. They're keeping tabs on me, and keeping track of what I do. So if I help the people here out with their lives, the boss will see that I'm actually a pretty good guy, and let me back in, and I can fix your files good as new."

"And how long will that take?" Shinji moaned.

"Who knows?" Kaworu shrugged. "Could be a few days, could be a few months, could be years…"

"And you expect us to believe all of this!" Misato screeched.

Kaworu just smiled as he returned to his window. "You just turned into a teenager and your charge turned into a girl overnight. Is my story really so hard to believe?"

"And Shinji and I are just supposed to WAIT for you to prove yourself with these good deeds!" That was Misato again.

"I'm afraid you have no choice," Kaworu shrugged, sounding a little too lighthearted about the whole thing. "You're stuck like this until I can fix it. But rest assured, I'm working on it."

Shinji began to shake. "We're…we're gonna be stuck like this forever, aren't we?"

Kaworu placed a hand on Shinji's shoulder. "Don't worry…I'll fix this up soon…you have my word…"

Misato grabbed Kaworu by the arm and yanked him away from Shinji. "Get your hands off him!"

Kaworu shrugged out of her grip. "Alright, alright, I can tell when I'm not wanted. Anyway, don't tell anyone about this – to the rest of the world, you've been this way all your lives. And if any of my bosses find out there's been a misfile, they'll make it this way permanently. They don't like mistakes, and they'll do whatever it takes to cover it up."

Shinji let out a sob.

"What about NERV?" Misato asked. "What about school?"

"Nothing else has changed," Kaworu assured them. "Everything is exactly the way it would have been had you been a born a girl," he nodded at Shinji, "And you were born fourteen years ago."

"Where's Asuka?" Shinji demanded.

"I don't know. Where would she be if you had been a girl all this time? The answers won't come to you by sitting there and asking questions. You've got to go out and look for them."

He stepped out the window with a wave.


Misato glared at his form as he disappeared out the window. The glare was somehow less threatening now that she wasn't even eligible to drive.

"What should we do?" Shinji mumbled, her eyes still red, her nose runny. Misato snatched a tissue out of a box on his desk and offered it to her, which she accepted slowly.

"We keep going forward," Misato told her, placing a hand on her head.

Apart from the lack of an Adams apple, subtle bust, diminished shoulders, and narrow waist, Shinji didn't look all that different. Her hair was still cut the same length, her eyes were still blue, and her body was still thin and lanky. Compared to herself, Shinji's physical appearance hadn't changed that much. Misato was much shorter now, skinnier and fairer of complexion. She had been an early bloomer, and it was clear that this genetic gift hadn't gone away. But of course, the differences that lay beneath Shinji's pajamas were a change on a whole different level.

"We'll have to help each other along," Misato said, thinking out loud. "I've at least been a teenager before, albeit not your average one…but you've never been a girl before, so there's some things you're going to have to learn…"

Shinji cringed. This was a thought she had been dreading since she had seen her newfound rack in the mirror. "I…I don't…I can't…"

"Take it easy, Shinji…take a deep breath…" Misato instructed. "I'm gonna need your help too, ok? I've never been to a real high school before, and its bound to be much different from college. And there's at least one other thing you're good at that I'm a complete beginner with."

Shinji's lip stopped quivering for a moment. "What's that?"

Misato let out a sigh, her expression helpless and defeated. She reached into her pocket and pulled out her NERV ID card. She held it out and showed it to Shinji. Sure enough, there was her face, just as young as she looked in person.

Misato Katsuragi.

Date of Birth: December 8th, 2000.

1st Child and Pilot of Evangelion Unit 00.

"I mean it looks like we're going to be working together a little more closely from now on…"