DISCLAIMER: I don't own Neon Genesis Evangelion or any of the characters associated with the series. GAINAX owns the rights to this series.

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Chapter 02 - Integration

"Shinji this is amazing!" Ritsuko exclaimed over the comlink. "It's unprecedented. We were pretty shocked a few days ago during your first synchronization with Unit 01, but this! Amazing. Just. Amazing!"

The command bridge was bustling with activity as technicians ran back and forth, comparing data and discussing possibilities. Everybody appeared excited. Just a few days ago, these technicians seemed on the verge of a nervous breakdown because they couldn't be sure if Shinji would be able to pilot the EVA so that he could face the invading monstrosity. Now, they looked at Shinji as if he would be the savior of them all. Shinji Ikari, the prodigy who had achieved a stable 81.3% sync rate on his first day of training. This was along the lines of what everyone observing the synchronization testing was thinking, except, of course, for a select few sitting at the highest point of the command bridge. That is, this was what they were thinking until Shinji was put into a simulation program for target practice.

"Shinji! You just point and shoot! Just point. And shoot! It's not that hard" Misato yelled for the fifth time, clearly frustrated beyond belief. The problem wasn't with Shinji's ability to control the EVA. He could move just fine with the simulated EVA. It was responding to his every thought with a negligible margin of delay. If they asked him to somersault over a building or do a cartwheel on the simulated streets of Tokyo-3, he could have done so with no problems. But he had never handled a gun before in his life, of course he had no idea how to shoot it! It was easy for Misato to say since she had gone through proper training with guns as a military officer. Shinji, on the other half, was just a fourteen year old boy.

Shinji winced as the angel tackled him yet again and sent his EVA crashing into a nearby office complex. Yet again, the simulation ended with Shinji having been defeated by the EVA. "Let's call it a day Misato" said Ritsuko. "I think the poor boy's been through enough-"

"I'm fine ma'am. I can continue." cut in Shinji. "I can't leave it like this right? What if an angel attacks tomorrow? Or even tonight? I would prefer not to be put into a situation like the last time, totally unprepared."

"Good. I admire your persistence." chimed in Misato. She was beginning to find more and more respect for the boy. It was almost as if she had never seen him break down that first day before he was forcefully put into the pilot seat of Unit 01. But then, who wouldn't break down in a situation like that? "Alright, let's try again!"

Shrugging, Ritsuko rebooted the simulation program and configured it to EVA Unit 01. As she did so, she risked a glance up at the Commander of NERV, who had been watching the entire training process. He did not look too happy. Gendo Iarki rarely did, when things were not going according to his plans. This new development with Shinji definitely presented a problem. Gendo knew that only Shinji could pilot the EVA so he could not replace him. At the same time, Shinji's new-found...confidence might pose a problem in the future. His son would have been much easier to manipulate as an insecure, unstable boy rather than...this. As the simulation started back up, Gendo stood up and turned to Sub-Commander Kozo Fuyutsuki. "Watch over the rest of this and report anything I might need to know, professor." Without waiting for the Sub-Commander's nod of understanding, Gendo strode out of the bridge room. He had a lot of thinking to do.

Shinji was now back in the simulation.

Point and Shoot. Point and Shoot. Why the hell is it so hard to point and shoot?!

The simulation always started the same way. A reconstruction of the battle against the third angel, Sachiel. Of course, Shinji had lost consciousness almost at the beginning of that battle, but he remembered what the angel had looked like and it still brought shudders up and down his spine thinking about it.

There it was. Shinji hid behind a tall skyscraper and carefully listened as the angel advanced further into the city towards the Geofront. He took a second to check that his standard issue EVA Pallet Gun was loaded and ready, and went back to scanning the area for any possible surprises.

"Distance to target, 800 meters." announced Misato. "wait for my mark."

"700 meters...600 meters...remember Shinji, you are aiming for its core, not the buildings to either side of it..."

"Wow. Thank you, I had no idea." grumbled Shinji.

"GO!"

Shinji ran out from the cover of the building, firing in bursts at, what he hoped, was the angel's core.

He missed.

Shit!

Shinji dove to the ground and rolled on to his knees as the angel's arm lance shot past where his head had been just a second ago. Stabilizing his aim, Shinji aimed and shot again. Miss. The angel was approaching rapidly. He could hear Misato yelling in the background but he was too caught up in the adrenaline rush to make out what she was saying. The angel was fast approaching, about 200 meters away now. He kept up the hit and run tactic, diving out of the way as Sachiel`s arm lances continued their assault.

Only 100 meters away now. Cursing, Shinji unloaded the rest of his magazine on a nearby building, causing it to crumble in front of the angel. Using the dust caused by the debris to buy him some time, Shinji tossed his gun away and took out his prog knife. He couldn`t understand why he couldn't hit the target. He was aiming straight at the damn thing and firing but it seemed to consistently miss. Dismissing those concerns for later, Shinji ducked behind a medium sized office complex and crept around the block to flank the angel.

Unfortunately, the angel seemed to realize what he was doing and fired a beam of laser from his eyes, destroying the building he was taking cover under.

Oh, to hell with this!

Cursing yet again, Shinji charged. Another beam of laser just missed him as he dove to the ground, rolled, and was charging again in one fluid motion. Shinji could feel sweat coming out of his pores and dissolving into the LCL as his heart pounded in his ears. Dodging the lances left and right, rolling out of the way of laser beams, Shinji felt like it had been hours before he was almost within reach of the angel. But then he was there, and squatting down to avoid another attack, Shinji sprang forward propelled by the mechanical muscles of the EVA and tackled Sachiel into the ground, burying his prog knife deep within its core as he did so. For a few seconds, Sachiel flailed, strugging to throw the EVA off its body, but then it was still.

He had succeeded. Not quite in the way they had hoped, but Sachiel was down for the count. Shinji finally focused back on the communication system, waiting to be scolded for ignoring orders, but no sound came from the comlink. Frowning, he turned on his visual monitors to see what was going on on the bridge.

The command bridge, once again, was staring collectively at the holographic projector with incredulous looks on their faces, completely dumbfounded. After a few moments, Misato recovered from the initial shock. "Shinji, that was amazing! I mean, you missed. It might have been much easier if you had just shot the damn thing, but your movements were spectacular! I had no idea the EVA could even move that fast!"

Needless to say, Shinji was more than slightly confused. He had thought that he would have gotten a lecture on the importance of obeying orders during combat and gibes about how he couldn't hit a target if it cost him his life, but...praise? He honestly hadn't planned on doing any of that; he had just been incredibly frustrated with his poor marksmanship and had just wanted to kill the damn thing for once. Thinking back on what he had just done, he couldn't really even understand what was so amazing about it. The angel had almost hacked him to pieces hundreds of times during those few minutes and he had barely escaped with his life. Well, hypothetical life, anyways. Deciding to ask Misato about it later, Shinji modestly dismissed the compliments, saying it had been chance, that he had had no idea what he had been doing, and if it would be ok to run the simulation again to improve his marksmanship.

A few hours later, at about 1 AM, Shinji and Misato collapsed on the couch in their living room, exhausted but content with the progress they had made that day. Shinji had finally been able to hit Sachiel at 500 meters dead on at its core and he had repeated the feat 3 times just to be sure he could do it. Even Ritsuko, a workaholic herself, had been amazed at Shinji's persistence and dedication to piloting. In truth, Shinji had enjoyed the experience. He relished the time he could stay connected to the EVA because he knew his mother was there, in essence, watching him and guiding him.

Misato lazily turned her head to face Shinji. "You were great today, Shinj. Just full of surprises, aren't you?" Shinji chuckled. "I try. So do I get a reward for all this hard work?" A mischievous glint appeared in Misato's eyes and Shinji quickly interjected, "I mean, I was wondering if you could maybe introduce me to the staff, maybe invite them over or something. I want to get to know them better." The glint had not disappeared from Misato's eyes, which worried Shinji. "Did you have someone in mind?" Misato asked, a slight hint of more teasing to come inflected in her tone of voice.

At being asked, an image of Maya Ibuko, one of the head computer technicians at the command center popped into Shinji's mind. Maya had shyly approached Shinji after his training session to welcome him to the team and to compliment him on the excellent work he had done today. She had been stuttering with her face crimson the entire time during the exchange, which had only really taken an upwards of 30 seconds as Shinji thanked her and excused himself to go get changed out of his plug suit. Shinji had figured that she was just naturally timid and dismissed her demeanor, but she had left a small impression on his mind. He thought she had a very nice smile, one full of sincerity and devoid of any personal intent. He could tell she smiled just because she wanted to smile. Dismissing Maya from his mind, Shinji replied. "Not really."

Misato inched closer. "Really? No one?" she asked suggestively. Sighing, Shinji pushed her away. "If I did, I would be crazy to tell you, wouldn't I?" replied Shinji. "Anyways, I'm headed to bed. Night Misato!"

Misato chuckled as she got up as well and headed towards her room. "Night Shinji, don't forget you have to be at school by 8 tomorrow! Don't want to be late on your first day right?"

Too tired to speak, Shinji waved a hand in acknowledgment and entered his room, falling asleep as soon as he hit the bed.

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The next morning, Shinji woke up to the sound of his alarm clock. Half-asleep, he made his way into the kitchen to grab a glass of water, then got washed up and ready for school. He could hear Misato snoring in her room indicating she was still asleep.

Lucky her.

Shinji walked out the door with a silent good-bye and headed to the school for his first day. It was actually a beautiful day outside. The sun was out, warming the air to a pleasant temperature with a slight breeze that kept the weather from being too hot. All in all, it felt like it would be a good day.

As he approached the school, he noticed two agents dressed in black suits standing at attention on either side of the entrance to the school. They seemed to be keeping an eye on Shinji and scanning everywhere for possible signs of trouble at the same time. As he passed by, they nodded in to Shinji in unison, which he returned. Unfortunately, what Shinji hadn't realized was that they never so much as blinked let alone acknowledge someone's presence. The fact that the two agents had gone so far as to greet Shinji caused an uproar.

As soon as he stepped into the school grounds, a crowd of students charged him, bombarding him with questions and demands for information. "Woah! Are you an EVA pilot?" "Are those men here because of you?" "Are you like the son of the president?" "Do you know Rei Ayanami? She's another pilot!" "Can I get your autograph?" "What's your name?"

"Uh..." Shinji stammered, eyes widening at the sudden onslaught of attention. He had no idea how to act towards crowds like this, coming from the country where there were scarcely five people together.

"Alright! Alright! Break it up you guys! Let him have some room!" came a voice from outside the crowd. "Move out of the way!" The crowd parted to make room for a slender girl with freckles and dark brown hair. "Hi there!" she cheerfully greeted when she made it to where Shinji was standing. "I'm Hikari Horaki. I'm the Class Representative for class 2-A, I was told you were coming today so I came to show you around."

Breathing a sigh of relief, Shinji nodded and let Hikari lead him away from the crowd of students and into the school. "Nice to meet you Hikari. Wow, thanks a lot back there."

"Oh no worries. Most of the students here are sons and daughters of NERV employees so they get pretty excited when a new face shows up." explained Hikari. "Don't worry about it though, it will die down once they realize you're not a pilot."

"...right."

Hikari let Shinji to the second floor of the school building to classroom 2-A, instructing him to sit down at one of the desks towards the back of the classroom. As she was explaining the school regulations and class schedules for the semester, Shinji noticed Rei Ayanami staring out the window at the far side of the classroom.

Rei Ayanami.

Mother's clone.

He remembered when he had first seen her in front of EVA Unit 01. He had thought she was beautiful despite her horrific injuries. She had looked so fragile and he had instantly been overcome with a desire to protect her. Even now, for some reason, that desire remained in him. Shinji knew he should be disgusted by the very idea of a clone created with his mother's genes in order to act as a vessel for an angel, but he couldn't help but feel sympathetic towards her. She was, to him, just another victim of Gendo Ikari's cruel and selfish agenda.

"Shinji?"

Blinking, Shinji forced himself out of his thoughts. "Sorry Hikari, I was distracted. What'd you say?"

Hikari sighed. "Just remember to stop by the office after class to talk to the principal, ok?"

"Yeah, sure. Thanks." replied Shinji, having no clue what she had been talking about. Why did he need to go to the principal's office?

Maybe it's something NERV related.

Deciding to worry about that later, Shinji got to work in configuring his new school laptop for personal use. Not long after, students filled the class one by one, most of them giving Shinji a curious look before taking their seats. A few more minutes later, the teacher came in and the class bowed at Hikari's direction, indicating the start of class.

No sooner had classes started, a message popped up on Shinji's screen.

'Are you the pilot of the robot? Y/N'

Curious, Shinji tried to track the source of the message, hacking into the mainframe to try to locate the IP address of the sender. This was another thing he had learned while inside the EVA. His mother had taught him how to retrieve information from behind most security firewalls, so of course, the school security system was nothing to Shinji. Suddenly, another entity started creating additional defenses in the network to try to conceal his identity. Smiling, Shinji looked around the class to see who it could be. Closer to the front of the class, he saw a skinny brown haired boy typing furiously on his laptop. Then, realizing that he had been spotted, the boy turned around and shrugged, chuckling nervously. Then, another message popped up on his screen.

'You are, aren't you?'

Shinji gave up and decided to play along.

'Yes.'

All of a sudden, everyone in the class got out of their seats and crowded around Shinji, much to his surprise. "So you are the pilot! Wow!" "What's it like?" "How were you selected?" "What does the cockpit look like?" "Were you scared?"

"Uhh...I'm actually not allowed to talk about it...it's classified." replied Shinji, trying to ward off the questions. He could hear Hikari in the background trying to get everyone seated again, but amazingly enough, the teacher had noticed nothing and was continuously droning on about the political and economic affects of Second Impact. Then, the bell rang signaling the end of school.

Shinji quickly escaped the crowd muttering some excused about having to stop by the principal's office. Once there, Shinji was relieved to find that all the principal wanted was to welcome him to the school and let him know that Shinji's "situation" was completely understandable. Having gotten that over with, Shinji made his way out of the school to head home. Just outside though, a student in training pants and jacket approached him. "Ya Shinji Ikari?" he asked.

"Uh, yes. Who are you?"

"Toji Suzuhara, I'm in your class. Can you follow me for a second?"

Slightly confused but too curious to refuse, Shinji followed Toji around to the back of the school. The freckled boy from earlier was waiting there with giving Shinji a sympathetic look. Starting to feel suspicious, Shinji turned to Toji to tell him he was going to leave when, all of a sudden, he was looking up at the sky. For some reason, he was down on the ground with a very sore cheek. As he was still trying to figure out what had happened, he heard Toji say "Sorry transferee. But I have to hit you. I wouldn't have been satisfied unless I did."

...what the hell?

The other boy, named Kensuke, explained, looking down at him. "Sorry, but his younger sister got hurt in the battle. That's the reason."

Incredulous, Shinji got to his feet and stared at the bastard who was stalking off. "That's it? You come lead me out here and punch me while I wasn't looking like a bitch and then just run away?"

Of course, that brought Toji back. He looked furious.

Coming up to stand right in front of Shinji, he said. "Then watch this one very closely, punk." Shinji actually did see this one coming. Just as it was about to make contact with his face, Shinji caught Toji's fist with his left hand and threw his right fist into the other boy's face. This time, it was Toji`s turn to fall.

Kensuke, who had been watching the whole thing, was gaping at Shinji, flabbergasted at what just happened. Toji hadn't fared much better. In fact, he looked like he was wondering what had just happened as well. Then, Shinji saw Rei as she walked into view around the building.

"An emergency call..." said Rei. "I'll go first..."

Needing no further explanation, Shinji nodded as Rei ran off and turned to Toji, who was still trying to get back up. "What's her name?" Shinji asked.

"Mari."

Shinji nodded. "Tell her I'm sorry." said Shinji, genuinely meaning it.

With that, Shinji ran off towards NERV Headquarters.

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AN - Sorry this chapter was so boring! Just needed to lay in some groundwork. Oh and I apologize if there were any grammar/spelling mistakes. Still trying to find a proofreader. Read and Review please!