A/N: After seeing several episodes of Evangelion and Naruto, I figured why not put the characters of one of the series into the other as a slight crossover? I know what you're thinking, I'd have to make some serious alterations in characters right? Untrue, I can keep some of the characters as they are now, but make them slightly OOC but still work out the kinks that would make this crossover work. Now please enjoy.

Disclaimer: I do not own Naruto nor do I own Neon Genesis Evangelion.

The Orphaned Shinobi

Chapter 1

Thirteen years ago, in Tentougakure the Village Hidden in the Heavens (A/N: I used someone else's idea with their permission. I'll post where I got the idea later.), a great tragedy occurred that only matched that of the attack of the Kyuubi no Kitsune on Konoha. The tragedy was known as the "Mountain Massacre" and many innocent lives were lost that day. A boy, no older than 3, was one of the many survivors of the tragedy and witnessed his mother's own death while she protected his life. With his mother's death his father abandoned him, leaving the poor boy to live on his own. Years later, the boy grew and joined his village's ninja academy and graduated with several other students; two of which became his teammates in a three-ninja Genin team.

The boy's name was Shinji Ikari, a boy with a past as hard as anyone's in the ninja world. He had short, brown hair and a pair of blue eyes that seem to make him plain; when in reality, he's a village heartthrob. While he was popular among girls, his two teammates didn't exactly fit the fangirl-type. To other girls, Shinji was as handsome as they come and he would go into a relationship with one if it weren't for his low self-esteem. Since he was orphaned, Shinji had lost all confidence in himself even when his skills as a ninja prove him to be a strong Shinobi.

His two teammates, as stated, were girls and yet they did not fawn over him like most did. The first of the two was a pale girl by the name of Rei Ayanami. She was unusual in both appearance and personality; she had short, blue hair and a set of red eyes that add to the oddity of her pale skin. Her personality would make her the perfect Kunoichi since she hardly ever displays any emotions; when she does, it's usually in front of her teammates and no one else. Like Shinji, however, she was also an orphan of the "Mountain Massacre" but with no memory of who her parents were.

The third of their Genin team was Asuka Sohryu, a blue-eyed, fiery-haired girl with a temper to match. While in public, Asuka seems like a typical girl that boys would die for; but in front of her teammates, it's an entirely different story. The girl would lose her temper to the simplest of things and would mostly direct it towards Shinji and Rei. She also acts as though she were the true leader of the team. She would even give negative comments to them even after she would start pushing them to assist her on their missions. But even with this vain personality, she still has a softer side and would often talk to Shinji about her problems. Ironically, she too was an orphan; but unlike her teammates, she was orphaned after her mother hung herself a year after the "mountain massacre".

While it may seem like a coincidence that these three orphans were on the same team, they still supported one another like any ninja team should. You would also think that if these Genin were under the tutelage of a sane, strong ninja like many teams; you couldn't be more wrong.

Their sensei, Misato Katsuragi, isn't exactly a good teacher even with her Jounin status. She drinks, she's somewhat of a slob, and her cooking isn't exactly a chef's dream. However, she does care for the wellbeing of her students and is like a surrogate mother to all three of them. She would often say that if she had the chance, she would adopt all three of them as her own children. However, she was their sensei and was still a ninja with great skills. She would often come to her students' rescue if they faced a Shinobi none of them were prepared for and come out on top. She often commented that she hated the thought of losing either of her three students in battle.

While this team had been Genin for nearly a year, all of that was about to change. The village leader, Sandaime Tsubasakage, had gotten word of movement near Fire Country, home of the Village Hidden in the Leaves, which Genin teams from other hidden villages were heading there. He knew that it meant one thing; the Chuunin Selection Exams were taking place there. It also concerned him since he also heard of ninja from the Village Hidden in Sound were also moving and there was rumors of a possible attack. The Tsubasakage knew that it meant trouble.

"The Chuunin Exams?" One of the Heaven Ninja in the Tsubasakage's office asked.

Sandaime Tsubasakage, or Kozo Fuyutski as he was known outside of his duties, turned to face all the Shinobi gathered in his office. "That is correct; with all of the movement within the borders, there is no doubt that they are going to start."

"But where will this year's exams take place and when do they start?" Asked a Chuunin.

"They will take place in a week from today," he said lowering his head before bringing it back up. "In Konohagakure."

Murmurs and whispers began to spread throughout the assembled Shinobi as they had all heard of various stories of great Shinobi from the Village Hidden in the Leaves. The Tsubasakage silenced the assembly by waving his hand before continuing. "However, only one team will represent our village in the upcoming exams."

This caused all the gathered ninja to go in an uproar; most of them were Jounin with Genin teams. The Tsubasakage then silenced them again by clearing his throat. "Because of this, I have already chosen the team that will represent us in the exams."

"Which team is it, Tsubasakage-sama?" Maya Ibuki, another Chuunin, asked from her seat.

Kozo smiled amusingly at the question before answering. "It will be none-other than Team Katsuragi."

Misato, the violet-haired Jounin instructor of her said team, looked at Kozo in shock before hesitantly pointing to herself. "M-m-m-my team?" She stuttered with a slight squeak in her voice.

Kozo grinned and nodded in affirmation. "That's right, Misato, your team."

"But, but, Tsubasakage-sama," Misato began with almost a pleading look. "My team has only been in the field for nearly a year; they're not ready for something as big as the Chuunin exams yet."

Some of the other Jounin instructors seemed to agree with her as they too have heard of Team Katsuragi's exploits since they began taking missions. While many of them were D-ranked missions that were very common to all Genin teams, her team had also completed three C-ranked missions as well as two B-ranked missions. While that was an impressive record, for many villages that wasn't enough for a squad to be even qualified for the Chuunin exams. The Tsubasakage, however, felt differently.

"I have seen your squad's record, Misato," Kozo began as he turned towards the window facing the village that his Shinobi resided in. "And I am very impressed with the successes your team has performed. I feel that they are, indeed, ready for the Chuunin exams."

Misato was at a crossover, she didn't want her squad in the exams so she had to come up with another argument. "But people die in these exams; my team isn't ready to handle that kind of pressure!"

Sandaime Tsubasakage didn't seem to be phased and continued his argument. "Have you forgotten what a Shinobi's life is all about, Misato?"

That stopped Misato dead in her tracks as she looked at the Tsubasakage apprehensively. "We shinobi always put our lives on the line when we go out into the field. Regardless of whatever the consequences, a shinobi must fight for his or her home even if it means their own death." Kozo explained. "Every other village knows that, and rumors say that Konohagakure will also be letting rookies into the exams. However, they are just rumors."

That shocked everyone, even Misato to the core. If Konohagakure was allowing rookies into the exams, that means they must have some very skilled ninja in their ranks. "Furthermore, I feel that of all the rookie teams that we have at the moment, yours is, by far, the most skilled of the entire rookie Genins. They have proven themselves a great asset to our village and should be recognized, as such, in the Chuunin Exams." He then turned to fix his gaze on Misato, who felt very small at the moment. "Any further objections, Misato?"

Misato was at a loss for words; to have her team praised by the Tsubasakage meant that they have, indeed, impressed him. But she couldn't shake the feeling that he wasn't telling her the entire truth of the matter. Seeing that it was useless to continue arguing with the Tsubasakage, Misato lowered her head and reluctantly said no.

"Excellent, then you are all dismissed." With that, every shinobi in the room began to exit. But before Misato could reach the door, the Tsubasakage stopped her. "Except you, Misato."

As the rest of the Tentou-nin exited the room, Misato stayed behind and stood in front of the Tsubasakage's desk as the door closed. The two were now alone and the Misato knew this meant he needed to talk to her privately about this matter. The Tsubasakage looked at her seriously before speaking.

"I know how you feel about this decision." He said as if he read her mind. "And I can understand why; but this is something that must be done and your team is the only team I can count on."

"But sir, if my team goes, they won't last very long, even if they make it to the final part of the exams." Misato pleaded as she stood in front of Kozo's desk trying to convince him to change his mind.

"Are you saying that you doubt your team's abilities?" Sandaime asked as he turned to her with a stern look.

Caught off-guard, Misato replied instantly. "N-no, I never said…" But Kozo interrupted her before she could finish.

"Then I am certain that your team can handle themselves." He stated before sitting in his seat and turned to face the window, which faced the village. Seeing no point in leaving, Misato stayed; she knew there was an ulterior motive behind the Tsubasakage's decision.

"There's more to this than what you're saying, isn't there?" She asked, point-blank.

Kozo didn't even turn to look at her when he replied, "Yes, as a matter of fact."

"What is it?" Misato asked, now more concerned for the motive than her team.

Fuyutski sighed heavily before turning to fully face Misato in his chair. "I have been receiving reports from our ANBU black ops along our borders with Sunagakure and they are quite disturbing." This caught Misato's attention as she listened inventively. "There are reports of unusual movements of their troops along the border of Konohagakure. It is quite possible that something big is about to occur and it involves those two villages and the Chuunin Exams."

Misato took all this in and thought about it carefully. "You're suggesting that the Chuunin Exams may be a ruse to start a war on Konohagakure."

Kozo clasped his hands together as he leaned in his chair. "Exactly," He then looked at Misato very seriously. "This is not only a good chance for your team to earn the rank of Chuunin, but it is also an A-ranked reconnaissance mission. I want you to gather as much information as possible before the final part of the Chuunin Exam. If this whole exam is, indeed, a ruse to start a war I want our village to be ready if it ever comes to us. Also, if the war is being involved with another Shinobi Nation, I want to know that as well. If it comes to war, I want you to assist Konohagakure as much as possible before leaving."

Misato stood perfectly emotionless; deep down, though, she was shocked to the core at the thought of another war. Even before the "mountain massacre", Tentougakure had suffered great losses during the Great Shinobi War and many of their best ninja were killed in that war. The thought of another war frightened her and she hoped that it wouldn't happen. "So, you want me to investigate the exams and assist Konoha, if possible is that it?"

"Precisely, Misato." The Tsubasakage confirmed.

Misato swallowed hard before asking, "When do we leave?"

"Tomorrow morning."

Later, Misato had told her team to meet her in their usual training area in an area near their village's walls. Asuka, in her red kunoichi outfit, Shinji in his brown jacket and pants, and Rei in her blue gui with a white sash tied around her waist all waited patiently for Misato. Asuka paced very impatiently from left to right, while Shinji and Rei sparred with one another practicing their taijutsu.

"Ugh!!! Where the hell is Misato-sensei!?" Asuka nearly yelled, causing Shinji and Rei to stop their training. "She should've been here two minutes ago!"

"Calm down, Asuka." Shinji said softly. "I'm sure she has a good reason for being late."

"I agree with Shinji-kun," Rei said almost in a monotone voice. "There is no reason for you to be upset, Asuka-san."

"Upset!? UPSET!?!" Asuka yelled as she stomped towards her two teammates. "I am WAY beyond upset, Wonder Girl!" Asuka yelled at Rei, using her nickname for her. "I am absolutely FURIOUS!!!"

"Someone mention me?" Came Misato's chipper voice from behind Asuka, who immediately spun around and pointed at her.

"YOU'RE LATE MISATO-SENSEI!!!"

Misato laughed as the tension settled. A few minutes later, after calming Asuka down, Misato had gathered her students to a bridge within the village. She had stayed quiet as they walked, which kinda bothered Shinji.

"I'm sure you're all wondering why I called you all out here." Misato said looking at her three kids.

"Yeah, what's up? Is it a new mission?" Asuka asked, almost eager to show off her skills as a kunoichi.

"Not exactly, Asuka." Misato replied.

"Then what Misato-sensei?" It was Rei who asked that.

"I'm just here to say that…" She said making a dramatic pause. "Congratulations on being representatives of our village for the upcoming Chuunin exams."

"Oh is that all? Well if that's…" Asuka began but her eyes widened as she registered her sensei's words. "SAY WHAT!?!"

"The Chuunin exams?"

"Us?"

"That's right!" Misato answered in a sing-song voice. "You three have been selected, by Tsubasakage-sama himself, to head to Konohagakure to participate in the exams."

"Awesome!" Asuka exclaimed, pumping her fist in the air. "Now I can show those Leaf-nin what I'm capable of!"

"When exactly do the exams take place, Misato-sensei?" Shinji asked ignoring Asuka's jubilation.

"A week from today, Shinji." Misato answered with a nod.

Asuka then shoved Shinji out of her way as she brought herself up to Misato with stars in her eyes. "When do we leave!?" She asked very quickly like a kid who had just found their presents under the Christmas tree.

"We leave tomorrow morning." Misato said simply, still keeping her smile.

"Tomorrow morning!?" Asuka whined like a child being punished.

Misato's face grew stern. "That's right, so I expect all of you to get a good night's sleep. We leave first thing in the morning and we'll be training along the way." Her face then turned solemn as she looked at them all as if she would never see any of them again. "When these exams come up, it is my hope that all of you pass and walk away as Chuunin of our village. I also hope all of you will be prepared for these exams. I can tell you right now; these exams will not be easy. I should know; I've taken them before. I must also warn you that other villages will be sending their genin to the exams and some of them may be stronger than any of you." She then wore a proud smile as she finished her speech. "But I have faith in all three of you and I know you will all come out on top. We leave at 0700 tomorrow so get some rest. Dismissed!" With that, the team dispersed and they all went home.

The next morning, Misato awaited her three students at the village gates. The Tsubasakage stood with her as her students approached. First Shinji, then Rei, and after a few minutes Asuka. Tsubasakage examined each one of them and noted their appearances.

Shinji adorned his usual attire, which was a fish net-patterned violet shirt covered with a brown blazer and a brown khaki pants. His shuriken pouch was wrapped around his right leg and he adorned his village forehead protector, which had the shape of a half cut maple leaf and he wore the standard blue shinobi sandals.

Rei wore a light blue doge-like t-shirt with a pair of light brown shorts with her shuriken pouch in the same area as Shinji's. Her forehead protector was wrapped around her neck and hung loosely above her chest. Around her waist was a white sash, which was wrapped in a bow behind her and she had bandages wrapped around her forearms.

Asuka wore a red one-piece Chinese-like outfit that had the left sleeve cut short while the right side had a fish net sleeve. Like Shinji and Rei, her shuriken pouch was wrapped around her right leg while on her left leg she had another fish net that extended from her thigh to the top of her knee. She also had a dark red cloth wrapped around her left arm while she wore her forehead protector like a headband while two hair pieces made a pair of bands in her fiery red hair.

Each of them wore their back packs and were ready for the long journey to Konohagakure and Kozo was there to see them all off. Misato, adorning her red Jounin jacket and violet clothes, waited for them and when all of them were ready, the turned towards the exit of Tentougakure and began their long walk to the Chuunin Exams.

Watching them, Kozo muttered quietly to himself. "Good luck to all of you."

TBC…

A/N: Well, this was the first attempt at an Evangelion/Naruto crossover and I want to know what you guys think so I expect some feedback. As for where I got the idea for Shinji, Asuka, and Rei's outfits I will post the link to my profile. So please click on the little button at the bottom of your screen that says "go" and click on it and post a review please.