Shinji: Path of the Shinobi

Disclaimer: I do not own Evangelion or Naruto

"Hello" – Speaking

'Hello' – Thoughts

"Hello" – Demon/Boss Summon Speaking/Techniques

'Hello' – Demon/Boss Summon Thoughts/Techniques

A small four year old child sat crying on a bench in a train station. This brown haired, blue eyed child is Shinji Ikari. It is the year 2005 and he has just lost his mother who was absorbed into the robot she was working on called Evangelion, but that memory was already starting to fade from the young boy's mind. Now a few days later he had been abandoned by his father who said that he no longer had a use for the boy.

The boy's father, Gendo Ikari, had said that Shinji would be picked up at the train station by his new care taker and had departed, completely ignoring the small child's cries for him to not go. Gendo had even ignored the tall, white haired, man with the antiquated clothes, red markings on his face, and a metal headband that had the kanji for oil on it. Jiraiya of the Three Legendary Sannin had witnessed the entire abandonment from start to finish.

Jiraiya was on an assignment to gather information on the world outside of the Hidden Continent that was the home to the shinobi world. He had just finished setting up his own personal spy network back in the Elemental Countries when the newly appointed Yondaime Hokage had requested that he work to update the one Konohagakure had for the outside world.

Jiraiya's mission hadn't started a moment too soon. Shortly before he left the Land of Fire there was a huge cataclysmic event called Second Impact. The following aftermath of death and destruction had left the spy networks of all the Hidden Villages in shambles, and with the recent war they had little manpower to try and repair them. So Jiraiya had spent the last four years wandering the world gathering informants, allies, and establishing methods to keep them in contact. He felt lucky that most information concerning the outside world was worth little in the Elemental Countries and he wouldn't have to handle it himself, with most of the handling of information from this network being done by a Chuunin squad.

Now Jiraiya had mostly finished with only Japan left to establish contacts in, and he still had a few months before he head to report back in. By sheer chance he had ended up at the same train station where Shinji had been abandoned and he had seen the whole thing. Now Jiraiya is many things, a legendary shinobi, a writer, a pervert (or as he says a SUPER-PERVERT), but what most people don't know is that he is a real softie for children. This softness is what led him to train three orphans in the war-torn Land of Rain. And it was this same softness the directed him to the crying child sitting on a bench waiting for some stranger to pick him up.

Being a master ninja it wasn't hard for Jiraiya to walk up and start talking to the little boy. He quickly gained the child's trust and soon knew the kid's entire life story. At first it was the same life that all children should have; all sunshine and giggles. But with the 'death' of his mother and the loss of his father Shinji had started to develop psychological scars that would hamper him later in life. On the bright side, the scars were still fresh and could be healed. As long as they weren't left to fester Shinji would become more or less a normal boy. Jiraiya felt that he could help heal the boy, the same way he helped Yahiko, Nagato, and Konan. Train him into a ninja.

Shinji had readily agreed to the training, although that might have been because he was under the impression that this was the man who was supposed to take care of him. But he's four, it's an understandable mistake. Now all Jiraiya had to do was put the guy Gendo assigned to watch Shinji under a good Genjutsu and they would be good to go.

(Time Skip – 4 months)

Jiraiya sat on a log in a forest clearing where he observed his latest student go through several exercises that would help improve his ability to throw shuriken.

It had been four months since he had picked up the small boy, and he felt those months well spent. Shinji had proved early on that he had a real knack for picking up skills and understanding the basic principle about how things were done and why.

At first the boy was incredibly shy and withdrawn from the world, but with the Sannin's help he had started to overcome that. He was now a lot more outgoing and responded better to new things. It had helped that he became eager to learn 'cool ninja tricks' after Jiraiya had shown him the basics such as the Henge, or when he cut a fly in half with a shuriken.

Shinji had quickly grasp what chakra was, even if he was a little young to understand how to control it, but Jiraiya figured that he would be doing the tree climbing exorcise long before most Genin do it. He was also developing nicely physically with the daily exercises his teacher had him doing.

Heck, Jiraiya would have been glad that he decided to bring Shinji along even if the boy wasn't turning out to be a student to be proud of. And that was because Shinji was helping Jiraiya with his research, even if the kid didn't know it. Anytime the two came to a hot springs, Jiraiya would somehow manage to trick Shinji into wandering into the women's side of the springs. The women would then swoop on Shinji and start proclaiming how cute and adorable while pinching his cheeks and musing his hair. Then Jiraiya would call through the door asking if his 'nephew' was in there. This was usually good for several minutes of free ogling of pretty women clad only in towels, sometimes not even that much. Shinji eventually wised up and stopped falling for the older man's tricks, but by then Jiraiya had already written one book and was working on the manuscript of another. But that's in the past and isn't important, well Kakashi would think it's important but he doesn't know about it.

"Hey Shinji! You can stop now, we have something important to discuss!" Jiraiya called to his student.

"What is it Jiraiya-sensei?" Asked Shinji as he stopped his exercises. The boy had figured out that Jiraiya was not the man Gendo had said would watch him, but he was happy now and didn't care.

"Listen, as you know I'm setting up a spy network. What you don't know is that I am about finished. When I am, I will have to go back to my home village in the Land of Fire. Remember what I said about the Hidden Continent and the world there?"

Shinji nodded, wondering what would happen to him once it was time for Jiraiya to leave.

"Well when I leave, you will be presented with two options that will change your life. First, you can stay here in Japan. I can have you taken to the teacher your father wanted you to be with. If you choose that then your training under me will be finished and you will never see me or anyone else from the Elemental Countries ever again." Shinji's did not like the sound of that option as it sounded exactly like what Gendo had done to him. "Or, you could come with me back to Konoha. There you can continue your training and become a shinobi, or you could try some other profession. I won't have the time to watch over you like I do now, but I will be able to drop by from time to time and give you a bit of personal training. What do you say?"

Shinji didn't even think about it for a second. "I want to go with you and become a shinobi."

Jiraiya grinned at the conviction in the boy's voice. "You know, I kind of had a feeling that would be the option you chose."

Jiraiya and Shinji casually strolled down a path in the forests of the Land of Fire. It couldn't be seen through the trees but they were drawing close to Konohagakure, the Village Hidden in the Leaves.

Shinji had to admit that this Hidden Continent was very different from Japan. For one thing, ever since they got off the boat they had walked everywhere, with not a single car or train. When he asked Jiraiya about this the Toad Sannin had replied that many of the technological conveniences of the outside world were considered either useless or more harmful than helpful, such as the internal combustion engine. Sure it could be used in a car to get a person from point A to point B quickly and smoothly, but there was no real need for it. Ninja with their stamina and speed were considered more efficient and cheaper then paving over the country side with roads then spending money to either buy or build the vehicles, not to mention the known pollution that came with them. And where would they get the oil from and still remain hidden?

That didn't mean that all modern conveniences were frowned upon. Electric lights and cooking appliances, indoor plumbing, and modern medical equipment and medicine were all received with open arms, although the medical equipment and medicine was sometimes found to be inferior to medical jutsus and shinobi medicine, but they were handy in places without ninja. They were even constantly importing and reprinting various forms of literature whether it is a science journal to manga to one of the classics by Shakespeare, although Jiraiya liked to brag that his books were a lot more popular then the playwright's.

Now this led to one question that Shinji had been wondering for some time. How did the Hidden Continent stay hidden? Jiraiya had said that that was one of the biggest mysteries in the world. No one knew why, but there was a barrier that covered a large portion of the Pacific Ocean. Within that barrier was every single one of the Elemental Countries from the northern Land of Snow, to the southern Sea Country. Some people theorized that it was the Rikudou Sennin, creator of Ninjutsu that erected the barrier. Other's thought it might have been the Bijuu who did it, or at least people who wanted to keep the Bijuu contained. The only thing that they did know was that barrier seemed to repel ordinary people, and the only way to get in was to be guided by someone who could manipulate their chakra as they were the only ones whom the barrier did not affect.

This left Shinji with a lot of information to think over as he and his teacher walked towards his new home. He found that over all their reasons for not having cars made sense as the only people who did a lot of traveling around here were generally ninja on a mission, and even though his training hadn't been going on for very long yet Shinji was not tired despite the days he had spent walking practically nonstop.

Eventually teacher and student made it to the tall large gates that were the entrance to the Hidden Village. And Shinji got to see some ninja besides Jiraiya for the first time.

"Hold it you two; we're going to need some ID before we can let you into the village." Said one of the two Chuunin that had gate guarding duty.

Jiraiya puffed himself up and started laughing boisterously. "HA HA!! ID!? Don't you know who I am!? I am the Great Sage of Mt. Myobokugama, known North, South, East, and West as the Legendary Toad Sannin Jiraiya!" This exclamation was accompanied by a short dance that involved a lot hopping around on one foot and finally summoning a horse sized toad at the end.

Shinji and the Chuunin sweatdropped at the sight. Shinji couldn't believe how ridiculous his teacher's introduction was, and the Chuunin couldn't believe that this was one of their strongest shinobi. But the ability to summon toads only belonged to one ninja, so that was proof enough.

"Ok…" said one of the Chuunin. "You're definitely Jiraiya-sama…Although I don't know if that's a good thing…but who's this child with you?"

"This is Shinji Ikari, a student I picked up on my travels. When I report to the Hokage I am going to see what I can do about getting him a place to live before enrolling him at the academy." Said Jiraiya as he presented his ward.

"Alright then, you two can go on in." Said the other Chuunin. "You should head straight to the Hokage Tower, we were told to expect you any day now and send you right there once you got back from your mission."

"Ahhh, damn gaki. He knows that I like relaxing at the hot springs as the first thing I do when I get back into town." Grumbled the white haired Sannin as he and his brown haired student made their way into the village.

The Chuunin looked at each other before the younger of the two said, "Doesn't he know about what happened three years ago?"

Shaking his head the elder said, "No, he left for a long term mission to the outside world shortly before it happened. There hasn't been a word of communication that's reached him since he left."

"Then shouldn't we have warned him? I mean he was the man's teacher."

"Nah, he should be told by someone who is close to him. Probably a good thing he's taken that kid under his wing though."

"Hey Jiraiya-sensei, what's the Hokage?" Asked Shinji as he and the perverted Sannin made their way through the village of Konoha.

"The Hokage is the leader of Konoha and is considered its strongest ninja." Explained Jiraiya. "If you look up there you will see the carved faces of the four Hokages that Konoha has had." He said as he pointed to the mountain at the back of the village that had four faces carved upon it. "The one at the left is the Shodaime Hokage a member of the Senju clan and who founded the village about 70 years ago. Then there is the Nidaime Hokage, who was the Shodaime's younger brother. Next to him is the Sandaime Hokage, Sarutobi-sensei as I call him since he taught me and the other two Sannin everything we know. And finally the spiky haired urchin at the right is the Yondaime Hokage, Minato Namikaze and my student. He's the guy who sent me out to set up a spy network in the outside world and he's the guy we're going to meet."

The two soon reached the tower and walked quickly and quietly through the lower levels, making their way to the Hokage's office at the top. The secretary outside the office didn't even try to stop them as she recognized the Toad Sannin.

Jiraiya, who usually preferred to come in through the window while sneaking up on the Hokage, decided that if you can't use Plan A go with Plan B. Kicking open the door he shouted, "HEY GAKI! DON'T YOU KNOW IT'S RUDE TO CALL A NINJA WHO'S BEEN ON A LONG, TIRING MISSION STRAIGHT TO YOUR OFFICE WHEN HE GETS BACK! I SHOULD GET A CHANCE TO RELAST AT THE HOT SPRINGS FRIST! IT'S BEEN SO LOng since I could enjoy the view…?" Jiraiya had trailed off in confusion at the sight of not his student the Yondaime but his teacher the Sandaime sitting behind the desk wearing the robes he gave up when he retired. "Sensei? What are you doing here? Where's Minato?" He asked.

"It's good to see that you've returned Jiraiya." He said while motioning to the empty seats in front of his desk. "Please seat down, there is much that needs to be discussed."

Jiraiya moved forward and sat down while Followed by Shinji who had been behind his teacher and had yet to be noticed by the Sandaime.

"Oh? And who is this young lad that you've brought with you?" Queried the Sandaime.

"This is a student I picked up while I was in Japan. His name is Shinji Ikari. Shinji say hello to my sensei the Sandaime Hokage."

"Hello"

"I'll explain later sensei. Now what is it you wanted to talk to me about?"

In the village of Konoha all activity ceased as a loud "WHAAAAT!?" could be heard from the Hokage Tower.

The news was such a surprise to Jiraiya that he practically had a heart attack. The Kyuubi had attacked Konoha almost a year after he left. In an attempt to stop the Kyuubi, Minato used a forbidden sealing technique that cost him his life. But if Minato was dead, then what about his wife or unborn child. Actually he had a funny suspicion about baby. "Sensei, what happened to Kushina and their baby?" He asked nervously.

Sighing Sarutobi said, "I'm sorry to say that one the same night Kushina died due to birth complications. As for their child, well there is someone I want you to meet." Pressing the intercom button on his desk he asked his secretary to have Iruka brought in.

Within a minute a young sixteen year old Chuunin walked into the office followed by a three year old boy wearing a white T-shirt with tan shorts and blue sandles. The child has spiky golden-yellow hair, cerulean blue eyes, and three whisker marks on each cheek. Shinji felt as if he had seen that face somewhere before but couldn't quite remember where.

"Jiraiya, this is Naruto Uzumaki. His birthday is October 10th." Introduced the Sandaime.

That was all Jiraiya needed to know who the kid was and what he was. "Shinji," he said, "why don't you go with Naruto here and play with him? You'll keep an eye on him…Iruka wasn't it?" He asked the Chuunin who answered in the affirmative. "Good now you three run along while I talk to sensei."

When the three had left the room Jiraiya turned to the Hokage and said, "We need to talk."

After several hours of discussion the two had gotten their stories told. Sarutobi told his student about the Kyuubi's attack and what Minato did to stop it. Then he talked about all the steps he had taken to protect Naruto from the dangers of being Minato Namikaze's son, and from the prejudice that usually came with being a Jinchuuriki. Unfortunately he wasn't quite as successful with the latter. Sure no one Naruto's age knew the truth and those who were too young at the time to understand didn't really know it either, but the fear and hate of their parents had rubbed off on the children and it leaves an impression on a child when a parent forces them away from someone while saying they were dangerous. Luckily there were those among the people like Iruka who were willing to look past the fact that Naruto contained a demon and got to know the true child that he was. Jiraiya in turn told Sarutobi everything that had happened while he was setting up his spy network. He highlighted most of it until the point he met Shinji. He talked of how he was in a train station when he saw a bearded man tell Shinji that he was no longer needed and was sending him away to live with some stranger. Jiraiya then mentioned how he talked to the boy and found out everything that there to the boy. Sarutobi had approved of how Jiraiya decided to help the boy and promised to arrange everything for Shinji to live in Konoha. But he was more interested in the organization GEHIRN. Jiraiya said that he managed to get a few informants in the place, but they were mostly low-level techs and other similar low-profile characters that would only be able to provide a little more information besides what was publicly known. The only real piece of interesting information that he had was the E-project GEHIRN was working on.

"Well, if that is all the information that you have Jiraiya then I will select a team of shinobi to handle your contacts there. For now I need you working here in the Elemental Countries." Said Sarutobi.

"Alright sensei, but what do you plan to do about Shinji's living arrangements? It's not like you can just put a small child in an apartment on his own."

"No your right. For a while now I had been planning to have Naruto live with Iruka. I feel that it will do Shinji good to live with them." Replied the Sandaime as he started filling out the appropriate forms. "Of course you do know that you are technically their guardian?"

"HUH? How did that happen?" Asked Jiraiya.

"Well, since Shinji is technically an orphan and you took him in as a student that makes him your responsibility. And Minato had decided to name you Naruto's godfather. As such you are their legal guardian. However we have a pressing need for you and your information gathering techniques, so they will be in Iruka's custody whenever you are not in the village."

"Man this is going to put a cramp in my style." Whined Jiraiya.

"Oh? You never complained when you had a Genin team. How is this different?"

"Because I was just a sensei to them. To these kids I will practically be their parent. It will be my job to give them a path to follow in life."

"Trust me, I'll make sure they follow Iruka's example before they follow yours." Said the Sandaime.

"Thanks for the vote of confidence sensei."

"Listen, it is getting late and I think it's time we got Iruka, Naruto, and Shinji to their new home."

By the end of the day they had all of Shinji's and Naruto's stuff in Iruka's apartment. Jiraiya stayed for a few days after that getting to know Iruka and Naruto while setting up a training schedule for Shinji and Naruto to follow until he got back. When it was time for Jiraiya to leave there were a few tears shed by Shinji but he brightened up when Jiraiya promised that they would see each other again in just a few months.

(Time Skip – two years)

Shinji was now six years old and would be joining the academy today. This was a day he had waited years for.

Over those years he had grown rather close to both Naruto and Iruka whom he saw as a little brother and an older brother respectively. Because Iruka was a Chuunin he was called away on a lot of missions, but that was alright since he always got someone to watch over his two little brothers. They were generally Chuunin like himself and were often very friendly to the boys. Although Shinji had felt that Anko was a little too friendly, bordering on amorous with Iruka. And did she have to keep throwing dango sticks into the wall trying to make a design?

He almost felt sorry for Naruto who was being watched by her right now. The key word being almost. He knew that neither would do anything to hurt the other and he was more excited about meeting the students and making some friends.

Entering the classroom he immediately spotted several students that made it there before him. One was a black haired boy with bushy eyebrows. The other was a girl wearing what he recognized as pink Chinese style clothes who was twirling a kunai around her finger from the handle ring.

It wasn't long after that the room filled up with other students and Shinji's eyes moved over to a boy with white blank eyes. He had seen others with those kinds of eyes and asked Iruka about it who said that they were members of the Hyuuga clan who were famous for their Doujutsu the Byakugan. After hearing about the Byakugan and its rival the Sharingan Shinji thought it would be pretty cool to have a Doujutsu.

Soon the class's Chuunin instructor walked in followed by someone very familiar to Shinji. "Hello everyone. I am your teacher Ryoga Hibiki and this is my assistant Iruka Umino. Today you will be starting your training as ninja, but I warn you now. Being a ninja is not a game. You will be called upon to complete missions that will require you to take another human life, or have your life taken instead. You will be asked to infiltrate fortified enemy positions in order to retrieve valuable information. Many ninja are killed before they are twenty, and from there it only gets more dangerous. So I ask anyone who doesn't think they can handle it to leave now."

Ryoga looked over the students and saw that some shook with apprehension, others shone with excitement, and some acted as if they were completely uninterested. But not one got up to leave, and he smiled at that letting his fang like canines show. "Very good you all just passed your first lesson. Always remember that battles between shinobi are more often mental rather than physical. If you allow yourself to be intimidated then you've already lost half the battle. So I congratulate you for not backing down, but remember that out in the real world you will face much tougher and more intimidating situations then this." The feral grin was soon replaced by a jolly smile as his attitude did a 180. "Now take out your texts and open to page five. We will now be studying shinobi history."

(Time Skip – four years)

Shinji loved his time spent at the Konoha academy. In the four years he had been attending he had developed several close friends. His best friend was Rock Lee (this is the only name I am putting in Japanese format of surname first and given name last, because it sounds a lot better than Lee Rock). Sure Lee wasn't that good in most of the classes, and for some reason he was unable to perform Ninjutsu or Genjutsu but that did not deter him from his dream of being an excellent Ninja. So to compensate he practiced his Taijutsu and he quickly rose through the ranks until the only two that good beat him were Shinji and Neji Hyuuga. Of course this didn't help his other grades and he was currently the dead last of the class.

Neji was more or less a pseudo friend of Shinji's. It might be more accurate to say that the two were rivals for the top spot in the class, which Shinji had held ever since the first day. It irritated Neji to no end that Shinji who came from no clan much less one as strong as the Hyuuga easily beat him an every subject they tested in. The only skill Neji came close to matching Shinji in was Taijutsu and he would often say that the only reason Shinji won was because he wasn't allowed to use Juuken (Gentle Fist) considering how damaging it was.

Another friend Shinji was close to was Tenten Higurashi. She was one of the top kunoichi of the class and was one of the best in projectile weapons, again second only to Shinji.

Shinji heard a lot of people muttering how he was a prodigy, but he laughed it off saying that his skills were due to the fact that he had been trained by Jiraiya of the Sannin ever since he was four. But still people kept saying that he was the best since Itachi.

Shinji was currently headed towards the principal's office. It had been decided that because of the skills Shinji had shown he would be given the Gennin exam early. When he got to the principal's office he was given a paper test that he quickly answered with 100 percent accuracy. Next was the weapons test which was observed by Iruka who had become a full teacher since Shinji's first year. After nailing all the targets right in their center he was taken to a Taijutsu field where he fought the assistant instructor Mizuki. Shinji had been underestimated because of his age and he accidently brook Mizuki's nose when he punched the teacher in the face. Finally Shinji was tested in Ninjutsu where he pulled off all three of the academy jutsu perfectly. And for extra credit he even performed the Katon: Endan technique that Jiraiya taught him.

Now he was back in principle Hibiki's office where his first teacher presented him with a brand new Konoha Hitat-ate. "Now Shinji you will have to come back Monday morning after you get registered so that you can be assigned to your Genin team." He told the happy boy who nodded in understanding before dashing off to show Naruto that he was an official shinobi now.

(Time Skip – four years)

Shinji snuck into the lair of his foe. He was a Chuunin now and was on an incredibly dangerous mission. One wrong move and everything would be ruined and the mission a failure. He silently closed in on his sleeping target, weapon poised in his hand. If the sleeping figure awoke then he was as good as dead. He looked on the face of his target who looked quite peaceful and almost angelic in his sleep. But Shinji knew better. Behind that innocent face was a sadistic monster that would make his life a living hell. He wouldn't be killed, oh no that is too easy for the beast. Instead it would torture Shinji into insanity, just has it had been for many years now. But now was the moment of where Shinji would get his revenge and it was going to be sweet. Shinji lowered his hand and let his weapon of choice fall onto his target.

The water splashed Naruto's face and the thirteen year old boy sat straight up spluttering. "Aniki!" He shouted as he started to shiver. Shinji had used ice water to make it more effective.

"Sorry bro, consider this the revenge I spoke of when you turned my hair blue last week." Said Shinji who had a great big grin of satisfaction on his face.

"I only did that because you put Jalapeño peppers into my ramen! You do not put Jalapeño peppers into ramen!" Naruto shouted at his older brother as he got out of bed to get some dry clothes before heading to the bathroom.

"And that was retaliation for putting hot sauce on my dango. You should feel fortunate that I didn't tell Anko what you did. She is as protective of dango as you are of ramen, and she is a lot more sadistic then I am. Remember what happened the time Jiraiya-sensei peeked on her while she was bathing?" He asked.

"Hey Ero-sennin had that coming to him." Retorted Naruto from behind the bathroom door. "You think that he would learn his lesson one of these days, but noooo. He has to keep peeking at naked or scantily clad women."

"Says the boy who invented the Oiroke no Jutsu." Shinji mutters as he made his way to the kitchen to finish cooking breakfast.

These was a fairly common occurrence in the Ikari-Umino-Uzumaki residence. Naruto liked to sleep past the time his alarm clock was set to and Shinji liked waking him up when he over slept. Eventually it had become common part of the prank war that Shinji and Naruto had. This war eventually came to include the whole village with the only people who were truly safe from pranks being the Sandaime, Iruka, and Anko. The first two out of respect, the third out of fear. Everyone else was fair game in their minds. Well Shinji tried to rein it back before it got out of hand but their motto was, "Just because we haven't pranked you, doesn't mean we won't."

After waking Naruto, Shinji would then go and finish breakfast preparations. It was usually just the two of them for breakfast as Iruka was very busy at the academy, so the task to make breakfast fell to Shinji. If he didn't fix the meals all he could expect to eat was ramen.

Soon Naruto was out of the bathroom wearing orange clothes with green goggles. Naruto had taken to training under Jiraiya whenever the Sannin was in town, and the effects of the training clearly showed. Sure he wasn't the top student, actually he was pretty close to the bottom, but that was because he was very good at academics which made up a third of their total grade. The other problem was that he sucked at Genjutsu and his weapons skills were pretty mediocre. His saving grace was that he was pretty good at Taijutsu and Ninjutsu, except for the Bunshin but Jiraiya tested the amount of chakra he had taught him Kage Bunshin to compensate. Shinji also learned Kage Bunshin as he had a lot of chakra for a guy his age, but he didn't have nearly the amount Naruto had and was forced to use it more strategically.

After a breakfast of miso soup and rice (much to Naruto's chagrin as he wanted ramen) Shinji started cleaning up as Naruto prepared for another day at the academy.

"Hey Aniki." Naruto called. "Didn't you say that you would be receiving a pretty important mission today?"

"Yeah I did Naruto. Hokage Ojisan had said that this was a B-ranked mission that he had been keeping reserved for me. Said that I would do better at it then most Jounin."

"Ah that is so cool. I wish I could go on important missions like that."

"Well this is your last year of the academy. Then you have to become a Genin and go on D-ranked missions. You won't get any real missions until you're a Chuunin and if your Jounin sensei is anything like me that will take a few more years." Indeed Shinji's sensei, Aoba Yamashiro, had trained his team for two years doing over 200 D-ranked missions and 20 C-ranked missions before he had deemed them ready for the Chuunin Exam. At the age of twelve Shinji was promoted to Chuunin after which he traveled and trained with Jiraiya learning the ins 

and outs of information gathering, only stopping by the village roughly every three months. Now at fourteen Shinji was already considered an elite Chuunin of the village who could get promoted to Jounin at anytime he wanted. When asked why he didn't want to Shinji said that he wanted to wait until Naruto became a Genin and when he had gotten the hang of elemental manipulation. "That is if you can graduate from the academy first." Shinji teased as he put on his Chuunin vest, knowing the kind of reaction that got from his brother.

"Hey I'll show you! I'll ace my exam and then impress my sensei so much with my awesome skills that he'll let me take the Chuunin Exam as soon as possible! And just you wait, before you know it I'll be the Hokage handing out your missions!" Naruto proclaimed.

Shinji chuckled as he handed the self-proclaimed future Hokage a bento and they left the apartment, Naruto to the academy and Shinji to the Hokage Tower. Truthfully Shinji really did believe that Naruto could become Hokage. He had the potential; he just had to tap into it.

When Shinji reached the Hokage Tower he was directed to the Hokage's office who was waiting for him.

"Ah, Shinji-kun it's good to see you." Said the aged Hokage whom Shinji had come to see as a grandfather alongside Naruto.

"It's nice to see you to Ojisan." Replied Shinji. "I hear you have a pretty important mission for me."

Sarutobi nodded. "That I do Shinji. This is a long-term spying mission that I feel that you are more suitable than anyone else." He said as he took out a manila folder that contained the specifics of the mission. "I will assign two other Chuunin who will help you and one Jounin who will act as team leader in case of emergencies, but you will actually be leading the mission. One of the reasons that you will lead is because you will be in charge of all the information. Also this will be good experience for you as I doubt you will run into any trouble. The time table for this mission calls that you will be finished in six months."

"SIX MONTHS!?" Shouted Shinji. "Hokage-sama that has to be some kind of mistake. Even border patrol missions don't last that long. And normal spying missions only last 2-3 weeks tops. The only reason Jiraiya stays out that long is because he usually only comes back when there's something to report." He said listing off the various reasons why that had to be wrong.

"Sorry Shinji but there is no mistake, and this will not be a normal mission." The Sandaime answered as he pushed the folder forward.

Shinji opened it and rifled through the first few pages. On top was his shinobi profile, followed by his teammates, the Chuunin being Kotetsu Hagane and Izumo Kamizuki, and the Jounin being a man named Yamato. But under that were files of the four people that did not look anything like their shinobi profile. Looking at his file he noted that it had all the normal information but also included a listing of schooling that he never had. When he noted the listed home address his eyes widened. Osaka, Japan is what it said. "Japan?"

"Yes Shinji. What makes this mission unusual is that it is outside of the Elemental Countries. Thanks to Jiraiya's spy network and Genjutsu we have been able to able to keep a false set of records that show a false life of you living in Japan. Since these are based on your original records, they will stand up to the greatest scrutiny from anyone. Which is more then we can say for the records we have for our other shinobi. Plus since you were born and raised for the first few years of your life there you will have an easier time blending in." Sarutobi explained. "You will gather information through the network Jiraiya set up years ago. Kotetsu, Izumo, and Yamato will contact informants outside of Japan and send the information to you, at a set time you will summon a toad and hand a report to it. Later Jiraiya will be given that report and he will supply it to me if he sees anything important. Are there any questions?"

"Yeah. You really expect me to be gone for six months?" Asked Shinji. "What about Naruto."

"Iruka can handle Naruto just fine and you know that. Besides he's old enough to watch out for himself."

"Yeah, but what will Iruka do when Anko decides that Naruto must die for some transgression. He's not exactly very stern with her." Shinji said as he remembered the one time they had pranked the snake kunoichi and how Iruka had not been much help. Shinji had long suspected that the two had a crush on each other.

"We'll cross that bridge when he get there, but this mission is too important."

"Then answer this Hokage Ojisan. Since when is it so important to have someone like me gather information of the outside world? It was never important before."

The Hokage took out several more folders and scrolls. "Recently our spies have reported that the UN military forces as well as the JSSDF have started mobilizing in Japan. Also our spies in NERV the organization that replaced GEHIRN have reported that they have been more active lately. As if they were preparing something." He said as he opened them up showing photos of various military vehicles as well as logistics reports. There were no photos of what NERV is doing. "We don't know why they are doing this as most of the informants don't have a high enough ranking position to give us much. But what we do know is that they are mobilizing for the same reason. Whatever this threat is the UN, JSSDF, and NERV all plan to fight it. Only NERV has gone and built some new type of weapon called an Evangelion to fight it. All information on the Evangelion is top secret and we have almost no information on it. What we do know is that that there are multiple units and they need children pilots."

Shinji raised an eyebrow in curiosity at that. What kind of organization would send children to the front lines? Sure they did that in the shinobi world, but they received extensive training and even then didn't go on the serious missions until they reached a rank that showed they were ready. "Sigh…When do I leave?" He asked.

"Tonight. That should give you time to pack your things and say your goodbyes."

"You're going to be gone six months!?" Exclaimed a dismayed blonde. "But you'll miss my graduation!"

"Sorry Naruto, but those are my orders. Besides Iruka will still be here." Shinji apologized as he packed up what belongings he needed. Setting a supply of emergency rations on top of an open scroll inside and intricate series of seals he brought his hands into the Ram seal and said, "Fuuin," sealing the food into the scroll. That scroll was one of many that possessed everything from Shinji's camping gear to spare weapons to techniques he wanted to learn. He had enough to invade a small country. But hey, he was going to be gone for six months and it wouldn't be easy to replenish his supplies in the outside world.

"But you promised to teach me how to walk on water this week. Ero-sennin said he wouldn't teach me the Rasengan until I know how to do that."

"I'm sure Iruka can teach you. He is a Chuunin just like me and he's very good." Shinji said as he put on his backpack. "Listen, the months will fly by and I'll be back before you know it." He assured as he headed out the door. "See you in a few months bro."

"Yeah and when you do I'll be a Chuunin like you!" Naruto shouted back, making Shinji laugh.

"Yeah, sure you will."

Within a few minutes Shinji found himself at the gate where his teammates were waiting. Izumo with his hat. Kotetsu with that wrap on his face. And the unknown Jounin Yamato who wore a shinobi helmet that protected the sides of his face. When Shinji arrived Yamato spoke up. "Is everyone ready?" The Chuunin nodded in the affirmative. "Alright, then let's go." He said as he turned and walked out the gate followed by the Chuunin.

"Man it's hot!" Complained Kotetsu as he fanned himself off with a paper fan, his normal Chuunin uniform discarded in favor of a white tank top and loose shorts. He laid sprawled out on the sofa of the apartment that were renting for the extent of their mission.

"Ya know, I went on missions to the deserts of the Land of Wind and I was perfectly fine but this place is torture." Said Izumo who was similarly dressed, sitting on a chair waiting for the moment when the rotating fan would pass over them.

"Actually the temperature in the Land of Wind far surpasses Japan. The source of your discomfort is the humidity which was usually very low back home." Explained Shinji who, being more comfortable then his companions since he already knew the climate, was dressed in a school uniform that was far from standard. For one thing he always wore his open Chuunin vest over the shirt. The pants looked normal but had been re-stitched so it would allow the maneuverability that was required of a shinobi. When he wasn't at school he wore his supply pouch and kunai holster. And he always wore his hitat-ate somewhere on his person. Today it was on his left bicep.

It had been a month since the Shinobi arrived in Osaka. They immediately moved into an apartment that was right next to the one owned by the very man Shinji was supposed to have lived with before he started training with Jiraiya. Of course to help keep their cover they had to enroll Shinji in school where they had used a subtly Genjutsu that made everyone believe that Shinji had always been in there, he was just quiet and didn't interact much with others. The 

Genjutsu would hold up as long as Shinji didn't really try to bring attention to himself. At first Shinji wasn't too keen to go back to school but it was necessary so he could learn how to use items like computers. Now the three Chuunin were waiting for Yamato to return with the information from the informant in Russia. They had to admit that phones and computers made their job easier.

The three heard the door open and shut and turned their heads when Yamato entered the room, in one hand was the info, the other contained the daily mail.

"Anything interesting?" Asked Izumo.

"The informant did not provide anything we did not already know. However Shinji did receive something in the mail. I took the liberty of picking it up from next door when I saw it." He said has he handed Shinji a large yellow envelop.

Curious has to who would send him something when he practically doesn't exist here Shinji looked at the return address. His eyes widened as he saw it was from NERV and he had a suspicion he knew who sent it. Opening it he let the contents drop onto the coffee table. Most of it were different sets of paper. Some were transportation instructions stating that he would take the train to Tokyo – 2 and then he would be picked up by a Captain Misato Katsuragi who would take him to Tokyo – 3. Accompanying those was a photo of a very pretty woman with purple haired tied into a ponytail, while wearing a tight pink tank top with cut off jeans. Her pose was rather flirtatious and it did not help that there was an arrow that said 'Look Here' pointing at her generous cleavage. But Shinji's attention was drawn to a small postcard sized piece of paper. The letter head said it came from the office of Commander Gendo Ikari. There was only one word written on it, "Come." Shinji's eyes narrowed in anger at the audacity of the man. He unconsciously started letting off a bit of unfocused killing intent.

"Hey Shinji, you ok?" Asked Kotetsu as he noticed the killing intent coming from the younger Chuunin. Shinji didn't say anything and just pushed the papers towards the others. Looking them over, it wasn't hard for the older shinobi to understand why Shinji was angry. They had been told about his past here in Japan as they traveled here.

"So what are you going to do?" Asked Yamato. Shinji was still in charge and this was not the kind of situation where he could step in and assert Jounin authority.

"As much as I would like to ignore anything that man sends, this is a good opportunity to get more information out of NERV. So for the good of the mission, I will follow the instructions in those orders and your three will relocate to Tokyo – 3." Said Shinji.

Yamato nodded in approval at the plan. Izumo also showed his support, but in a different way. "Hey look on the bright side. At least your ride is hot." He said, sounding a lot like a certain perverted Sannin as he picked up the picture and started ogling the figure on it. Everyone else sweatdropped at this.

Author's Notes: This is my second Eva fic and is another side story that I will work on when I feel like it. I had never seen this crossover before and decided that I would give it a try. Anyone familiar with my Naruto stories will have noticed that I am writing the names in the English format of given name first then surname. That is something that I will always do in any Eva fic I write.

Next chapter is Shinji's introduction into NERV as well as the fight with the Third Angel. I will also introduce Shinji's first love interest. Can you guess who?

Please Read and Review. I love reading any comments people have to say about my stories and it helps inspire me to write.