Naruto: Aftershock

Blanket disclaimer: I do not own Naruto or Neon Genesis Evangelion

AUTHOR'S NOTE:

I've wanted to do a Naruto/Neon Genesis Evangelion crossover for years but could never figure out how to do it to my liking. I shelved the idea as a result. Then recently I bought the manga and it rekindled my interest in the idea. Hopefully the story will turn out to be a good one.

It is assumed the reader is already familiar with Neon Genesis Evagelion. Otherwise it's going to be very difficult to follow. This story is based on both the Evangelion anime series and the manga series. In particular, Shinji's character will be like the manga in that he will be apathic as opposed to somewhat spineless. There will be pairings but at this point they are undecided. I will be adding a sprinkling of technology from the Rebuild movies (like new EVAs) but none of the plot. There also may be a bit of the Shinji Ikari Raising Project manga for the additional characters and humor at the school.

On the Naruto side of things Konoha and Naruto's background are quite different and it will be revealed in the story. Naruto can use chakra and jutsus but he doesn't have Kurama sealed in him. He's also a bit more mature due to circumstance. Let's see how this goes. Here is chapter 1 of Naruto: Aftershock. Enjoy!

{ } Signifies a foreign language

[ ] Signifies hand signals

Chapter 1

Tokyo-3, Japan, 2015 A.D.

Uzumaki Naruto was reading his orders as he rode the train into Tokyo-3:

….

Orders for Chunin Uzumaki Naruto:

The Third Angel code named Sachiel was the first Angel seen since the Second Impact fifteen years ago. According to our contacts; Sachiel attacked Tokyo-3 two days ago with the apparent intent of destroying the city and more importantly NERV Headquarters. It was unstopped after battling UN Forces, Evangelion 01 piloted by the 'First Child' Ayanami Rei and an N2 mine attack by the UN. Shortly thereafter the Angel was destroyed via self destruct while in combat with Evangelion 01 piloted by the 'Third Child', Ikari Shinji . (For details of the actual battle see the attached report). Your current duty is to infiltrate the NERV Organization as the 'Seventh Child' as chosen by the Marduk Institute. (Information also attached). Your partner in this mission will be your fellow apprentice to the Sanin Haruno Sakura who has also returned from her training trip. She will be the 'Sixth Child.' Your contact will be your cousin*① Kaji Ryoji who is going to be taking you in as his ward. He currently is a NERV Special Inspector.

Presently Kaji is in Germany watching over the 'Second Child' Soryu Asuka Langley so you will be 'on your own' the first few weeks after your arrival. Use this time to set up your own network as Kaji Ryoji has his own agenda (as you are well aware). Be alert that there are multiple forces at work besides NERV. The Japanese Department of the Interior and the shadow organization SEELE are also involved. Use your training under your Master Jiraiya and your last year abroad wisely in order to learn as much as you can about them and await further orders. Konoha is counting on you Uzumaki Naruto. This is an S-ranked mission.

-The Third Hokage, Sarutobi Hiruzen

….

"Gods Jiji; you always give me the simple missions." Naruto shook his head. "So I'll be seeing my cousin Kaji again for better or for worse." the blonde thought aloud. 'He claimed he couldn't become a ninja and left Konoha….So what does the idiot do? He becomes a spy!' "….On the positive side I'll be seeing my friend Ikari Shinji again. I wonder if he still has such a dreadful outlook on life…." Naruto burned his orders to ash with a fire jutsu. 'I wonder how Sakura is doing. I haven't seen her in years. I guess we're both fourteen now and chunins.' He closed his eyes and thought about his life so far….

….The blonde just turned fourteen and like so many of his generation in Konoha he was an orphan. The Second Impact destroyed the original Konoha Village forcing them to retreat into the mountains as a tiny, secluded village in the mountains of Japan. They were among the few villages left that practiced the ancient ways of ninjutsu using chakra. It was a fact every living thing had chakra but being an Uzumaki; Naruto had an ocean of it. He was raised by his Godfather Jiraiya who taught him the shinobi arts as soon as he was old enough walk and talk. Naruto was taught the strategy and tactics of unconventional warfare, guerrilla warfare and espionage practiced by the ninja since ancient times. He learned the Gama style of taijutsu, fuinjutsu (sealing), shurikenjutsu (shuriken arts), kenjutsu (swordsmanship) and kyujutsu (archery) among others. The blonde's ninjutsu repertoire was impressive and well rounded but his true strengths lay in wind jutsus and chakra manipulation.

Jiraiya reckoned Naruto was a solid jonin level shinobi a year ago in skill except for his lack of experience. Therefore the young ninja was sent to wander for a year to learn about the world the hard way. It was just like young hawks were kicked out of the nest by their parents to make the young birds tough. You learned to survive or the weight of the world would crush you. Naruto ended up travelling to Musashino*② in the old Tokyo District (that was rebuilt to some extent) where he enrolled in school as a homeless orphan. There he met a depressed and seemingly apathic boy named Ikari Shinji. Naruto could tell there was something special about the dark haired Ikari boy and befriended him. Naruto attended school and observed the behaviors of others his own age so he could seamlessly blend in to society. When the year ended Naruto returned to undergo the grueling trials to become a chunin and passed with flying colors….

….And the rest, as they say, is history. The Uzumaki chunin went on many missions for Konoha ranking from C to A as well as a single S-ranked assassination he pulled off flawlessly. As a result the Third Hokage chose him to infiltrate Tokyo-3 as the 'Seventh Child' -someone chosen to pilot the giant Evangelions and serve in 'the admirable job of defending humanity.' Naruto wanted to laugh. NERV's purpose and that of SEELE were clearly not to serve humanity. Whatever their true purpose was; Naruto figured would become apparent to both him and Sakura in due time….

….

Naruto got off the train at Track 2 of the Tokyo-3 Train Station and saw the damage from the battle against Sachiel. Then he saw armed guards in sunglasses watching him. It was subtle by civilian standards but to a trained ninja he could have spotted them several kilometers away. 'NERV Public Security Forces and Intelligence Bureau….' thought the ninja. A very pretty woman with bleach blonde hair and a white lab coat was with them.

She walked up to Naruto slowly and asked, "Uzumaki Naruto?" The whiskered blonde nodded and the woman smiled. "I'm Doctor Akagi Ritsuko from NERV. I'm here to pick you up in Inspector Kaji Ryoji's stead. He unfortunately is out of town." 'Kaji you lazy bum. You owe me one. You weren't even here to pick up your own cousin. I haven't got time for this.'

The blonde ninja grinned and said, "It's nice to meet you Doctor Akagi. I'm sorry you had to do this for my cousin. Last I heard he was in Germany."

Ritsuko nodded to the two security agents and they promptly left. She said, "You don't bear a strong resemblance to Kaji physically but you have the same air about you. I can tell you are cousins. I've known him for years and I don't remember him ever mentioning family before."

Naruto explained, "Kaji left before I was born; I've met him but I guess you'd call us estranged. It's of little importance."

She raised an eyebrow. "I was wondering why he suddenly had a ward. Did he invite you here to live with him? The circumstances seem rather unusual."

The ninja chuckled and said, "He invited me here due to a report from the Marduk Institute whatever that means."

Doctor Akagi's eyes widened and Naruto gave her a flirty smile that looked just like Kaji. Then she noticed that Naruto had his spiky blonde hair pulled back into a tail just like Kaji. Ritsuko thought to herself, 'The Marduk Institute?! But that would mean he is a candidate for piloting the Evangelions!' She coughed and asked, "Did Kaji explain what the Marduk Institute is?"

The whisker faced blonde shrugged and answered, "I don't have a clue. Kaji said it was very important though." 'The Marduk Institute doesn't even really exist; it is a dummy organization composed of 108 front companies and Eva pilots are actually hand-picked by NERV.'

Ritsuko sighed in relief and said, "Well, it's of little importance. Let's get your luggage and get you to your new home." 'It seems he's ignorant of what we do here. Good.' The car ride to Kaji's apartment turned out to be a quiet one. Ritsuko did ask about Naruto's unique whisker marks and he explained that they were birthmarks. She accepted this answer and figured she'd have a chance to look into them later.

The blonde ninja appeared to be playing a game on his phone but he was looking up intelligence data on Ritsuko. 'Let's see what I have on the good doctor here.' he thought as he tapped some buttons.

….Chief of Project E, Doctor Akagi Ritsuko of the Bureau of Technology's First Division. She is NERV's chief scientist and is in command of the Technical branch of NERV HQ which is responsible for the research and development of the Evangelions as well as their maintenance and repair. Akagi is a polymath genius whose disciplines include physics, biotechnology and computer science….

Naruto mentally frowned. 'That doesn't help me much other than the woman is a genius and her position in NERV. I guess it's better than nothing….'

….

Kaji Ryoji's Condo

Naruto had a key to his cousin Kaji's condo and once Ritsuko was sure the blonde ninja could get in and out okay she returned to work after giving Naruto her phone number just in case there was an emergency. Naruto thanked her and the bleach blonde scientist was soon on her way. The ninja looked around the darkened condo and turned on the lights. "This place is fairly neat and tidy." he thought aloud as his eyes scanned the place over. Checking the various rooms he saw a note on the kitchen table with his name on it.

….

Naruto-

Sorry I couldn't be here to welcome you in person. The condo has three bedrooms. The main bedroom is mine but the other two are open so pick the one you want. I should be back from Germany in a few weeks. I've already enrolled you in school and you've been assigned to Tokyo-3 Middle School Class 2-A. (The paperwork for your transfer is on the table). I hope that the transition is an easy one for you. The whole situation of you moving in was a bit of a surprise to me but I'm sure we'll get along fine after you settle in. The utilities and other bills are taken care of and you have your own bank account through NERV. I asked Doctor Akagi Ritsuko to watch over you until I get back but as busy as she is I doubt you'll see much of her. I'll see you in a few weeks.

-Kaji Ryoji

….

"Well, this is interesting." pondered Naruto aloud. 'I guess I should check for security cameras and whatnot. The last thing I can afford to have is someone watching me.' The blonde ninja searched the apartment thoroughly and found there were no hidden cameras or listening devices. Then he painted silencing seals on the room he picked to be his. "Now that I have that done I'd best start scoping this town out. It's Friday and I have to report to school on Monday…."

….

Tokyo-3 Middle School, Class 2-A

A week later Naruto had concluded that Class 2-A was nothing short of a NERV set up. All potential Eva pilots were transferred to Class 2-A to keep them safe and on hand should NERV require them. That aside the class was an incredibly mind numbing and listening to the old instructor drone on about the Second Impact was downright painful. The blonde ninja was fighting to stay awake and everyone else was too. 'By the gods; this history teacher is so boring I'm falling into a coma. Watching paint dry or grass grow is more exciting.' He caught a glance from Aida Kensuke whom he had gotten to know a bit in the last week. Kensuke wore glasses and was a bit of a military geek and Evangelion otaku. Naruto also interacted with Horaki Hikari who was the class representative. Hikari was a cute and considerate girl but could be very stern….

….After lunch Naruto was pleased to see they had a new transfer student. It was someone the blonde knew well. A pink haired, green eyed girl was at the front of the class and introduced herself. "Hello everybody; I'm Haruno Sakura and I just moved here to Tokyo-3. I hope we can all get along." she spotted Naruto and made eye contact briefly.

Several of the students were interested in Sakura and thought she was cute with her shoulder length pink hair. Naruto looked the kunoichi over and realized she'd grown more womanly in the last four years. 'Of course the last time we saw each other we were ten years old. She cut her long hair off too.'

"Sit anywhere you like Miss Haruno." said the homeroom teacher.

Sakura looked around and saw that there was an empty seat in back by Naruto. She asked kindly, "Is this seat taken?" Naruto indicated it wasn't and the kunoichi sat down beside him. The two acted like they were newly introduced but they were rapidly conversing with each other though ANBU hand signs. ["I'm living in my own apartment; it would be good if you could stop in and set up some silencing seals for me."] signed Sakura.

Naruto replied, ["It shouldn't be a problem. My cousin Kaji is in Germany so I'm free to do as I please."]

["I didn't know you had a cousin Naruto."] signed the rosette.

["It's a long story but he left Konoha before we were born. He's not a ninja."] explained the blonde.

Sakura signed, {"We'll talk later. Looks like class is about to start."]

….

NERV Headquarters

Doctor Akagi Ritsuko was talking with NERV Commander Ikari Gendo and Vice Commander Fuyutsuki Kozo about some unexpected news. She was a bit panicky. "Did SEELE force these children upon us? And why the 'Sixth' and 'Seventh' children? We're always involved in the selection process! What about the 'Fourth' and 'Fifth' children? We haven't even picked them yet. This is highly irregular!"

Gendo sighed. "SEELE is the only logical answer to this strange situation. Given Rei is injured and the 'Third Child' is unstable we may actually need the 'Sixth' and 'Seventh' children as backups. Bring them in and test them. We have nothing to lose." He looked at the dossiers compiled on Naruto and Sakura and frowned. 'They are completely clean according to our intelligence division. Uzumaki is an orphan from Musashino and Haruno grew up in the countryside although she shows an incredibly keen intellect….just how much harm could two teenagers do?'

….How much indeed….

Fuyutsuki asked Ritsuko, "What do you think Doctor Akagi? You've at least met this Uzumaki Naruto. Was there something about him that makes you apprehensive?"

Risuko sweat dropped. "He seemed like an ordinary teenage boy that knew absolutely nothing about NERV…." 'But he's Kaji's cousin so that alone makes him suspicious to me!'

"Test them and see if they are compatible with the EVAs." ordered Commander Ikari. "I'm very curious if these two are even capable of linking with an EVA."

….

Tokyo-3 Middle School

That afternoon Naruto and Sakura were leaving class with the other kids when Ritsuko pulled up in her car and waved the blonde ninja down. The NERV Chief Scientist smiled and called, "Naruto; who is your friend?" The whiskered ninja looked around acting oblivious before Ritsuko pointed towards Sakura.

Sakura pointed to herself and asked, "Me Ma'am?" The bleach blonde scientist nodded and the rosette said, "I'm Haruno Sakura and I just transferred in. I just met Uzumaki-san today."

Ritsuko smiled and said, "I need to talk to you both for a few minutes…." 'Better me than NERV Intelligence hauling you in against you will….'

….

The two kids carefully listened from the back seat as Ritsuko drove along and gave them a job offer to pilot the EVAs. Both shinobis did their best to look surprised and dumbfounded. "You want us to get inside those giant robots we've heard about?" asked Sakura. "That doesn't sound too safe. I mean; going into battle with these Angels?"

Naruto acted a bit more enthused, "Well, I know some martial arts so maybe I could fight. Is there a reason we were picked in particular Doctor Akagi?"

"Both of you just call me Ritsuko when we're not on duty." said the bleach blonde in a disarming way. Then the scientist explained, "Only children born since the Second Impact are capable of piloting Evangelions for some reason. If you join NERV you'll be paid handsomely. Right now we just want you to get in an Evangelion and see if you can synchronize with it. If it doesn't work then no harm done right?"

["I wasn't expecting this to happen so soon."] signed Sakura. ["We haven't had much time to acclimate to our circumstances."]

Naruto nodded. ["Things are happening too fast. We're just going to have to adapt. I have a bad feeling about this."] The blonde ninja said to Ritsuko, "I guess if all I have to do is sit in it then I'm game."

"I guess I will too then." said Sakura in a nervous tone.

"Good. That's all we can ask of you." said Ritsuko. 'That was simple enough. I was afraid things would be difficult. Their reactions seem like normal kids….maybe I'm just too suspicious.'

….

NERV Headquarters, EVA Test Bay #1

"So this is an Evangelion…?" asked Naruto in genuine awe looking at the gargantuan form of Unit 01. He reached out with his sensory abilities and his blue eyes widened. 'This isn't a machine….It has chakra! IT'S A LIVING BEING!'

Sakura was equally shocked at EVA 01. "It's….It's colossal!" she whispered. That's when she saw Naruto give her some ANBU hand signals.

["It's not a robot. It has a chakra. The EVAs are living things!"] signed the blonde ninja.

Her green eyes widened in wonder and fear. 'If it's alive….does it have a soul?' she wondered. "Ummm….Ritsuko?"

"Yes Sakura?" asked Doctor Akagi. She was pleased at the children's awestruck reactions.

"Why were the Evangelions constructed in a human form?" asked the rosette. "For the sake of balance alone wouldn't it have been simpler to make a four legged form?"

Ritsuko was surprised and pleased at the insightful question. "They are made to mimic the human form so they can interface directly with their human pilots. You feel what it feels when you are linked; see?"

"Then they must be alive as well." said Sakura. "I wonder if there is a consciousness floating around in there somewhere."

'What a bright girl!' thought Doctor Akagi. 'But she's a little too close to the truth….' "No one truly knows Sakura; but it is true that there are a few living components. It's nothing to be concerned about."

Naruto's blue eyes narrowed. 'Liar! I'm sensing a fully developed chakra system just like a human being's….It's just on a massive scale!' He looked at EVA 01 and thought, 'Who are you?!'

….If there was an answer the EVA remained silent….

….

Pilot's Locker Room

Sakura looked at the ridiculously thin white Plugsuit and wondered if it was thicker than a millimeter when she activated it and it conformed to her body. It was a spare suit of Ayanami Rei's. The rosette looked in the mirror and thought, 'I guess it's better than being completely naked….I've been in bikinis that don't expose as much though.' She sweat dropped. 'On the positive side it is opaque and I can't see the color of my veins.' The green eyed girl blushed slightly and wondered, 'I wonder what Naruto will look like in his.' Then the kunoichi clipped her white interface headsets into her pink hair and was glad she wasn't going to be seen in public this way….

In the next stall over, Naruto was wearing a suit that was designed for Shinji. It had a white top with the mid torso down being blue. "Well, this thing has zero coverage." he grumbled to himself. Activating the slim suit so it stuck to him like a second skin; Naruto noticed it was easy to move in but aside of that it left nothing to the imagination. 'I wonder what Sakura thinks of her suit. I guess I'll be able to tell how well she's grown up….' he thought perversely. Then he hung his head. 'Of course, I'm on display as well.' Clipping on his interface headsets he whispered, "Here goes nothing!" as he stepped out into the main area.

The two teen shinobis stepped out at the same time and got an eyeful of each other. Blushing profusely they filed out to where Doctor Akagi Ritsuko was waiting along with Captain Katsuragi Misato.

….

Katsuragi Misato was a lithe, shapely woman with dark eyes and purple hair. She was good friends with Doctor Akagi and she commanded NERV HQ's Tactical Operations branch which was responsible for coordinating the Evangelions in actual combat. Misato was normally a lively person but was very concerned for Rei and Shinji who were both still in the hospital at the time. The purple haired woman smiled at the two shinobi and said, "So you've been chosen to be our backup pilots? I'm Captain Katsuragi Misato of NERV. I'll be your Tactical Commander in combat situations and your direct superior. I hope we all get along."

The kunoichi smiled weakly and thought, 'What a way to meet a person dressed like this….' "I'm Haruno Sakura; it's nice to meet you."

'She's quite a woman!' thought Naruto. Then he caught her scent and wondered, 'Why does she smell like beer?' The ninja said, "I hope we get along too. I'm Uzumaki Naruto." Then Naruto smiled in a familiar way.

Misato raised an eyebrow and thought, 'Why does this Naruto remind me of somebody?' The Captain sighed softly and explained, "Our crew hasn't recovered from the last battle so we are a little undermanned at the moment. Since you are both suited up we're going to test each of you in Unit 01. I don't expect your compatibility to be very high since you are new but don't worry. Our first qualified pilot Ayanami Rei took nearly seven months before she was combat ready."

"Seven months seems like a long time to me." said Naruto in dismay.

Misato laughed. "Don't worry. I'm sure you'll do fine. It's a lot more difficult than just learning to drive a car."

Both teens sweat dropped since they weren't old enough to drive….

….

Entry Plug to Unit 01

After discussing it with Sakura in ANBU code; Naruto went first. They agreed that the fact he was a sensor might be to their advantage. The whiskered blonde sat down in the entry plug and waited as the three bridge Lieutenants rattled off the process over the radio:

Naruto felt like he was in an elevator when he heard Shigeru Aoba's voice: "Inserting entry plug".

"Direct hydro-transmission system, connection prepared." said Ibuki Maya

The plug stopped and jolted the blonde ninja. Aoba continued, "Plug fixed in place."

Hyuga Makoto reported, "First stage connection initiated."

Maya said, "Filling the entry plug."

As the plug started filling with the amber colored LCL*③; Naruto's heart rate skyrocketed at the sensation of drowning. Ritsuko tried to calm him down. "Don't be alarmed Naruto! It's just like I explained. Once your lungs are saturated with the LCL; you'll be able to undergo direct oxygen exchange. You'll get used to it in a minute."

The ninja growled, "This is completely unnatural!" as he calmed down. "Breathing liquid that tastes like blood is just wrong! Breathing a liquid at all is just wrong!"

Misato asked, "Are you okay in there Naruto?" Seeing him nod the purple haired woman said, "All right, let's continue."

Aoba resumed after getting a nod from Misato. "Connecting the main power. All circuits are fully functional. Now initiating the power up sequence."

"Set the thought configuration to Japanese." said Doctor Akagi. "All preliminary contacts established."

Maya reported, "Commencing secondary contacts. A-10 nerve connection, normal. Bi-directional circuits are open. Synchronization rate at 11.4%"

"Not too bad…." said Ritsuko. "Try focusing a little harder Naruto. Think what you want to do."

"Give me a minute to find my center." said Naruto. The blonde reached out to the EVA with both his thoughts and his chakra. 'Hello there. I'm Uzumaki Naruto. Can you speak to me?'

The Eva remained silent but a thought flashed into Naruto's mind. It was an image of Ikari Shinji both as a child and then as a teenager. A strong urge to keep Shinji safe was there.

'You want to protect Shinji?' thought the blonde. 'I went to school with him for a year and we are friends. I'll keep an eye out for him. I hope you and I can be friends too.'

As the ninja conversed with the silent EVA he felt it was warming up to him a bit and his synchronization rate started climbing steadily.

"His synchronization rate has climbed to 31.6%!" said Maya excitedly. "It has leveled of and is holding steady."

"Good job Naruto. That's exceptional for a first try!" exclaimed Misato over the radio. 'Not on Shinji's level but still….' she thought.

Naruto was soon out of the cockpit and said, "She seems nice enough but a bit apprehensive."

"She?" asked Ritsuko and Misato as one.

"Yes, EVA 01 is definitely a she." replied the blonde ninja. He smiled like his cousin and said, "I can tell a woman from a kilometer away."

Misato giggled at his antics and Ritsuko sweat dropped. 'He even acts just like Kaji.' thought the bleach blonde scientist. Sakura just rolled her eyes….

….

"You kids both exceeded my expectations by a wide margin!" said Misato enthused. "Naruto ended up with a 31.6% synch rate and Sakura was slightly lower at 29.2%. For first tries that is superb and either of you should be able to operate an EVA effectively. Now all we need to do is begin your training as pilots. This weekend our other pilots are getting out of the hospital so you'll receive your first orders Monday. Well get you your own plugsuits ready as well."

….

NERV Hospital

Later that day; Ikari Shinji was in hell. He'd been in the hospital recovering for over a week and had been plagued with some truly horrific nightmares all centered around the EVA. His Father Ikari Gendo never even bothered to acknowledge Shinji's existence although Captain Katuragi had checked up on him a number of times. Now he was out…. 'Out of the frying pan and into the fire.' he thought acidly as he rode along with Misato in her Renault Alpine to their new condo. 'So what if I wanted to live alone?'

….

Flashback….

Shinji was ready to leave the hospital and Misato was wondering why he didn't want to live with his Father…. "It's none of your business Misato!" growled Shinji.

Misato looked shocked. "Hey, what's with that tone of voice? I'm just worried about you; that's all…."

The boy roared, "Don't you have enough to worry about?!"

Then the purple haired woman frowned and a vein bulged on her forehead. "So gloomy….like some kind of mood disorder!" she said. "I'll fix that personality of yours!" Misato then proceeded to make arrangements for Shinji to live with her at her condo much to his disbelief.

Shinji was too shocked to react until it was too late. When he regained his wits the teenager screeched, "Are you kidding me? Why do I have to live with you?! It's crazy! Who are you to tell me what to do, huh?!"

"Oh, you mean me? Who am I?" growled Misato. She froze poor Shinji in place with a terrifying glare. "What part of 'Commanding Officer' don't you understand?"

'H-her eyes -paralyzing me…!' the boy mentally whimpered as she dragged him off by the wrist….

Flashback end….

….

Ikari Shinji's life with Misato began with a shock. The condo was a pigsty, the fridge was full of beer, all there was to eat was TV dinners and somehow the young man ended up with the vast majority of the chores….Then to top it all off Shinji found out about his other roommate, a hot springs penguin named Pen-Pen. Shinji just sighed over dinner. 'What have I gotten myself into?' he wondered forlornly.

….

Tokyo-3 Middle School, Class 2-A

Monday morning Shinji was sitting towards the front center of Class 2-A. He had been introduced to the class that morning but after a weekend of Misato and Pen-Pen's beer laden antics the boy was running on autopilot. He really didn't notice anything in particular. The dark haired young man did notice the enigmatic Ayanami Rei sitting over by the window bandaged up with her right eye patched. He wasn't sure what to think of her. For some reason his Father Gendo paid attention to Rei and that made Shinji curious about the light blue haired girl….

All the while; Naruto was sitting at the back of the class keeping an eye on Shinji. 'Ikari is as oblivious as ever. He didn't even notice me….' thought the blonde with a mental chuckle. Naruto had been using his sensory abilities rather liberally since returning to class that morning and he noted that both Ikari and the Ayanami girl had active chakra networks just like a shinobi. They were both far above average for a civilian. Both displayed high genin level capacities from what Naruto could tell. 'Must be from interacting with the EVAs.' thought the young ninja. The rest of the kids in class displayed higher than average chakra levels as well but their chakra networks weren't active. Naruto and Sakura had been communicating through ANBU code all morning theorizing about this.

["Perhaps an active chakra system is a necessity to interface with an EVA"] said Sakura. ["My guess is being in close contact with an EVA and its massive chakra system jump starts the pilot's system in some way. It's a shame I can't study it directly instead of just theorizing."]

Naruto signed in agreement. ["Well, for what it's worth your theory makes sense to me but then again I'm no medic. That's your area of expertise. It's too bad you and Doctor Akagi can't punt ideas around. I get the impression she likes you and your mega intelligence."]

Sakura smiled. ["Are you trying to butter me up?"]

["Nah….I'm just stating a fact. You've always been super smart."] replied Naruto with a grin.

The two continued to banter throughout the morning. Nothing really exciting happened in class until lunchtime….

….

Lunchtime….

….Shinji suddenly found himself the center of unwanted attention. A girl asked him, "So the rumor's true, isn't it?"

The dark haired boy looked confused and asked, "….Rumor?"

Another girl exclaimed, "Don't play dumb. The rumor that you're that you're that robot's pilot!"

"….It's true…." replied Shinji timidly.

"THAT IS SO COOL!" shrieked the first girl. "How did they choose you?"

He was barraged with questions but one was louder than the others. "What was that monster? Is it some country's secret weapon?"

Shinji paused and answered, "I don't know much about it. They called it an 'Angel.' ….But nobody seemed to know exactly what it was…."

That's when a tall boy in a tracksuit came in and yelled at Shinji, "You think you're all that but you don't know anything do you?!"

The class rep Horaki Hikari said, "Suzuhara Toji! You missed a whole week of school without permission…."

"It's none of your concern!" snapped Toji. "Shaddup!"*④ Suzuhara turned back to Shinji. "You, new kid! Step outside now!"

Shinji followed Toji outside to see what the athletic boy wanted. Finally they made it up to the roof and Suzuhara rounded on the EVA pilot. He growled, "Listen up! My younger sister was hurt bad….She's still in the hospital! Don't you feel sorry for her?" The jock's eyes narrowed and he asked, "Whose fault do you think that was…?" Then Toji exploded. "It's your fault! She was pinned under rubble because you had to go crashing around in that robot!"

Shinji was a bit dumbfounded at the outburst and quietly replied "….Sorry."

"Sorry just doesn't cut it!" roared Suzuhara as he decked the Ikari boy.

Shinji rubbed his cheek where he'd been punched and asked Toji, "Don't you get worn out from being angry all the time…?"

The jock lost it and yelled, "YOU BASTARD! I'm drawing the line right here…!" He lunged at Shinji….

….Then Toji suddenly felt an incredible grip on his shoulder that stopped him dead in his tracks. The athletic boy felt a chill up his spine when Naruto's killing intent laden voice said, "That's enough. You back off or I make you back off. It's your choice."

Toji looked over his shoulder and saw the blonde ninja's eyes were cold as death. "W-who are you?!" asked the frightened jock.

The whiskered blonde answered, "I'm Uzumaki Naruto. I just transferred in. I'm sorry for your sister but if Shinji hadn't defeated that Angel then you, your sister and everyone else in this city would be dead. Did you think about that?"

The jock looked taken aback. He obviously hadn't thought about that. "Ummm…." said Toji.

"Just go." said Naruto. "There's been enough fighting as it is."

Suzuhara nodded and saw his friend Aida Kensuke standing there looking distressed and left with the glasses wearing boy. After they left Naruto turned back to Shinji and held out his hand. "Need help up Ikari?" he asked kindly.

Shinji took the offered hand and Naruto pulled him up. The dark haired boy rubbed his jaw and smiled. "Uzumaki Naruto….I'm glad to see you but what on Earth are you doing here in Tokyo-3…?"

"I arrived here a week ago." explained the blonde ninja. "I got headhunted to be a backup pilot for the EVAs so I live here now. I guess we're stuck working together just like when we were lab partners in school last year."

Ikari remembered the two of them 'accidentally' filling the science lab with green smoke back at the Musashino Middle School and laughed. Naruto was always up to no good and pranking somebody…. 'Maybe this won't be so bad….' thought Shinji with a mental chuckle….

….

NERV Headquarters, Captain Katuragi's Office

Misato watched the film of her ward as Suzuhara Toji punched him in the cheek and Ikari hit the ground. She sighed. 'Shinji….I guess I'll wait until I get the NERV Intelligence report on the cause of the trouble. Maybe this is just a misunderstanding.' Then she saw Naruto intervene and help Shinji up. They obviously knew each other and Shinji smiled and actually laughed. The purple haired Captain blinked. "That's the first time I've seem Shinji actually smile. He's a cute kid." 'Still, I need to know how Shinji and Naruto know one another. This slipped right by NERV Intelligence and that can't be good….'

….

POSTSCRIPT:

*①: Kaji Ryoji: He is Naruto's cousin on Namikaze Minato's side. He was born in Konoha but left before the Second Impact. He is not a ninja.

*②: Musashino: This was where Ikari Shinji was living just before the series started according to his address on the letter he received from Misato. Musashino is a part of Tokyo. The reason I point this out is Tokyo was supposed to have been destroyed during the Second Impact so Musashino must have survived or at least been rebuilt.

*③: LCL is an amber-colored, translucent liquid which allows an EVA pilot to mentally link with their Evangelion Unit. The entry plug of an EVA Unit is completely flooded with LCL and because it is oxygenated; the EVA pilots can 'breathe' the liquid.

*④: Suzuhara Toji is depicted as having a Kansai accent. Your author is no good at accents in the long term. I'll occasionally throw in something in but generally I'll keep his language close to normal. If nothing else it wreaks havoc with spell check….

Evangelion has a lot of structure and timelines that I'm going to be throwing out the window. That isn't to say that canon elements will be gone but a lot of things will be changed. There are so many differences in the different Evangelion media (like manga vs anime) that reconciling them all would be impossible anyway. This story is going to be different to write as well. In most of the crossovers I've done they take place in the Naruto universe with Konoha and the ninjas being the center of the action. In this case we're in Tokyo-3 and Konoha will play a minor role. Hopefully it will turn out interesting. See you next time. Blue out. 4/17/19