A Different Beginning

A/N: Every one is probably wondering what the hell I am doing this but this is the remake to my story Ninja of Tokyo3. I have changed my writing style so much since then and I have improved as a writer since then. There were some horrendous plot holes in it, mostly from my inexperience and some from just bad plot work...and giving Naruto a really bad case of god mode. This one will be an improved version.

It is still a NarutoxHarem with Kaji bashing. I like Kaji usually but sadly I am going to have to sacrifice his character at one point for my plot. There is no real Gendo bashing because Gendo is just an ass, plain and simple.

This will be mixed with things from the manga, the original anime, the Rebuilds, some of the spinoffs, other sources, and original ideas.

This is mostly based off of my theory of the Rebuild of Evangelion. I believe Rebuild to be a sequel to Evangelion for several reasons.

SPOILERS SPOILERS SPOILERS

The ocean is blood red, the Lance of Longinus is on the moon rather than in Antarctica, Kaworu seems to know about Shinji, and a few minor ones. The big one is at the near end of Rebuild 2 when Kaworu mentions "This time I'll definitely make you happy". He is referring to Shinji and makes me think that at the end of Instrumentality in EoE, some sort of event was triggered where everyone but Kaworu remembered what had happened but some of the changes in the world, such as the blood-red water, were unable to change.

SPOILERS end

Disclaimer: I do not own Naruto or Evangelion.

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Shinji couldn't help but let tears flow from his eyes as he watched Third Impact unfold. He had hoped that he could stop it but he wasn't good enough, he wasn't strong enough. After having to watch those he cared about die, he now had to know that everyone in the world would be killed. "I mustn't run away. I mustn't run away. I mustn't run away..." The mantra continued from Shinji's lips as if with the speaking of these words he could turn things around for the better. 'Asuka-chan, Rei-san, Misato-san, Toji, everyone...I'm sorry.'

"Shinji..."

The ethereal voice shattered Shinji's self-loathing as he saw the form of the boy he had killed with his own hands, or at least those of the Evangelion's, Kaworu Nagisa. "Kaworu-san, you're alive?"

The silver-haired boy smiled. "Hello again, Shinji-kun. What has you so sad? Come on, tell me." Kaworu had a disarming smile, one that Shinji was familiar with.

"I couldn't do it. I wasn't strong enough. I'm not the person that should have been fighting, if someone had been born instead of me. If I had never been born then tou-san would have had to find someone else to pilot Unit-01, someone that would have the abilities to stop Third Impact!" By the end, Shinji was sobbing as tears stained his face

An eerie smile graced Kaworu's lips. "Well it just so happens Shinji, that will the activation of Third Impact, there has been plenty of energy gathered where such a wish can be fulfilled. You would never have to fight and someone else, someone stronger would be the pilot of Unit-01. All you need to do is say the words and I can do so."

He could hardly believe his fortune. As the world turn blood-red around him, there was a glimmer of hope thanks to Kaworu. "I wish that someone would take my place, I wish I had never been born!"

Kaworu's grin split his face now becoming maniacal as a laugh soon accompanied it. "Very well, Shinji Ikari. Never will you have been born and one shall be born in your place, one of sterner stuff and one of action. Farewell, Shinji...enjoy your eternal rest in the abyss." The color around the world shifted as it was covered in a blinding flash, all that could be heard was the laughter from Kaworu...from the Angel Tabris...and then a final sentence. "Hmm, he will do nicely..."

- A Second Age -

In a city, a blonde haired boy of fourteen wearing a pair of jeans and a orange t-shirt listened to the phone against his ear. "...did you say 'bent your Ferrari'? If not, please hang up and try ag..." A dial tone sounded in his ear as the boy smashed the phone back on the receiver breaking it in the process. "Fucking automated service! No, I said 'Gendo Ikari' you fucking piece of shit. Damn... Everything has been shut down and now I can't even reach Gendo-teme. Now what am I supposed to do."

This was Naruto Ikari, adopted son of Gendo and Yui Ikari. Ten years ago, after Yui's mysterious death, Gendo left a young Naruto behind saying that he could take care of himself. Since that day, Naruto decided to follow Gendo's words in spite of the man and became his own man. It required some aid for the first few years but he was able to get into an advanced specialty school of innovations. Like his adoptive mother, Naruto was very interested in technologies and this thirst for knowledge on the subject resulted in several degrees in multiple technological fields. Unfortunately, the advancement of his school life had hindered his social development to the level that he was considered anti-social. It started out with Naruto just not having any extra time but with no one his age to interact with, he secluded himself. As he grew up, he just became used to his life and the rest, as they say, was history.

Naruto looked at the letter that had started this whole journey. A letter with a single word "Come", a return address, and a postcard with a very beautiful woman on the front named Misato Katsuragi who apparently was quite comfortable with her "assets". 'Well, hopefully she will make the trip worth it. Beauty and a sense of humor, a refreshing combination that may just make up for that teme of a father of mine.' Naruto pushed off of the telephone and began to walk down the deserted street. 'Guess I'll walk the last two stations. What the...?'

A noise from over head put Naruto on alert as a fighter jet flew low to the ground and was followed by a sonic boom as it fired a cruise missile. "Holy shit! Has the whole world gone to hell?" When he looked at what the cruise missile had been fired upon, he literally smacked himself across the face. "Naruto, when the hell are you going to learn to keep your big mouth shut?" The thing looked like a humanoid black mass with bits of bone covering it and a bird-like mask on it's "face".

Though the VTOLs fired a barrage of missiles at the monstrosity, not a single one made a dent on the being. The being moved its arm to the side at one of the VTOLs, a beam of energy shooting out of it's hand and spearing into the machine, sending the disabled machine to the ground not far from Naruto.

As the VTOL neared the ground in it's crash, Naruto was forced to leap away from the machine, landing several feet back nearly on all fours. It was at that moment that a blue-steeled stead came with a busty knight to his rescue...or it could be a purple-haired woman that was a REALLY bad driver, the door opened to reveal it to be the latter. "Sorry to keep you waiting, Naruto! C'mon, get in!" Naruto didn't need to hear it a second time and hopped into the passenger side.

With Misato's crazy driving and the constant missiles being fired from the VTOLs, Naruto was beginning to fear for his life as his thoughts of the woman turned from praises to curses. 'Oh dear Kami, I swear I'll be a good boy from now on if I survive this insane woman's driving. I give more offerings at shrines, I'll stop playing poker and making grown men lose their hard-earned money against me, I'll even...ugh...be kind to people even though they don't deserve it. Just PLEASE save me from this insane woman!' "What the hell is that thing ugh...AND WATCH THE FUCKING ROAD!" It was close but Naruto could almost feel his lunch come up as Misato nearly drove off the road.

"That thing...we call them 'Angels'." Misato looked over at Naruto as she said that, completely ignoring his advice as a missile exploded in front of her car and caused them to turn several times over. The two got out of the crash relatively unharmed, Misato's car was a different story entirely. "NOOOO! I still have thirty-three payments left on this car!"

A sense of dread filled Naruto and he quickly turned around to see that the monstrosity that had been wreaking Tokyo-3 was just above them. Before fear could rush through him, the Angel was knocked back by a purple humanoid machine. Naruto and Misato got back into the car but Naruto's vision was transfixed on the battle between the Angel and the purple machine. The machine seemed to have a better chance than the VTOLs had but it wasn't enough as the Angel threw the machine nearly a mile away and the machine disappeared as it went down large hatch and was lowered somewhere beneath Tokyo-3.

A siren sounded throughout the city and Naruto could see all of the VTOLs flying away from the Angel. When Misato told him to brace for impact, he felt an tremor and then the car was lifted from the ground and turned over. The explosion only served to give the two a chance to get to where ever it was they were heading. As they pulled into an underground road, Naruto saw them stop at a metal panel that had the word "NERV" before the panel opened to reveal it was a door. As the car exited the dark road, Naruto could see buildings above and a forest below. "A geofront...but I thought it was still only a theoretical dream? To actually see one, I can see why so many people are hoping for it's success."

Misato gave him a smile as she handed him a book that said Welcome to NERV. "This is our secret base of operations, NERV HQ. The Keystone for the resurrection of the world and the stronghold of humanity."

It didn't take too long to enter NERV HQ and pass through the checkpoints but with Misato's sense of direction, Naruto felt they would never get to their destination. "Katsuragi-san, we've been walking for a while now, are you sure we are going the right way?"

Misato's flinch was visible. "Call me Misato, Katsuragi-san makes me sound old and don't you worry, I know where I'm going...I hope." The last part she whispered under her breath but Naruto's short chuckle let her know that he had heard her.

The noise of a mechanical door sliding open sounded to Naruto's side as a blonde woman walked out. "You two, where are you going? You're late, Lieutenant-Colonel Katsuragi."

Misato and Naruto turned around. "Oh...Ritsuko. Sorry, so sorry, I g-got lost I guess. I still don't have the layout of this place down yet." Misato rubbed the back of her head with her hand in embarrassment.

Ritsuko looked over at Naruto with a look of interest. "So this is the Third Child? I am Ritsuko Akagi from the First Engineering Division and the supervisor of Project E. Pleased to meet you."

Naruto let out an overly dramatized sigh. "Finally, someone more on my intellectual level, thank goodness. I am Naruto Ikari." Naruto ignored Misato's annoyed huff.

"You two should follow me. There is something I would like to show you before you meet your father, Naruto." Ritsuko led Naruto and Misato down a hallway until they reached a room that seemed to be filled with a orange colored liquid. "We'll need to take this boat to reach the other end of the room. Please, get in." Ritsuko started the boat and the three made for the other end of the room.

The entire time the boat crossed the "river", alarms were going off as Misato and Ritsuko talked about something called "Unit 01". Naruto didn't know what this Unit 01 was but he had an idea. Once they reached the door on the far end of the room, Ritsuko opened the door that lead into a dark room. When the lights turned on, Naruto was face-to-face with a large, purple, robotic head with a single horn and two eyes. "This is...that robot that was fighting the Angel."

Ritsuko walked up to Naruto's side. "Strictly speaking, she's NOT a robot...she's a man-made, all-purpose battle weapon: Artificial Human Evangelion. And the last chance for humanity. This is the first unit."

Naruto looked at the Evangelion in wonder. "So this is what Gendo has been spending all of his time with. It looks impressive but really...purple?"

"That's correct. And I'll have you know purple is a very manly color. It has been a while, Naruto." On the upper deck above the Evangelion's head was a man with a short beard and wearing and interesting suit, this was Gendo Ikari. "Naruto, listen carefully to what I am about to tell you. You are going to pilot her and you are going to battle the Angel."

Naruto simply gave Gendo a look that asked "what the hell have you been smoking". "Wait a moment, Commander! It took even Rei seven months to synchronize with the Eva...remember? And you want a boy that just arrived today to be able to do what took a matter of months for a trained pilot in a matter of minutes? It's impossible!" Misato couldn't help but doubt Gendo, it just didn't make sense.

'Rei...so that is the pilot that prevented us from getting crushed. I'll have to thank her for that.' Naruto stepped forward, staring the Commander right in the eyes. "And if I were to refuse, Gendo? Your only brought me here to pilot your little toy and you think I would just because you told me to? You lost the right to order me around when you abandoned me." The words flowing from Naruto's lips with little emotion.

Gendo looked down on his son. "The very existence of the human race rests on your shoulders, you would damn all of humanity just for a childish sense of revenge? Fine, then I have no more use for you...go home. Cowards are useless in a battle where man's future is at stake." Gendo pressed a button on a screen to his left. "Fuyutsuki, wake Rei. Have her transported her, she's not dead yet." Moments later, a door opened on the opposite side of the room and in came two men in lab coats and someone on a gurney. On the girl was, in Naruto's honest and surprising opinion, a beautiful girl with light blue hair and exotic red eyes. "Rei, our back-up has proved useless. You will need to pilot the Eva once again."

The now identified Rei attempted to sit up from the gurney, obviously in pain. "Yes, sir." Her body was shaking and she gripped the sheet on the gurney as the pain racked her body.

A noise came from above them followed by a large tremor. The tremor caused a light fixture to fall onto the gurney, barely missing Rei, and tossing the woman off the side. In a quick reaction, Naruto slid underneath Rei and prevented her from hitting the floor. As Naruto looked on at Rei in the pain she was feeling, he made his decision. He gently set her down on the floor and stood up straight. "Gendo, I'll pilot your little toy...but I want compensation for piloting." The only response he got was a nod of Gendo's head.

- A Second Age -

Naruto found himself inside the "cockpit" of this Evangelion, his hand gripping on the controls. The seat was comfortable and he was secured into place. A voice filled the "Entry Plug" that he was in. "Cooling-down cycle complete. All Internal cage systems in docking position. Pilot has reached the cockpit position within the Entry Plug. Inserting Entry Plug." Naruto could feel as the cockpit he was in was put into the Evangelion. "Flooding Entry Plug."

From the bottom of the Entry Plug, a similar orange liquid to that of the previous room began to fill the cockpit. From the speakers, he hear Ritsuko's voice. "Don't worry Naruto, this is LCL. Once your lungs are saturated with it, you'll be able to undergo direct oxygen exchange."

As the LCL filled his lungs, Naruto was amazed by what this NERV had come up with. "Ritsuko, can you display the details of this Evangelion for me? I want to see just what makes this thing tick." With only a few moments, schematics and details pop up on the screens. "Okay, controlled with a combination of manual controls and a neural interface. Multiple screens for communication and the screen is connected with the 'eyes' of the Evangelion. Current weaponry is a Progressive Knife that uses uses sonic vibrations to slice and stab. Has an internal battery life of five minutes unless attached to an energy source via a cable. Hehe, this is going to be fun." The screen soon turned to a rainbow of colors and soon the view on the screen turned to the view through the Evangelion's 'eyes'.

As Misato announced the Evangelion's imminent launch, Naruto relaxed his breathing. It wasn't something he had ever done, as he was more of a inventor than a fighter, but it was something that seemed to work as his nerves calmed just as Unit 01 shot up the lift. 'Here we go.'

- A Second Age -

Naruto could feel the g-forces as he was launched, the intensity exceeding anything he had felt prior to this. It wasn't just he g-forces that he felt but also his instincts were yelling at him, giving him only two choices. 'To fight...or run away... Fight or flight, the basest of instincts in all living creatures for survival when facing conflict. My instincts, they're screaming at me to run but I won't...I can't. This is something only I can do and, while I don't like the situation or that I had no real choice in the matter, this is something I must do. Of course, this does mean I get to try out Gendo's little toy here and who am I to pass up a possible chance to gather more data.' A fierce grin appeared on Naruto's lips as his hands gripped the controls. Once the lift stopped, Naruto could see the Angel in front of him. "Alright fuckface, you've caused me to have the most annoying day of my life so I believe I owe you a bit of payback!" Naruto had no idea where it came from but he KNEW how to move this machine, this Evangelion, and he was going to make use of it. The Evangelion moved forward as Naruto willed it to move, closer and closer he came to the Angel.

The Angel Sachiel lifted it's arm at Unit 01 and this caused a flash in Naruto's mind, like his entire body was warning him. In a quick decision, Unit 01 moved away from the hand and just in time as a lance of pink energy shot out of the Angel's palm. Naruto used this moment to send a straight punch at the Angel but before he could even touch it, an orange barrier repelled the attack and gave the Angel time to counter. Naruto wasn't able to move Unit 01 in time, even though he knew the Angel was about to attack, and was lifted into the air by the Angel.

Naruto's eyes widened as he saw the pink energy form in the Angel's palm through the screen in front of him. The energy shot into Unit 01's head again and again, the pain rushed through Naruto's body. 'The pain...why am I feeling this pain?' The pain only increased with each strike until the 'lance' pierced the armor and shot through Unit 01's head and sending it back into a building.

As the Evangelion stopped moving, a red blood-like liquid shot out of the open wound and shut down Unit 01. Naruto was hardly able to process anything through the pain and was frozen in a state of shock. He could almost hear voices that were screaming at him but they sounded muffled and like they were coming from far away.

Naruto looked upon the image of the Angel in front of him...a fire began to burn inside him. Naruto's face began to contort into a look of absolute rage, now bearing elongated fang as a growl emanated from his throat. His eyes dilated into slits like that of an animal's and his irises turned red. The entirety of the entry plug was covered in a red energy. '...kill, kill, kill, kill, kill, KILL!' Unit 01's eye glowed once again only this time in a red hue, the mouth broke open and a roar let loose from it's throat.

- A Second Age -

Those on the command bridge could only watch in horror. "Synch rate rising! 70%, 80%, 90%, it's stopping at 100% and isn't deviating even a fraction." Maya's eyes were glued to her terminal but was otherwise shocked.

Ritsuko took over Maya's station and went over the data. "This can't be right, there aren't any fluctuations in his synch rate. It's now going berserk but...what could this possibly be..."

Unnoticed by anyone, Gendo's grin turned into a frown. 'Already a deviation from the scenario? It matters little, SEELE won't recognize a difference so in the end it is no problem.'

- A Second Age -

Shogouki charged at the Angel like and angered beast, the predator now becoming the prey. The overwhelming forward attacks from Shogouki and the force of each attack was not giving the Angel a single moment to react and slowly forced it back. A punch, a kick, a knee, all parts of it's body were used as Shogouki unleashed it rage and began to break the body of the Angel.

The Angel's eye flashed and Shogouki was sent backwards by an explosion but not for long as the mechanical force of nature twisted in the air and collided with the Angel's AT field. The red eyes of Shogouki appeared to narrow as a rumbling grow emanated from it's throat when it reached the field. It pushed it's hands into the field and attempted to rip it open like sliding doors

- A Second Age -

"Unit 01 is deploying it's AT field! It's neutralizing the Angel's Phase Variance!" Maya at her terminal was trying to keep up with the data that crossed her screen as Ritsuko shifted her gaze from the woman's terminal to the main screen with a like akin to fear.

Misato had more of a shocked look as the main screen showed the Evangelion tearing through the Angel's barrier. "My God, the Eva has forced open the Angel's AT field!" Horror grasped the hearts of those on the bridge as they saw the Angel's eyes flash again.

- A Second Age -

Shogouki wasn't effected this time by the Angel's attack and deflected the attack with it's own AT field, giving the Angel a taste of it's own medicine as this time the Angel was being sent backwards and colliding into a building. Shogouki leaped into the air and heel dropped the Angel on it's red orb, causing it to crack. As the Angel attempted to grab onto Shogouki, it was stopped as the Evangelion's hand pierced through the red orb which stopped all movement in the Angel as the "life" left it's eyes. It seemed the Angel had a last ditch attack as it's red orb glowed brightly and Shogouki was caught in an explosion.

While those on the command bridge in NERV HQ could only watch as the explosion caused a giant cross of energy to appear from the center of the suicidal attack, Shogouki walked out of ground zero with minimal damage as the eyes soon returned to normal and the mouth shut.

Inside Unit 01, the red energy that had filled the entry plug had dissipated and Naruto was now back to normal. "This is Naruto Ikari requesting someone to get me the hell out of this fucking machine as soon as possible. I'm feeling pain like a motherfucker and I promise to take it out on the first person I see if you don't hurry the fuck up." With that message, communication were cut off from Unit 01 as the last of it's power ran out.

- A Second Age -

Naruto woke up alone inside a hospital room with a small headache. "Note to self: Avoid damage to the head in general. It gives one hell of a headache." He slowly got out of the hospital bed and checked to make sure everything was still working, making sure that he hadn't lost anything or that anything had been removed from him as he never did trust hospitals or want to stay in them longer than needed. As he walked out of "his" room, he walked onto a nurse. "Excuse me, could you tell me where the room of a girl named 'Rei'? I don't know her family name but I know she was injured." The woman pointed him to a room not far from his own, just on the other side of the hall.

When he entered the room he had been told, he saw the blue-haired girl asleep on her hospital bed. Naruto sat down in a chair near her bed and a small smile grew on his face. 'She looks cute when she's asleep like this... Come on Naruto, you can't go changing so much after all these years. Besides...a girl like her would never want to be with a selfish guy like myself.' A sort of sad chuckle left Naruto's mouth before he turned around and left the room.

The hallways of the hospital were nearly empty except for the rare nurse or doctor, it made sense when Naruto noticed the wall had the NERV logo on it and this was probably a private hospital for NERV personnel. As Naruto was just about to talk to the nurse at what seemed to the the front desk, he stopped when he heard a familiar female voice. "There you are Naruto, I was looking for you." When Naruto turned, there was Misato Katsuragi. "I've already arranged your release now we just need to find you a place to stay. Your father wanted you to live on your own but would you rather stay with someone say...me? I have a nice apartment and it would be better than any normal living that NERV would arrange for you."

Naruto was surprised by Misato's generosity and found himself smiling a bit. Until now, he had always been supporting himself be it through his inventions or tutoring but for once...someone wanted to help him, not since his mother died had he felt like this and it was lightening on his shoulders. "I...I'd like that."

A look of remembrance appeared on Misato's face. "Oh before I forget." She started to rummage through her purse in search of something and then pulled out a card. "Here is your NERV ID card. It also is linked to a private bank account where five hundred thousand yen will be deposited every month with a bonus of one month already being in your account." Misato handed the card over, missing the evil grin on Naruto face.

- A Second Age -

After a long and nearly homicidal/suicidal car drive and an elevator ride up several floors, Naruto and Misato arrived at her apartment. When Naruto took a look inside he noticeably shivered, no place should have this much trash laying about unless it's a dump...and that word seemed to fit the place pretty well. "Come on inside, Naruto, and make yourself at home. I only just moved in here myself a few months ago even I still have some unpacked boxes. Go ahead and put your things away in the first room on the left while I make dinner, that room will be yours for as long as you stay."

Naruto could only sigh in response. 'Just moved in here my ass. That's no excuse for all this trash. She may be drop-dead sexy but the rest needs quite a bit of work. I guess it won't be too bad. I get to play around with tech that other can only dream of and I can possibly advance my theories into a physical trial if I am lucky. Yeah, I think that things are going to be just fine...'

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There we go. Now, just to assure you all, Naruto may know how to move Unit 01 but that doesn't mean he can pilot it well or properly. Now, I separated the personality of Unit 01 and Shogouki. While Shogouki is the proper name of the Evangelion in Japanese, I use it to show that the Evangelion is in majority control and I use Unit 01 when Naruto is in control. I will be leaning more towards that manga and the Rebuilds for most of this and expect this to be a harem by the time this is finished and I do have a way to explain why Naruto would be able to have a harem.