SHINJI AS NARUTO
by Gunman

Disclaimer: I do not own Eva nor Naruto

Summary: Shinji is teleported to Konoha, where he merges with Naruto Uzumaki after he is killed by the village and takes over his life along with Hinata.

Yet another response to Invincible Shinji's Romance Fanfic Challenge.

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The Nine-Tailed Fox reared up on it's hind legs and let loose a fearsome screech as it's nine whipping tailed lashed out and crushed every building, wall and fence it could.

Below it, scurrying back and forth like ants, the terrified and shell shocked citizens of Konoha were caught under the weight of it's massive feet and claws, or crushed underneath the tons of debris that was knocked back and forth by the demon's tails.

The only one that the demon seemed to miss, was the body of a blond-haired boy with dozens of stab and slash marks all over his body.

His name was Naruto Uzumaki, also known as the prison of the Nine Tailed Fox who once tried to destroy the ninja village years ago. However, the villagers of the Hidden Leaf, in their ignorance, thought that Naruto was the demon and, after several years of attempts, succeeded in killing him. They thought that with his death, their village would be safe. But all it did was to free the demon to complete it's original purpose and destroy their village... and everyone in it.

It was during all this chaos, that Shinji Ikari teleported in from an alternate dimension, via the 12th Angel, right on top of Naruto's deceased body, merging with him, and taking over his life. Because of this odd merger, and because Naruto's body was so damaged, he remained unconscious while he healed... allowing the Nine-Tailed Fox to rampage and kill to it's hearts content.

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It was hours later when the Nine-Tailed Fox, satisfied that it had destroyed everything and killed everyone, finally left the rubble that used to be Konoha and went on it's way.

In the middle of the former village lay the body of Naruto Uzumaki. This made it easier for a certain lavender-eyed girl, who was actually the last of her entire clan, to locate him.

She wandered over to where Naruto lay, and fell to her knees, tears flowing down her soft cheeks and onto the whisper marks that adorned his cheeks.

"Naruto-kun... I'm sorry. I'm so sorry." Hinata Hyuga cried, burying her face in her hands.

Several minutes past, before a soft moan came from the blond boy.

"Ooooohhhh..." he said.

This moan caught Hinata's attention and she looked up to see Naruto blink his eyes open.

"H-Hello?" he said weakly, looking at the girl.

"NARUTO-KUN! YOU'RE ALIVE!" Hinata suddenly cried happily, diving down to hug the boy tightly.

"I'm... alive?" Shinji said weakly, his body and head covered by the girl. "W... what? Who are you?"

Hinata froze as she pulled away to look at the blond boy. "You... you don't know me?"

Still weak, and extremely confused, Shinji looked at the lovely young woman, taking in her soft skin, pale lavender eyes that were almost completely white, her long dark-purple hair, and tan and purple coat and pants she wore.

"No. Are you... my girlfriend?" Shinji asked, wondering if he had imagined the level of her concern.

Hinata practically glowed at that question.

"I-I-I'm... H-Hinata Hyuga. And...I...yes. I am." she stuttered out.

"You are? Really?"

"Y-yes." she smiled.

Shinji smiled as he sat up, Hinata helping him, and looked around at the disaster zone that used to be a village. "What happened here?"

"The villagers stabbed you. And... you died."

"I died?!" he gasped.

Hinata nodded. "I tried to stop them, but... I wasn't strong enough. I'm sorry." she apologized as she wiped her tears away. "Anyway... when you... died... the Nine Tailed Fox was released from your body and... it destroyed the village."

Nine-Tailed Fox? Released from my body? Shinji thought with fear in his eyes. What is going on here? He wondered.

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"I still don't get this. I... I died? Then... shouldn't I be dead? Or... is this death?" Shinji asked as he splashed his face with water from the river a small ways away from the village.

"No. You are not dead... even though the wound they gave you was fatal. It was right to your heart." Hinata said, sitting next to him as he stared at his reflection in the water.

Shinji opened up his shirt and saw the multiple knife wounds. He gasped.

"I don't know how you survived, or how you came back, but... I'm glad you did, Naruto-kun." she said.

Shinji looked back to Hinata and sighed.

I don't think this girl is lying... she seems like a real sweet girl. And pretty. Real pretty. But... what happened to me? I was inside Unit 01 for hours and then... I passed out. The next thing I remember is... waking up with this girl crying over me. Did I get reborn in this body... after this Naruto person was killed? But... that would mean... I died in my world. He thought as he looked back to see his new face in the water.

He couldn't have been over 15 years of age, which was perfect for Shinji, but the spiky blond hair, sapphire blue eyes, strange whisper marks on his cheeks, not to mention the mostly orange and black track suit he was wearing, was a little odd to him.

"Naruto-kun?" Hinata said to him, breaking him out of his musings.

"Oh. Sorry, Hina-chan. I just... I don't really remember anything."

"It's alright, Naruto-kun. You're probably just had a shock since you... died."

"Yeah. That part is still kinda hard for me to accept."

"I am sure. I don't even understand it myself. But.. you're back and I'm..."

Shinji looked over at Hinata as she paused, looking like she was trying to work up the courage to say something. Anything. He sighed as he reached out his hand placed it over hers.

Hinata gasped, freezing at his touch.

"Wha-what are you doing?" she asked.

"Uh... trying to hold my girlfriends hand? Isn't that what we do? Or... did we do anything?"

"Uh... well..." she said, blushing and thinking quickly, "We hadn't even been dating for... a week... when you were..." she said, lying a little bit, which she hated really.

"Oh. I see." he said with a sigh. "So... do you mind if I hold your hand?"

Hinata smiled and took his hand into her own.

"I'm sorry, Naruto-kun. I just... I've never had a real boyfriend before." she apologized.

"It's alright. I've never had a girlfriend. I think." he said.

Hinata smiled as she shook her head. "No. I am your first."

"Oh, good. I'm glad."

"You are?"

"Yes. You're kind and very pretty. I feel lucky to even know you."

Hinata smiled happily as she launched herself into Naruto's arms, hugging him tightly and knocking him backwards in one shot.

The pair laughed as they tumbled to the ground.

She's even prettier than before. Such a pretty laugh. Shinji thought.

Naruto-kun is so different than I remember. He has lost so many memories of his life. Maybe it is because of his death. But... he came back. Back to me. She thought, then felt guilty. But I'm taking advantage of him, of his amnesia. But... I can't lose him again! I didn't have the courage to tell him my feelings before. And now that he has returned...no! I won't lose him again!

"Hina-chan?" Shinji asked, noticing the girl was hugging him tighter and was crying into his chest. "Hina-chan, are you alright?"

"No! No I'm not!" she cried. "I... Naru-kun, I have something to confess."

"Confess?" he asked.

"I... I have had a crush on you since the academy."

"You... have?"

"Yes. Back when we were learning at the academy... I used to watch you from the back of the class. You never noticed me before. I... I never had the courage to tell you my true feelings. And... when I thought you were... dead... I swore that I would never hide my feelings again, if only you would return to me!" she said, still hugging him tightly.

She did? But... I didn't return to her. She loves someone else. I'm... I'm not him. Shinji thought as he hugged the girl to try and calm her. But... I can't just leave her like this. If I tell her the truth... it could break her heart.

Shinji just hugged the girl as she held onto him tightly, stroking her hair as she cried into his chest. Eventually she cried herself to sleep, leaving Shinji to try a figure out a plan while Hinata's head rested against his chest.

What am I going to do? From everything she told me, this Naruto was some kind of ninja. I don't know anything about being a ninja. I don't know anything about taijutsu, or genjutsu, or kenjutsu, or ninjutsu, or... he paused as he realized that he had just rattled off a list of ninja systems. And what's worse... he knew what they all were.

But how did I know... I can't have known that. But... I do. He thought as he lifted his arms up above Hinata's head, his hands suddenly preforming different gestures.

Now Shinji had never done them before, but he knew how... and what's more... he knew what they were for.

Shinji suddenly vanished from underneath Hinata, appearing right next to her. He looked down and saw that there was a human-shaped stuffed dummy in her arms, where he had been.

WHOA! Did I just...that was a substitution jutsu? How did I know that? I knew it. I don't know how I did, but I do. Shinji gasped, his hands shaking. This is impossible! I... I have special powers?

Scared out of his wits, Shinji backed away from Hinata and walked as far as he could so that he could still see her but not wake her.

I need to figure out what I can do. He thought.

For the next three hours Shinji exhausted himself preforming every technique and move that came to mind. He just started doing things, not really thinking, just doing, and was completely amazed that his body, his new body, seemed to almost preform these unusual techniques on their own.

He even managed to pull off Naruto's Sexy Jutsu, Harem Jutsu, and even the Rasengan.

It was nearly midnight when Shinji finally walked back to where Hinata was still sleeping. He smiled as he watched her sleep.

Didn't even wake her up. He thought with some relief. I don't know what this Naruto's life was like before I came here. Maybe he and I would have been friends. Maybe he had another girlfriend before Hinata... maybe he didn't. Maybe he wanted to ask her out, but never had the chance. It's so weird. I remember how to preform all those different jutsu's and ninja moves like it's second nature... but I don't remember anything about his personal life. I don't remember my parents... or HIS parents... his friends... anything. It's like a... a big void.

Just then, Hinata started to stir. Panicking, Shinji preform the hand signs and switched back into her arms before she woke up completely.

"N-Naru-kun?" Hinata blinked her eyes open to look at him.

"Hina-chan. Are you alright?" he asked.

"I... I am alright... why are you sweating?" she asked, noting the dampness of his clothes and the strange odor coming from him.

Shinji gulped. "I... I think it's a little hot out."

"Oh! I must be making you hot by lying against you. I'm sorry." she said, trying to lift herself up off his chest.

"No, no. It was nice. You... you just looked so peaceful I... I couldn't help but watch you sleep." he said, keeping his hand tightly holding her own.

Hinata blushed as he said that, then leaned up to kiss him on the cheek.

It was Shinji who blushed at that kiss as the moonlight came out from behind a cloud to shine down upon Hinata.

Suddenly, a memory flashed past his eyes.

Shadowy images lite by moonlight... of a beautiful girl dancing on the surface of the waterfall they were at now.

"N-Naruto-kun?" Hinata asked. "Are you... alright?"

"Uh, yeah, I..." he said, pausing as he stared at Hinata when he suddenly realized something. "You... have the same face."

"Wha-what?"

"Hina-chan... I... I just remembered something. A girl... dancing on the surface of the water... in the moonlight."

Hinata gasped.

"I... I couldn't see her face, but... I realize... the outline of her silhouette... it's the same as yours now. Was it you?"

Hinata stared at him for a few seconds before tears broke out from her eyes.

"Hina-chan? What's wrong?" he asked.

She smiled as she spoke. "You remembered. Of all the things you remembered, the first was... of me dancing at the waterfall."

"So... it was you."

"Yes. You didn't know it was me when we were on that mission, but... you saw me that night when the moon came out. I... I wanted to tell you it was me, but... you figured it out on your own." she smiled and hugged him again.

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At first sun-up the pair returned to Konoha to look for supplies. It was there that they found a dog buried under some debris.

"Akamaru-kun!" Hinata shouted.

Shinji preformed a Shadow-Clone Jutsu and created a dozen clones to remove the debris. Hinata hugged the large white dog once it was free.

"Oh, Akamaru-kun! I'm so happy to see you!" Hinata cried as the dog licked her face. "But... where is Kiba-kun?"

"Uh... Hina-chan?" Shinji said to the pair, lifting up another piece of debris that was next to where Akamaru had been.

"Oh... Kiba-kun." Hinata cried as Akamaru cried as well.

Their trio buried Kiba in the training grounds and then continued to search for supplies. They found some food, a few tools, even a some weapons.

They even found some survivors.

The first was Anko who was buried underneath an apartment building. The second was Iruka, who had been in the school when it was attacked. The third was TenTen, who had been at her parents weapons shop. The fourth was Choji, who was hiding in his favorite restaurant. And finally Tsunade, who had been in her office when the attack came.

Naturally they were all glad to see that Hinata was alive, but confused as to how Naruto was also alive.

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"So... he doesn't remember anything?" Tsunade asked the lavender haired girl.

"Not really. He remembers bits and pieces, but... nothing extensive. I think he knows how to do his hand signs for the jutsu's, but that could just be instinctive knowledge." Hinata said.

"Makes sense. Naruto did practice a lot. It makes sense some part of him would remember." Iruka commented.

"Not his conscious mind, it seems." Tsunade said.

While the adults were discussing what to do now, Shinji, Choji, TenTen and Akamaru were still scrounging for food and supplies, finding more bodies of the villagers and ninja.

"Who was this?" Shinji asked as he lifted the body of a girl with pink hair.

"Sakura Haruno. You... don't remember her?" TenTen asked.

"No." Shinji said, glad that he hadn't had anything to eat or he would have thrown up long before now with all the body-policing he had done.

"Probably better. She gave you such a hard time when you were at the academy." Choji said.

"Was it because of the Nine-Tailed Fox?" Shinji asked as he set the body down next to another girl he didn't know.

The pair looked at him in shock.

"Hina-chan told me." he said.

"Oh. Well, no, it wasn't." Choji said as he continued searching.

"That's why the village hated you." TenTen said.

"Sakura didn't really like you because she liked someone else."

"Who?" Shinji asked.

"This guy." Choji said as he pulled back a wooden plank to reveal a certain raven-haired boy.

"His name is... was, Sasuke Uchiha. The Academy's Rookie Of The Year." Choji said.

"I... guess we didn't get along?" Shinji asked.

"No. You didn't."

"Somehow, that's not surprising."

The group of survivors eventually found Neji, Kakashi, Rock Lee, Guy Might, Shizune, TonTon, Shino, Kurenai, Asuma, Ibiki, and dozens of others.

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It took several days for the small group to properly bury all their friends.

"So... what do we do now?" Iruka asked on the seventh day, once all the bodies were buried.

"The village is a complete loss. We need to move on." Tsunade said.

"But to where?" Anko asked, wiping the dirt from her face.

"Well... I do know of a place." Tsunade said.

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Tsunade Iruka and Anko made sure all their provisions were secured in scrolls before they set out to their new home. The adults were in the lead while Shinji, Hinata, Choji, TenTen and Akamaru brought up the rear.

"So... you don't remember anything?" TenTen asked Naruto.

"I remember some things, but... they're mostly things about Hina-chan." Shinji said.

"Really? I didn't even know you noticed her." Choji said, stuffing his face again.

"Well... that's what I remember."

"Nothing else? Like... how much you love Ramen? How you were beat Neji in the Chunin Trials? How you and Sasuke kissed?" the 'fluffy' young man asked.

Shinji paused in step.

"I... what?" Shinji gasped.

"Choji!" TenTen snapped at the boy.

"Sorry." Choji grinned sheepishly.

"But... Sasuke is a guy. I Kissed A Guy?"

"You didn't do it on purpose!" Hinata said.

"You were having a staring eye contest with him in class and... someone bumped into you, and you just kinda... liplocked." Choji said.

Shinji felt lost at that. "I... I feel so dirty."

"Then... let me cleanse you." Hinata said as she boldly took Naruto's head into her hands and kissed his lips with her own.

TenTen, Choji and Akamaru blushed as Shinji retaliated the kiss, adding his own passion to the girl.

Wow. She's really getting bold! TenTen grinned.

Eventually, the pair broke free and stared into each others eyes, blushing furiously.

"Wow." was the first word out of Shinji's mouth.

"Umm... that was... that was..." Hinata said. Oh Kami! My heart won't stop racing. That kiss was... incredible! She thought, her face threatening to overheat.

"Uh... Hina-chan?" Shinji asked.

"Y-Yes?"

"Can I... may I kiss you again?"

Hinata smiled. "Yes."

The pair kissed again, until a deep cough caused them to break apart.

"While it's nice to see you have gotten your feelings aired out, we really must be going." Tsunade said, standing over the pair.

"Uh, yes ma'am." Shinji said.

Ma'am? He really did lose a lot of his memories. She thought as she turned around and continued walking to their destination. Still, he doesn't seem to be in bad spirits, all things considered. At least he acts more mature... and has finally admitted that he likes Hinata.

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Eventually the group reached their destination.

It was at the end of a small canyon where a large group of trees stood straight up, like a fence. Behind the large trees was a group of buildings. All of them looked fairly old, at least ten years, yet they all seemed to be complete and functional. The large outcrop of trees covered the main entrance to the village, but also acted like a roof over their heads, keeping the village hidden even from the air. It was less than half the size of Konoha.

"What is this place?" Anko asked, looking at the small village.

"Konoha's back-up village." Tsunade said.

"Back-up village?" Iruka asked.

"You mean..." Anko started to say.

"Yes. It was started by the Third Hokage as an emergency hideout in case Konoha was ever attacked and such." Tsunade said. "I read about it in one of the scrolls Sarutobi left me."

"But... is anyone here?" Shinji asked.

"Hinata. Use your Byakugan and see if anyone is here." Tsunade said.

"Yes, Hokage-sama." the pale-eyed girl replied.

Activating her eyes, Hinata looked around and after nearly a full minute deactivated her Byakugan.

"There is no one here, except for a few insects and lizards." Hinata said.

"Alright then." Tsunade said as she turned to address the group. "As of right now... this is our new home."

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Everyone eventually found their own personal lodgings.

Choji found a restaurant. TenTen found a smith shop. Iruka found the school. Anko found the guardhouse. Tsunade found the Hokage's office.

Shinji, Hinata and Akamaru found their lodgings at an apartment building with a large balcony that overlooked the village.

Another plus was that there was a hole in the tree-roof that let both sunlight and moonlight through and down onto the balcony itself.

Night time eventually came and found both Hinata and Shinji sitting on the balcony on a bunch of pillows with Akamaru lying next to them.

"Are you alright, Hina-chan?" Shinji asked the pale-eyed girl.

"Actually, I am, Naru-kun. Despite everything that's happened... I'm actually happy." Hinata said as she rested her head against Naruto's.

"I know what you mean. I'm glad I met you, Hina-chan." Shinji said as he rested his head against hers while petting a sleeping Akamaru on the head.

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The next ten years found the new Hidden Leaf Village slowly rebuild itself. Tsunade was able to keep their existence hidden from virtually all of their enemies, recruiting and training a new group of ninja with a wide variety of skills and talents.

Shikimaru had been in Suna during the attack and managed to track down the last of the Leaf ninja to their new home. When he arrived, along with Ino and Konohamaru, the small ninja group was overjoyed to see him and the others.

The Sand Ninjas of Suna helped out the new Hidden Leaf Village as best they could, also keeping it a secret until the village was back to full strength.

Choji opened his own restaurant.

TenTen started up her family's weapon shop.

Iruka was the head of the new ninja academy.

Anko was the head of their Jounin ninja squad.

As for Shinji... he quickly accepted his life as Naruto, taking the blond boy's name as his own. Also, because of the strange merger, Shinji developed some of Naruto's old characteristics, namely his unbeatable determination. Though he did feel guilty from time to time about not telling Hinata the truth, it was quickly allayed by the happiness he realized he could bring her. And having found love with such a kind and beautiful young woman, he and Hinata eventually married and raised their three children (Sasuke, Sakura, and Shinji) to be good and honorable ninja.

And while several people were curious and even suspicious as to Naruto's miraculous resurrection, they were content to just let him go about his own life and business seeing as he was only a little bit different than he had been before. Their reasoning was that death can have 'life-altering' effects on anyone.

Hinata never suspected that her Naruto wasn't the same person who had died all those years ago at the hands of the village. She was just happy that the person she had been in love with for so long was willing to return her feelings, promising to both love and protect her.

Akamaru also found a mate and had a dozen puppies to continue his family line.

The Nine-Tailed Fox was never seen again.

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Author's Notes:

How did everyone like this new Shinji Romance Challenge Fanfic? While some of you might criticize me for killing off Naruto and pulling Shinji into his body, I really couldn't think of any other way that wasn't a one-shot story. If I did have Shinji and Hinata hook up, like normal, then it would have to be a multi-chapter story. This way... it's not only shorter, but it's less uncomfortable for the pair. Hinata being in love with Naruto, and Shinji wanting to be loved by someone who could be kind to him.

Let me know what you think.