Missing-Nin Naruto Namikaze

by stixz35

After the Pein Attack, Naruto is sentenced to death. Watch as Naruto becomes a missing ninja and still fight for world peace. But will he have to fight against those he loves? AU Kind of ish. Terrible with summaries.

1. Chapter 1

CH 1

Eyes wide open. Mouth agape. No other emotion then pure shock. He could not even move.

"W-what?"

Homura leaned forward. "Did I stutter boy?"

"YOU CAN'T DO THIS!" Naruto screamed taking a step forward, fists clutched so hard blood trickled down his fingers.

Koharu shifted her hands to her lap. "The decision has been made."

Naruto slowly look around the room to all the elders and the members of the council who were invited.

"You have no right to do this!" Naruto yelled pointing at all who were present.

A man cleared this throat in a smug and rude way, then spoke in his emotionless voice. "Respect your elders boy. We came to this decision for the protection of Konoha. For its citizens, for its ninja, for its future. A future without you." The smug smile formed on the face of Danzo.

A FEW DAYS BEFORE

Sakura and Naruto stroll down the of the newly constructed streets of Konoha. The attack by Pein left the Village Hidden in the Leaves completely in ruins. Not just the destruction of homes but the destruction of the people's hopes and stability. Yet there was one thing that held everyone together. Not a thing, but a person. One person.

Naruto.

Sakura glanced at Naruto out of the corner of her eye. His hands were behind his head making a make-shift head rest. His typical orange and black jacket was completely unzipped giving him a relaxed aura. Sakura could not help but smile. He had come so far in life, started off as the annoying little brat that everyone wanted to get rid of to someone who everyone needed in their lives. Especially her own. He was her pillar. That unmovable rock that no matter what was happening, she could rely on him. She could not imagine life without the Kyuubi vessel.

"What's up Sakura-chan?"

The question brought Sakura out from her musing to full out look at Naruto. His gaze at her was quizzical.

She was slightly embarrassed. "u-uh, n-n-nothing Naruto. "

He lightly chuckled. "You sure?" he teased.

She looked away from him, crossing her arms. "Humph. I'm sure."

He laughed out loud at her antics. He narrowed his eyes at the pink haired girl. "I was just playing Sakura-chan."

Sakura turned her head back around to stare right into those beautiful cerulean eyes of the blond boy walking next to her. Scratch that. Not a boy. A man. No boy can do the things he can.

"Well I hope you are done playing around because I am starving." Sakura stated leaving no room for negotiations.

"Me too. Ichiraku?" The blond asked with much hope.

Naruto's favorite stand reopened just a few days ago but was bigger because people figured out it was his favorite place to eat at. The poor old man and his daughter never got a break because they were always so busy. But they were ok with that, especially since it was all because of Naruto. They always had room for Naruto when he came around for his eight bowls of almost daily ramen.

As much as Sakura did not want to see Naruto devour many bowls of ramen at inhuman rates, she was so hungry she did not care. "Sure."

Naruto stopped in his tracks almost not believing in what he just heard. She wanted to get ramen? With him? This was a dream come true!

"But it not a date," the pink girl stated loudly so he could hear her.

Scratch that. It was still a dream yet to come true.

Feeling somewhat defeated Naruto stuck his hands in his pockets and continued forward to catch up with her, but with no real rush. As always he threw on the smile just for her sake.

They turned the corner to see the stand already full of people but there were only two spaces open. They sat down and Sakura ordered her usual while Naruto….inhaled all of his own. They just enjoyed each other's company. They noise around them ensured they were just in their own little world. Just the two of them. They laughed. Sakura play slapped him when he make a stupid joke or just plain annoyed her. But neither of them would trade this for anything. They finished their meals and paid for it. And headed along their way.

"So what do you want to do now Sakura-chan?" asked Naruto.

The pink haired girl crossed her arms and tapped her chin with a single finger. "Well I do need to shower first. But then I need to stop by the hospital and see how things are going with the expansions. And I need to stop by and see Tsunade-sensei to see how she is doing and give Shizune a break."

Naruto lowered his head. "I hope Granny gets better soon."

Tsunade still had to wake up from her coma from protecting everyone in the village. People were starting to doubt if she would ever recover.

"Me too." Sakura agreed. "Well, I have to get going see you around Naruto!"

Sakura ran off in the direction of the temporary living quarters for most of the village's ninja. Naruto waved after her giving her that big smile that he reserved for her alone.

"See ya Sakura-chan!"

Naruto returned his hands to his pockets and turned the other way. As he turned he glanced off the corner of his eye at a shadow out of place on top of a roof. He continued on his way like he did not see anything humming a sweet tune to himself. He wanted to train some more and to see what that misplaced shadow would do.

Returning to the training ground he was surprised to see his sensei leaning against a tree, but not surprising he was reading his favorite smut book.

Naruto ran over to him. "Hey Kakashi-sensei!"

Kakashi moved only his eye above his favorite book to see Naruto standing in front of him. "How are you doing Naruto?"

Using one hand he scratched the back of his head with a big smirk on his face. "Not too bad sensei. Wish things could be going a little better…"

With so many things going on and the rate Naruto had been going recently Kakashi was surprised to see that was doing as well he appeared to be. Almost too good. Like Naruto's whole aura was different. More calm. An air of almost complete peace and knowing.

Kakashi narrowed his eye at his students. Naruto could tell that Kakashi could see right through him and almost see he was hiding something. Naruto had not told Kakashi about meeting his dad, the Fourth Hokage. And, in extension, the fact that the seal is strong again like the day the jutsu was cast. Naruto did not want to have a conversation like that in the open. Not here at least. Maybe Kakashi was good enough to figure this out on his own….

"Hmm…is that so?" Ok maybe not. I wonder what he is hiding….

Naruto looked away at a seemly random tree in the distance. Kakashi glanced away to the same point, only to look back at his student. "Feel like a spar?"

Naruto's smile grew as he looked back at his sensei. "Sure!"

The cyclopes closed this smut novel, pushing himself off the tree and stowing it in his tool pouch. "I want to see how much you have grown since you left."

Naruto smile disappeared, getting serious, as he back flipped away from Kakashi to give them some space.

"Ready?"

"Go."

After an hour of intense fighting, Naruto found himself on a large branch high in the trees looking out for the copy ninja. A familiar hand sign was made, suddenly, eight more blonds appeared in smoke. Seven clones immediately vanished to find Kakashi while one disappeared to remain hidden. The original took a second to relax his thoughts and take a deep breath. Unfortunately, Kakashi had other ideas. Two clones were taken out together giving Naruto enough information to head out. Jumping from branch to branch, Naruto quietly made his way to where his clones were defeated to, obviously, find no sign of the copy ninja.

Staying out of sight, Naruto silently made his way around. Something was telling him Kakashi was nearby. But where? He stopped. Closed his eyes, sent out a mental thought to his hidden clone. A small ruffle to the left caught Naruto's attention. Kakashi appeared next to him with a fist cocked back ready to strike. Naruto waited. Kakashi thought he had Naruto taken by surprise until he was surprised when a fist stopped his attack. The eyes of the copy ninja widen, as he was the one taken by surprise. Using his non trapped hand to block Naruto's counter strike, Kakashi hoped to soften the blow. But, unfortunately, he was sorely mistaken as Naruto's strength seemed to surpass even Tsunade's heaviest punches.

Kakashi was sent flying through some trees to find Naruto in the air next to him, punching him a different way into a clearing. Then one final Naruto appeared above him and performed a double hand hit, slamming Kakashi into the ground. Before he could recover from out the crater was formed from his body a kunai was at his throat. He looked up to seem a smirking Naruto.

Kakashi closed his eyes, smiling in defeat. "You have definitely improved."

Naruto offered a hand up. Once Kakashi was up, he covered his sharingan, finally getting a good look at Naruto. His first observation was the change in Naruto's eyes and the orange rings around the eyes.

So, this is what he looks like in Sage mode… Thought Kakashi.

The blond grinned widely and rubbed the back of his neck with one hand. "You really think so Kakashi-sensei?"

Kakashi's eye smiled and he nodded in approval. As Kakashi opened his eye he saw Naruto looking off in the same direction he was before their fight began. Kakashi looked and tried to sense anyone out there. Nothing. Was Naruto seeing something even the jonin was not?

"Do you sense them sensei?" inquired Naruto without even looking back.

Kakashi tried again. Again nothing. "Nope." Taking a step toward where Naruto was looking, "What do your new senses tell you?" Sage mode must be incredible if he can pick something up I can't.

Naruto pointed. "They are that way, five hundred meters. They are trying to hide their chakra, but they are not very good about hiding themselves." Suddenly Naruto's eyes widened.

"What is it?" asked Kakashi looking off the corner of his eye.

Naruto closed his eyes. The rings around the eyes faded away and opened his eyes to reveal his normal bright sapphire eyes. "They must have seen us pointing them out they quickly ran away." Naruto walked to beside Kakashi. "Should we chase them down?" Naruto had an almost playful look in his eye.

The older ninja shook his head chuckling slightly. "No. We don't know why they were here. Plus, it could be an admirer of yours." Kakashi loved to tease his students with anything he could.

Naruto sighed heavily. "Too many already," Naruto said in a mock pout voice.

The silvered haired ninja tilted his head slightly. "You mean there is only one special person you wish would be your biggest admirer." Too easy.

Kakashi knew of the love triangle in his now separated squad of young ninja. Again too easy to tease about.

Naruto looked down. Smile on his face gone. "Yea. But she is for Sasuke."

Kakashi walked up to the young blond and put his hand on his shoulder smiling under the mask. "Cheer up, she roots for you more than anyone else. I can see it."

Naruto's head perked up with a smile. "Thanks sensei."

"No problem. Let's go find Yamato and grab some grub. I'll buy." Yup, the jonin really knew how to talk to people. His tongue was as silver as his hair.

"Sure!"

Sakura sigh as he propped her tired feet up on a table in the nurse's break room. Ever since she left Naruto she did not stop moving. She was beyond exhausted. She closed her eyes. Every part of her body was screaming in pain, yet ironically at the same time was completely numb. Can't her body just make up its mind?

"What's up forehead?" Don't even need to look up to know who it was.

"Hey Ino. Did you finish your rounds?" Peeking one eye open to see her way too perky best girl friend sitting across the table from here with tea in each hand.

"Yeup. Heard you could use this." Ino handed her best friend on of the steamy teas.

Sakura thankfully accepted the tea and let the hot liquid run down her throat. The tea seemed to loosen up the muscles and relax her. Ino may not have all the best talents but Sakura was thankful for one thing, Ino could miracle teas.

"Has it really been that bad for you?" Ino ran her eyes up and down her pink haired friends frame seeing just how tired she was.

Sakura took another sip of tea then shook her head. "No, it is never this bad, even with the amount of wounded we still have. I made the mistake of training with Naruto before coming. He may not be the smartest guy but can he put up a fight and push you to your limits."

Ino leaned her head on her hand and looked at Sakura. "Yea he has come a long way from being that annoying brat he always was. I mean look at him! Hero of the village! It would not surprise me if they made him Hokage!"

A smile crept on Sakura's face as Ino spoke. "Yea there is nothing that can stop him now."

She looked at the Hokage monument that was out the window. She could almost imagine Naruto's face carved into the rock face.

On top of the Hokage monument, on The Fourth Hokage's head stood the very blond Sakura was thinking about. The sapphire eyes of the village hero gazed out on the reconstructing village. He could only imagine how grand the new and improved village will be when everything is done. Easily one of the greatest things the world will ever see. He took a deep breath. As he stood, both Kakashi and Yamato were behind him. Kakashi a few feet behind him, and Yamato leaning against the rock face.

Naruto had just finished telling them what happened during the fight with Pein. He told them how we went eight tailed state before the Fourth Hokage intervened and then they learned a darker and more terrifying secret. He withheld the fact the Fourth was his father.

Yamato was not happy. "So you're telling me that someone much more powerful than our Fourth Hokage was controlling the world's most feared organization and wants all of the tailed beast from some evil plan?"

Naruto turned around to face his two superiors. "Yea. And he is also manipulating Sasuke."

Kakashi nodded in agreement. "Naruto, did the Fourth Hokage tell you anything else?"

Naruto's fists tightened. Yamato perked up.

"Fathers usually have a lot they want to tell their sons." Kakashi was smiling under the mask.

Yamato's eyes were wide as saucers. The resemblance was undeniable.

Naruto looked up with the widest smile. "He said he was proud of me. That I could find the answer to peace."

Pushing off the wall and walked to beside Kakashi. "Y-y-you're the son of the Fourth Hokage?"

Naruto did not jump and scream like most would expect him too. He seemed to have a more of a calm air about him now. But still that playful and free spirit. "Yea. He left his dream to me. I will make it happen."

A couple of days later Naruto was walking down one of the streets towards Ichiraku. Yesterday all of the rookies got together and had some grub at one of the new barbeque places that were opened. It became their new hangout spot when everyone was home. Everyone had a great time. Naruto was enjoying himself but he could not shake the feeling of being watched. He had the same feeling right now.

Suddenly two ANBU appeared in front of him. "Uzumaki-san, you are to report to the council immediately. We are here to escort you."

Naruto should have known it was ANBU. He just nodded and started walking towards where the council was temporarily meeting until a more permanent structure was completed. What were ANBU doing here and why did he needed to escorted? He knew where to go. Something was not right.

They got to a large meeting room and the double doors opened up.

The entire council was here. Naruto stood before silently.

Koharu cleared his throat and spoke. "Naruto Uzumaki. Much has happened recently, most of which has revolved around you. Many regard you as some sort of hero. After much discussion the council has decided-"

"Don't you mean what you want." Shikaku interrupts with his eyes closed and arms crossed. He was obviously not happy.

Koharu continued as if never interrupted. "The council has decided that you have become too much of a danger to this village and should be put to death immediately."

Eyes wide open. Mouth agape. No other emotion then pure shock. He could not even move.

"W-what?"

Koharu leaned forward. "Did I stutter boy?"

"YOU CAN'T DO THIS!" Naruto screamed taking a step forward, fists clutched so hard blood trickled down his fingers.

Homura shifted her hands to her lap. "The decision has been made."

Naruto slowly look around the room to all the elders and the members of the council who were invited.

"You have no right to do this!" Naruto yelled pointing at all who were present.

A man cleared this throat in a smug and rude way, then spoke in his emotionless voice. "Respect your elders boy. We came to this decision for the protection of Konoha. For its citizens, for its ninja, for its future. A future without you." The smug smile formed on the face of Danzo.

"What are you talking about? All that I have done has been for Konoha and it's protection!" shouted Naruto. "how can you do this? There is no Hokage!"

"We do have a Hokage." Said Homura. "Lord Danzo."

Danzo sat with a smug look on his face. "And it is the decision that you must be eliminated for the good of the village. Now, Naruto Uzumaki, will you come quietly and die a glorious death for the village or we will have to do this the hard way."

As if on cue ROOT ANBU burst in the door and began to surround Naruto.

During the whole thing Naruto was shaking, but now he had to calm himself. He closed his eyes thinking about what he should do.

He did not want to die. That much was obvious. There were so many things he still had not done yet. He could not die until he was Hokage. And he was not Hokage. Danzo is. It started to make sense now. Danzo must have had Naruto followed recently to keep tabs on him. The slimy snake. Vile creature. All Danzo craved was power. Now he had it.

So what could Naruto do? As much as he wanted to, Danzo was off limits. Attacking the Hokage even if he is a terrible person, comes with severe heavy consequences. Naruto has to get out. And fast.

Naruto heard Danzo. "So what's it going to be boy?"

Naruto opened his now frog like eyes in full Sage Mode. "I choose neither."

All of the ROOT agents attacked at once. Naruto decided to take one from Sakura's book. He cocked his hand back and with all of his strength and pouring as much frog kumite he could into it, he punched the ground. Wood, debris, and even people were blown away from the impact as part of the building was blown out.

Not even waiting for the dust to settle Naruto leaped as far as he could from the destruction. He could here Danzo order his men after him. Using the strength and speed granted to by his Sage Mode Naruto pushed himself to get away from his pursuers. He needed to leave. He had to leave.

He stopped on top of a random building and it all came crashing down of what that really meant. Should he ask for help for someone to go with him? No. too dangerous. He did not want his friends to be dragged down and hunted like him. Closing his eyes, the now on the run blond, took a deep breath to harden his resolve. There were a few things he needed to do before he left for good. Sensing the more ROOT ANBU behind him, Naruto took off for his little camp he made waiting for a place for him to live to be built. Bursting into the tent he threw all of his belongings into his pack and then strapped it to his back. Exiting the tent he had two things to do before his left. Taking two scrolls he wrote on both and signed them and took off to deliver them. He found where Kakashi stayed and threw it on the pillow. Finally made it to where he knew his favorite pink haired teammate stayed. How he longed to see her but he knew he couldn't. Gently he placed the scroll down on her belonging pile. Took a second to take it all in then sprinted out before anyone could see him, he still felt the agitated chakras of ROOT ANBU searching all around him.

A few minutes of running Naruto managed to make it to the top of Hokage monument. Silly ROOT agents, don't they know who they were chasing? Naruto Uzu….no, they were chasing Naruto Namikaze. The boy who ran from ANBU as a child. Of course they would not catch him… unless he allowed it.

Naruto looked out at the village below him. Everything has changed. Only days ago he was looking out over the village as its hero, a son of one of its great leaders, a bright future ahead of him, now, he was on the run.

Reaching up he, untied his forehead protector. Tracing the symbol with his figure he remembered how excited he was to get this. It was the same one as Iruka gave him. He was so proud to wear this. He still is but with the events of today, he had a funny feeling about it.

Narrowing his eyes he felt some of the ROOT agents finally closing in on his location. He needed to do this. He had to make sure people thought he was gone or he would never get a day's rest. This new way would take all of his strength and all of his humanity to make it through. But he was ready.

Hearing the ROOT behind him closing in he took a second to gather more Nature Energy.

"Naruto Uzumaki, you are under arrest come quietly."

Naruto chuckled to himself. "If you are looking for him you are looking in the wrong place."

Behind him some of the ROOT looked at each other not getting his meaning.

"Naruto Uzumaki-"

"Is dead," interrupted Naruto. Looking at his head band he took out one kunai, and in one fluid motion scratched a single line horizontally in the metal. Wasting no time he quickly tied the headband around he head. Slowly turning around he looked at the lead ROOT with an intense glare. "I am Naruto Namikaze."

All the ROOT agents hesitated for a second taken off guard by the announcement. But then, by order of the leader, they attacked Naruto at once. Dodging, ducking, blocking and simple side stepping, Naruto evaded all of his attacker's blows. Finally one of his attackers overstepped and lost his balance, Naruto took the opportunity to shove a Rasengan into the attacker's back blowing him off the cliff. Unfortunately, this left Naruto open so a ROOT agent had to opportunity to stab Naruto in the shoulder. Naruto hissed in pain, thanks to Sage mode he did not feel as much pain. He punched the ROOT in the chest, caving it in and throwing the body away. Grabbing his shoulder feeling the massive blood erupting from it, Naruto had an inspiration.

Root kept up their attacks. But now they were landing blows on the Sage. Nothing too severe, just enough to draw blood. It was all for the show. Finally Naruto had enough and using a quick Sage Mode enhanced Wind technique, the blew all the attackers away. Summoning two clones Naruto prepared his greatest attack. Soon a howling wind surrounded Naruto and fully formed Rasen-Shuriken. He looked around at all of the ROOT agents, feeling their fear.

"If you stay, you will die." Naruto warned. Most of the ROOT took the advice and immediately started to flee, sensing the great danger. But a few unfortunate souls decided to stay or try and attacked.

Leaping high into the air, Naruto came hurling back to the ground throwing the Rasen-Shuriken right where he would land. The Rasen-Shuriken impacted the ground expanded and blew up, tearing apart all of the trees around and the ROOT agents who stayed. The shock wave blew off of the mountain and traveled over the village. Everyone in the village turned the attention to the explosion ripping apart the top of the monument.

The ninja hoped into action. Many ran to the explosion as it started to die down. Some knew exactly who it was.

Sakura was walking down the street with Ino when they were hit with the shockwave. Both turned to see the power of the Rasen-Shuriken.

The blood in Sakura's face drained, "Oh no."

Not a moment's hesitation was wasted when she took off in the direction of the wind based jutsu. Why was Naruto using that attack here? And against who? She was going to make that baka's head roll when she catches him. That jutsu was too dangerous to use. Especially, in the village. But who would attack Naruto in the village, except the Akatsuki? Either way she had to make sure Naruto was ok. Then shake him senseless.

Many ninja arrived before she got there. The devastation was obvious. A huge crater was in the ground with splintered trees and three dead bodies. She pushed through the crowd to get to the rim of the crater. Something orange caught her eye. She hoped into the crater without thought and sprinted to the middle, hoping she would not find her worst fears realized. Sliding to a stop at the bottom, her breath hitched. Laying in the middle was a torn up and bloody orange and black jacket.

Sakura fell to her knees. Tears streamed into her eyes. She shakily reached for the jacket. Her worst fear had come true. Naruto was gone. She checked the jacket hoping to find anything to show he was alive. But with so much blood she knew, medically, that was a lot of blood to lose.

Finally she broke. She cried out in agony. Her pillar was gone. She hugged the jacket to her as if it was the only thing keeping her alive. Shudders racked her body and the full force of emotions hit her of losing her best friend. Her teammate. Her sunshine. How could she live on? She needed him. All she could do now in cry out for him.

"NARUTOOOOOOOO!"