Naruto: The missing nin

What if Naruto didn't belong to the world he has always lived in. Everyone believed that Obito's mangekyō sharingan was a space-time jutsu, but what if it wasn't. What if Obito's sharingan was a dimensional plane jutsu. Find out what happens when both of Obito's sharingan eyes are destroyed during the fourth shinobi war.

"The" - normal speak

"The" - normal thinks

"The" - Demonic speak

"The" - Demonic think

AN: The story begins where Kakashi and Obito were fighting in the separate dimension during the Fourth Shinobi War. This is my first fanfiction so I hope that all of you readers enjoy it.

I OWN NOTHING! Well that's not true, but I don't own Naruto so please support the official owners.

Chapter 1 - The World Was Torn Asunder

A Shinobi.

This simple seven letter word describes a plethora of individuals. For some it was the title of a warrior, for others it was the mark of an assassin. The word is even able to describe healers whose abilities can save those who are more dead than alive. Even for all the wonders that a shinobi can perform most thought of them as nothing more than tools. A simple means to an end. They are however, so much more.

Looking past all the abilities and skills they honed for their entire lives, they were individuals like any other. Each held their own hopes, dreams, and aspirations.

And just how the complexity of an individual is hard to define, so is an accurate definition of the word shinobi. If one was asked to give a definition of the word, many would simply say it is 'One who endures'.

Kakashi Hatake endured more than most had for their entire lives and he only recently began his thirties. A father renown as a genius was drove to depression by those he saved. A man so great that none thought he could be killed in battle ended up dying by taking his own life. A teammate no a comrade who was still young enough to be considered a child sacrificed himself to save Rin and Kakashi. Rin the only women he ever loved, died by his own hand in order to save their village from the demon sealed within her. A teacher who treated him as family was killed by the same teammate that was thought to have died all those years ago. Watching the son of his teacher bear the burden of a monster forced on his shoulders as a newly born only to be scorned and feared by those he was protected.

The pain and suffering that this man had endured is what shaped him into the man, no the shinobi that he was today. Even with all the experience Kakashi had, he was at a loss of what to do as he stood across from Obito in the world, or more accurately put alternate dimension that they were in. As Kakashi looked at the scarred man who was once the teammate who sacrificed himself for him, the absent minded gesture of running his hand over the scar that caused him to gain the right eye of Obito's wasn't missed.

Obito stared at his right eye that he gave to Kakashi for a few more seconds before his posture relaxed and audibly signed. "I'll need you to return that gift I gave you all those years ago Kakashi."

Even as Obito visibly relaxed it only caused Kakashi to tense more. The distorted man before him was not Obito but a warped body and mind that was not to be trusted. A man who started the fourth shinobi war only to say it to be done in the name of peace caused anger to brew within the white hair nin. Perhaps it was the anger, and emotion that Kakashi hadn't felt in years or maybe the desire to understand such broken logic that prompted Kakashi to question his former teammate.

"Why are you doing this Obito? If you truly do desire peace then why are you doing all of this? Because of you there have been tens of thousands of deaths. You single handedly in a sense started the fourth great shinobi war." Taking a pause to see if Obito reacted to any of his words was met with the same black expression Obito donned before his tirade. The disinterest displayed only brought another spike of anger from Kakashi. "All of this bloodshed and all of this hatred! How can you possibly claim peace to be your goal!?" Kakashi asked his voice beginning to lace with mixed emotions.

Obito sighed again, in a manner very reminiscent of a parent forced to explain logical arguments to a head strong child. "Kakashi, you understand nothing. There will never be peace. People will never be able to understand one another, that is why I will force peace onto them with an infinite Tsukuyomi." was the reply Kakashi received in a voice devoid of any emotions. Obito actions were not like those of a fanatic who sought recognition for his choices, but an individual so distorted that they truly believed their reasoning's of logic was the only correct one.

Such a convoluted though process is what prompted Kakashi to roar "Then explain to me how this war is a justifiable action for your ideal of peace. You claim nothing more than an illusion of peace for the price of a thousand lives."

Kakashi's argument prompted Obito to think of the points made against him, but the mind of a distorted individual cannot simply be swayed with mere words or bouts of irrefutable logic. "It's really simple Kakashi. By using the infinite tsukuyomi with the power of the Juubi, I can cast the genjutsu on the whole world. With the fruition of my plan the revival of those who died will be a simple endeavor in this grand scheme." Leveling a patronizing look at Kakashi he continued. "Everyone will be happy and have everything they ever wanted. We can even bring Rin back Kakashi." Obito affirmed with a smile reminiscing of events long ago.

I can't save him...' Kakashi thought. A quick self-assessment of his combat potential caused him to frown. He was almost out of chakra, with only enough left for one more high level jutsu. Killing Obito was almost next to impossible since anything short of an instant death would allow him to teleport back to the Juubi and heal any damage done. As Kakashi began to formulate scenarios to bring the seemly unattainable victory to light Obito changed his causal stance into one with the intent to attack.

Obito decided to give one last verbatim before he attacked. "Sorry Kakashi, but I need my eye back. You having access to my sharingan has proved itself more of a danger than I anticipated. Please give it back before I take it back by force."

With that statement an idea burst into Kakashi's head, 'I don't have to kill Obito… if I just destroy our sharingans then we'll be stuck here forever.'

"You shouldn't be concerning yourself over the sharingan. If I have to kill you, so be it Obito." He began to charge the last bit of his chakra into a final raikiri. "It seems like I've never been able to keep any of my promises, but Naruto has kept every single one he has made so I'll put my faith in him like everyone else." Idle banter aside as long as Kakashi planned a lethal attack while simultaneously setting himself up for a second attack to Obito's eye, the possibly that Obito would predict the second strike with his sharingan was there. A very real risk with the likely hood of failure, but one he was willing to take.

Kakashi's admission made Obito frown. "You truly are scum Kakashi, first you kill Rin, and now you try to take my life too. Do you still place missions above friends Kakashi? Killing you would truly be a gift to the shinobi world." Kakashi flinched at Obito's statement. "You can't stop me Kakashi, you are almost out of chakra. I can sense the last of your chakra being funneled into that justu. No matter what you do I'll be able to read the attack with my sharingan." Obito words didn't deter Kakashi in the slightest so he signed resolutely. 'I don't even have to dodge this attack. Once I kill Kakashi I can teleport back to Madara and seal the Juubi in myself. When that happens the condition of my body will be irrelevant.

Taking one more look at each other, both their faces twisted into something akin to remorse they begin to move. A mere blur to all but the highly trained eye they flew towards each other. Not a second later the sickening wet crunch of flesh being torn was the only sound heard in the desolate dimension they dwelled in. Both had their arms pushed through the other in a gruesome display of the strength that shinobi had at their beck and call. A few seconds of registering the pain was enough for the two seasoned shinobi to identify the extent of their wounds. A gaping hole where his heart should be was the blow Kakashi dealt to Obito who in turn received a hole of similar size in his right lung.

Tears began to freely fall from the sister set of sharingans. Even with one being a seasoned shinobi and the other a man distorted to his very core, the act of killing the person who you considered your best friend was enough to draw tears from these two. Using his left hand in a gesture to wipe the tear away Kakashi moved he hand with his thumb resting right below Obito's eye while his fingers cupped his head. The simple mouthing of "I'm sorry" was the last thing Obito saw with his left eye. With the speed Kakashi was known for forming hand seals he destroyed the pair of sharingans with the minuscule amount of lighting chakra he ran into his thumb.

The second Obito registered the attack with the acute sharp pain from having his eye destroyed; he used his left hand to begin crushing Kakashi's throat while ripping his right arm out of the dying shinobi. "DAMN IT KAKASHI!"

The act of being strangled seemed pointless to Kakashi since his body would no longer be able to supply the necessary oxygen to survive with one lung. That was considering he died of asphyxia before blood loss. As blood vessels began to rupture in his neck form the force of Obito's grip blood began to pool out of Kakashi's mouth. Despite dying Kakashi couldn't help but smile. Obito reflexively stopped when Kakashi tried to speak in what was most likely his last words. Speaking with a throat that was more along the lines of crushed while sporting a hole in one of his long caused the words spoken to adopt a blood curling chill as they came out in vibrating rasps. "Sorry Obito… looks like you… are going to be stuck… here with me…" Kakashi wheezed out in a voice too alien from normal to be properly described.

Kakashi's last words prompted Obito to begin crushing his throat with more vigor. Kakashi knew Naruto would find a way break any obstacle in his way so he smiled one last time while he looked at Obito with his only functional eye. All of his memories of his once dear friend began to flicker through his mind. The copycat nin was so close to death that he didn't notice how the world froze as a darkness consumed everything in it's path.

With Naruto

Sitting down Naruto was exhausted. Faced with crippling exhaustion he was forced to wait as Sakura healed his heavily damaged body. The green chakra felt like pure ecstasy throughout his nervous system as it repaired his damaged muscles and organs. As his body was being treated he focused his thoughts on how he would deal with Madara and a partially revived Juubi. Not really sure how he would stop the two he entered his mindscape to council with his newly formed friend, Kurama.

The first thing he realized was that his mindscape no longer resembled a sewer with murky water swirling at his feet. With the Biju having free reign to change the scenery of his mind it looked like he chose a place a regular fox would most likely call home. Instead of Kurama residing in the recently opened cage that acted as a seal, he sat in the middle of a meadow with a forest surrounding the two. Naruto walked up to Kurama and after a few seconds of a lack of acknowledgement Naruto he spoke up by saying "Yo".

"What's up kit?" Kurama asked in a strained tone while he sat in a meditative position which focused on restoring his recently exhausted chakra supply.

"Any clue how we can beat those two, dattebayo?" Naruto asked calmly as his hands rested in his pockets.

Kurama didn't even consider the question for a second before he responded with "Yes, it's quite simple, really. We rip the two to shreds until there is nothing left of them," Kurama answered with a cheeky grin.

"I don't know if we can do that buddy, the Juubi is the size of a mountain after all." Naruto reasoned as he attempted to visualize such an outcome.

Kurama had to suppress groan. Leave it to that idiot to try and think logically now of all times. He hoped that the kit could behind his usual pattern of action which considered of kicking ass first and thinking later. "Listen kit, it doesn't matter if you think we can or can't stop them, because we will stop them. You have never let me down before and I don't expect you to start now. Now leave me to rest and gather my chakra, I suggest you do the same."

With that, Naruto left his mindscape in order to check his current chakra levels and look for vulnerable areas on the Juubi's body. When he opened his eyes, his breath hitched because in the scope of his vision everything before him was frozen. Ninjas in the air seemed to be stuck as their bodies forgot the meaning of gravity. The entirety of the world was brought to a standstill as if frozen in time as the laws of physics seemed to be broken. Not only was the sight off putting, so were the sounds since not a single one could be heard. The situation being more than a little eerie caused a chill to run the course of his spine. What stood out the most was that the Juubi was no longer wildly thrashing about, but instead it stood completely still. The most powerful known force in the world was being frozen in place by an unknown force. "Sakura, do you see this?" Naruto questioned. After a few seconds without a reply and noticeable absence of her healing ninjutsu he swiveled around and saw Sakura frozen with her face stuck in a mask of concentration.

"Yo, Sakura what are you doing?" asked Naruto.

No response.

"Hey Sakura, are you even listening to me?"

No response.

He snapped his fingers in front of her face, to which she still did not react at all.

Naruto could do nothing but gape. The idea that he was under some sort of genjutsu caused his heart to begin to hammer in his chest as thoughts of panic began to race around. He tried to focus chakra out of his body in an attempt to break the genjutsu he thought he was under but he wasn't able to push a single drop of chakra outside his body. The momentary panic began to shift to fits of hyperventilation, but then something began to happen. The world began blackening and from all sides he could see the darkness was racing towards him. Doing a quick three sixty degree scan showed the abyss all racing towards one spot. That spot was right where he was standing.

In a matter of seconds the void would reach him. Frozen by fear he felt the dark abyss reach him before he could react and the second it did, he could feel himself falling. Unsure of what to do, or for that matter what was happening, he began to focus all of his energy to sensing the world around him. Again no matter how hard he pushed the chakra would not push through the threshold of his body. The large quantities of energy now freely floating in his body forced him to stop circulating chakra in his body for fear of harming himself.

Fear. An emotion that he hadn't felt for years began tearing into his heart. Not sure what to do as he suffered from the fear of the crushing paralysis he was currently facing. Shaking his head he knew he wasn't out of options yet. His sensing abilities drastically improved ever since he learned sage mode so he began to prod around with that six sense that only those who knew how to manipulate chakra could feel. The sensing was just as disheartening since he could not feel anything, not a single form of life or a structure for that matter anywhere around him. He was sure he pushed his senses are far as a mile in the distance; surely he would have felt something, a stone, grass, hell even a grain of sand would make him happy.

With this unsettling information Naruto began to panic thinking that the infinite tsukuyomi was just preformed. However he pushed that thought out because Madara wouldn't have been able to cast it without absorbing the Juubi's chakra to power the technique, which he knew didn't happen because he was watching and sensing him the entire time Sakura was healing him before the abrupt cut off he was currently facing.

Not knowing what to do, Naruto relaxed as he began to free fall through the abyss. After a minute or so he began feeling a tickling sensation at the back of his head. He moved his hands to check his head but felt nothing but his blond locks and his skull completely undamaged.

Even though Naruto knew nothing was on the back of his head the tickling sensation began to increase until he began hearing an audible ringing sound in his head. As seconds passed by, the ringing grew louder and louder making him wonder if cracking his own skull for stop the damn noise. Thinking the worst, he entered his mindscape and saw Kurama deep in thought with his eyes closed.

"Kurama! What's the fuck is going on! No wait, never mind that why the hell does it feel like my head is going to explode."

Kurama's eyes slowly began to open and when he did he looked at Naruto and frowned.

"Kit there is something I need to show you..." Kurama said somberly.

Naruto frowned since Kurama always had a certain amount of emotion to his tone. It was usually filled with hatred and not until recently, when the two had bonded, had he ever heard the fox in a different tone, one more akin to pride. With this, Naruto began to fear the absolute worst. He never expected Kurama to talk in such a way that was so resigned… it just didn't seem possible for him. He was the Kyuubi, the most powerful of the tailed demons. "What's up Kurama, do you know what's going on?"

"No... but you have to see this, kit. This is the first memory you have ever had and until a second ago I did not exist. How a memory that doesn't exist coming to existence is beyond me."

With that said, Kurama extended his fist to the blond. Naruto more than confused and uncertain waited a little before a sign as his shoulders began to sag. Bringing his fist up he lightly tapped his to the giant foxes' and the second he did, an explosion of sights, sounds, and smells rushed through his body.

Opening his eyes only for them to be extremely blurry caused him to try and squint which made him realize he was no able to perform the biological action for some reason. Sounds caught his attention but he was having trouble distinguishing what they were. They came in more of muffled whispers than anything else.

"Fou... hoka... ito get away from the jin... Other ise...this...ilds... ilf... ill end... one min... " was all he was able to make out. A few more things were said but Naruto wasn't able to recognize any of it. As seconds began to tick by, Naruto's vision began to improve along with his hearing. Since he couldn't control any part of his body as he realized it was a memory he was currently reliving.

Over the sound of himself crying he heard a voice he knew he heard before but couldn't place who or where he heard it from.

"Wait! Calm Down!" said the foreign yet, at the same time, familiar voice.

At the sound of the voice, his eye through the memory focused and what he saw as he looked up was none other than Obito, wearing his orange mask that had a swirling pattern to a hole where his left eye should be.

At that second Naruto realized that the memory he was seeing, and everything that was happening down to every detail, was as Minato explained to him when the seal was broken years ago from the night when the Kyuubi attacked Konoha.

Something happened though that Minato didn't say. He saw Obito use his mangekyō sharingan before the battle between the two began. Naruto was sucked in with Obito, but instead of entering a different dimension, he was right where they were before Obito used his Sharingan. Everything after that played into perfect detail on account of what Minato told him.

After the memory ended Naruto looked up to Kurama who held a neutral face. Naruto searched Kurama's face for answers but the fox's mask didn't betray a thought so he stated, "Everything that happened went exactly as the Fourth told us, but why do you think he didn't include the part when Obito used the mangekyō sharingan before the two began fighting?"

"I don't know kit, but I have a few guesses as to why. I would tell you now but we don't have time for it. Something is happening, head back to your body now."

When Naruto regained his senses he opened his eyes to see a light in front of him, rapidly approaching. The second he hit the light, his body was flooded by a variety of senses before he abruptly blacked out.

AN: Hey everyone I know this is quite the cliff hanger but I will try to get the next chapter uploaded this weekend. I have half of it written already but I want to wait a little before I release it to see if anyone reads my story. If you are enjoying it so far and you have friends who also read fanfiction I would greatly appreciate it if you recommended the story to them. No matter how much fun I have writing this story I write in hopes that I give people some entertainment. On that note everyone I would like to wish you a good day, and as always I will see you in the next chapter.

AN UPDATE: Hey guys sorry about how short the chapter was and how many mistakes were in it. I will revise much more thoroughly before I upload now. The chapter isn't that much different I just wanted to add more things seeing as how I kind of skipped and glossed over some parts. Anyway I hope you enjoyed the revised chapter I will try to get the second one done and uploaded later today. 7/12/13

AN UPDATE: Well this chapter has finally been revised. It is actually readable now to woo hoo! Please be sure to thank awesomenaruto my beta reader for these more than amazing revisions. These revisions would NOT have happened without her and would NOT be nearly as well done without her so please be sure to not only review but add a thank you to miss awesomenaruto for her more than superb job as my beta. 11/25/13

AN UPDATE: The final vision to this chapter is finally out. 1/11/2015, here to hoping the other chapters come out just as fast.