Author's Notes: Hey everybody, this story is going to be epic in length and pairings so far are undecided. I'm open for almost any pairing as long as is isn't yaoi. It isn't because I hate yaoi; I just don't like writing it. Also, forgive me for any grammar or spelling mistakes, I need a beta-reader.

Disclaimer: Today a bar of soap told me I didn't own Naruto, worst day of my life…

Chapter 1

Coolness woke him. His eyes shot open, hands grasping for a kunai, he found one. Head still swimming from the fall, he tried to jump to his feet, almost falling flat on his back when his foot landed smack dab in the middle of a puddle of water. Growling angrily Naruto extracted his foot from the water and tried to shake it dry.

Dull yellow walls lined with dripping pipes stood to either side of him, their once shiny surfaces marred with sooty blackness and cracks. The floor was riddled with puddles of water. But what really drew his attention were the massive gates directly in front of him. To say they were huge wouldn't give them due credit. They were even larger than the entrance of Konoha. Strange cryptic symbols ran from every corner of the room to a small piece of paper with the word seal inscribed upon it, stuck squarely in the middle of the gates. Weirdly enough, the paper seemed to be the only thing holding them shut.

The gates consisted of metal bars larger around than Naruto himself, and taller than the Hokage building. Curious, Naruto began edging toward the entrance, wondering what lay beyond.

Two cat-like crimson eyes appeared amid the inky blackness behind the gate. Burning red as coals, they looked down at Naruto. A dark hatred lurked within those eyes, ancient and foreboding. A terrible, snarling smile grinned into existence below the massive orbs, wicked fangs gleaming threateningly in the dim light.

"So, the hairless ape has decided to show its face." The bodiless mouth grinned wider at its own words before the rest of its form flickered into existence. It was a thing born of nightmares; a colossal, foxlike beast that reeked of blood and death. Nine tails unfurled behind it, coiling and uncoiling like snakes preparing to strike.

"Kyu-Kyuubi…" Naruto whispered, tripping over his tongue when a suffocating wave of killing intent hit him.

"Why are you here boy?" The demon snarled, its lips pulling back to further expose its fangs.

Naruto stalled for a moment. Why was he here anyways? The last thing he remember he was training with ero-sennin and… oh shit! The bastard tossed him off a cliff!

Fear cast aside he matched the fox's unblinking glare. Whether he liked it or not, he needed the demon's help.

"I've come here to borrow some of your chakra!"

Kyuubi laughed as if in disbelief. It was a deep, bark like laugh that shook the very room, sending dust flying into the air.

"You've got balls kid, I'll give you that. But what makes you worthy to use MY power?"

The killing intent rolling off Kyuubi intensified, but Naruto refused to flinch. He couldn't die, not like this, not before he became Hokage!

"You're trapped inside me right? If I die; you die." Naruto strode purposefully toward the gates, stopping less than an arm's length away. Trying his best to hide the fear welling up inside his chest, he carefully placed one hand on the paper seal that held back the beast. It was warm to the touch, and rough, feeling more like a think leaf of parchment than normal paper.

"This seal binds us together, it connects us." As he spoke Naruto traced the symbols inked upon its surface. They pulsed with an inner power, and somehow served to calm his nerves. "We are going to be stuck together for a long time, assuming this fall doesn't kill me. I don't want us to spend the rest of our lives hating each other."

Naruto paused, trying to find the right words to articulate his thoughts.

"I've felt enough resentment for one lifetime. Enough hate. I'd like it if someday we could learn to work together, maybe even become friends. But for that to happen I have to live. I need you to loan me you're power."

The Kyuubi was quiet for a long while after that. Naruto wasn't sure if that was malice, amusement, or understanding that filled the crimson eyes of the fox, but he was banking on one of the later. After all, from this distance it wouldn't be to hard for the fox to skew him with one of those wickedly curved claws.

"You're either very brave, or very stupid."

Silence.

"But I would rather my container be a headstrong fool than a coward. Just this once human, I'll do you one better. The seal would have forced this to happen sooner or later anyway."

Naruto blinked dumbly for a moment, "What do-?" But it was too late, his surroundings were already fading away to be replaced with the real world.

And he was still falling.

I don't feel any of the Kyuubi's Chakra… Naruto realized. Still a little dazed, he looked back at the top of the crevice to see Jiraiya's face staring down him. He was surprised to see that everything was moving much more slowly now. And the detail! Every hairline fracture in the rock walls to every freckle on old pervert's face was visible to him.

His surprise turned to anger when he realized Jiraiya was smiling. Smiling! Here he was, plummeting towards an onslaught of rushing water and certain death, and the old perv was smirking like it was some kind of joke!

Rage bubbled up in him, anger long stuffed away, coming to the surface. Why did this always happen to him? Why did he always have shit for luck? He wanted to be up there, to yell at the idiot for throwing him off a cliff. To punch him right in that smirking face of his. There was a twinge in the back of his eyes, and for a split second he felt as if he had lost all definition. He had no body, no consistency, nothing. Then it was gone.

Thawk!

Naruto hit the ground. Hard.

"Ugh." he grunted, the wind knocked out of him from the impact. Grass poked up on either side of his head, tickling his ears. Straining his muscles he tried to get up, only to find he was too dizzy to do so. His head was swimming.

At least I'm not falling any more. He thought to himself.

"Naruto, how-?" A large mane of white hair popped into Naruto's field of vision. Was he at the top of the the ravine? Lolling his head to the side he saw he was just about an arm's length from its edge.

"-the fuck was that for!" Naruto managed to breathe out before vertigo overtook him and he blacked out.

A bell chimed as the door to a prominent flower shop opened and closed with a soft thud. A young girl with pink hair walked up to the counter, where a young blonde-haired girl sat reading one of the newest fashion magazines.

The girl at the counter looked up. "Hey Sakura," was all she said before she returned to the magazine.

The pink-haired girl replied with a sigh, "Ino, can I have a rose?"

"Go ahead. Is it for Lee?" the blonde asked with a frown. She knew that Sakura had been visiting the overly-zealous teen. That fight with Gaara had really done some damage. After all, the kid had protected her from those Sound-nins and pledged to protect her to the death.

"Yeah," Sakura frowned.

Ino sighed, "Well, how is he?"

Sakura suddenly became very interested in the floor, "The doctors said that the damage may be permanent, he may have to end his ninja career."

"I'm sure that they will find a wa-" a tremor, the ground had vibrated. "Did you feel that?" Ino asked.

"Yeah, what was it?"

"I don-" there it was again. The vibrations were bigger. Both girls were silent; waiting to see if it would come again. It did, the ground trembled, the ceiling shook, and the water in the vases rippled.

Simultaneously Ino and Sakura ran towards the door, both fighting to get out at the same time so they could investigate the source. They fell into the street, standing up they brushed off and looked towards the gate.

Just in time to see a toad the size of multiple houses hop over the wall. What was that sticking out of its mouth? A pipe?

In shock, they could only stare dumbfounded as the frog jumped again, towards the center of their village. It landed about ten blocks away, sending tremors that caused the dust in the streets to fly up. It jumped again, not even a block away now, they could see the cement crack when it landed.

On top of the frog an old man with white hair was standing, holding what looked like an orange blob with blond hair. "Naruto," Sakura's eyes widened. She knew what its destination was now. It was making a beeline for the Hokage's Tower. Steeling herself, she grabbed Ino's wrist and took off running as fast as she could after it.

"What is that boy doing now?" Sarutobi knew Jiraiya was in town, so naturally when he felt the earth begin to quake, he had some inkling as to the cause. Pinching his nose between his thumb and forefinger, he prepared himself for the headache that was surely to come.

Getting up, he trudged slowly, almost remorsefully towards the window. True to his prediction, he was met with the sight of Jiraiya going for a joy ride on Gamabunta's back, through the MIDDLE of the village. Sarutobi almost whimpered. The complaints that would be filed, the damages that would need repaired! This would mean a whole new mess of paper work for him!

As he continued to watch his former student progress through the village, a crowd seemed to be growing near the Hokage tower. It seemed quite a few people had figured out where Gamabunta was headed.

ANBU were already gathering around the tower, working as crowd control. Many of them seemed confused or dazed; it must have been their first time seeing a summon of such size.

Why must Jiraiya always make a commotion…? Sarutobi groaned.

Gamabunta made one final leap, landing with an earth shaking thud right outside the tower. Jiraiya leapt off, the large toad dissipating into smoke behind him. Sarutobi frowned when he noticed his former student was carrying an unconscious Naruto.

This ought to be good. Sarutobi sat back down in his seat, rubbing his head. Only a minute or so later the self-acclaimed 'super pervert' strode through the door, kicking it shut behind him.

Jiraiya was visibly shaken. That worried Sarutobi. Not much took his student by surprise anymore, and this obviously involved Naruto.

Jiraiya laid Naruto down on a bench against the wall, his back to his sensei. The silence grew, lasting minutes, neither party saying a word, until-

"Who were Naruto's parents?"

Silence and a harsh look met his words.

"WHO were they?" Jiraiya repeated, more loudly this time.

"I'm afraid this is a conversation for another time, Jiraiya." Sarutobi's eyes flickered towards a shadowy corner of the room, as if to say, we still have company. In an act of pure speed Jiraiya disappeared, reappearing in the corner of the room. Charging his pointer finger with chakra, he flicked the air. There was a ripple as the well constructed genjutsu unraveled, exposing the ANBU hiding behind it.

"Leave us." Jiraiya voice was stern, but soft. He knew only the Hokage had the authority to dismiss his personal guard. The ANBU looked towards Sarutobi, who waved him off. Without a word the masked ninja moved towards the window before phasing threw it and disappearing.

Their company gone, Jiraiya continued his rant.

"I've suspected it for long enough, but I need to hear it from you. Who-"

"Enough!" Sarutobi growled out, anger and frustration leaking into his voice. "Last I checked I was the Hokage and you, even at your station, are still required to speak to me in a manner fitting my office.

"You storm through my village, cause untold amounts of damage, and scare the populace into a frenzy! It is my turn to ask questions Jiraiya. So why? Why are we having this conversation?

"Why now?"

Now it was Jiraiya's turn to look a bit uneasy. He wasn't so sure his former sensei would approve of his 'training methods'.

"I was trying to help Naruto learn to control the Kyuubi's chakra," ...Jiraiya paused, taking a hesitant breath, "sooo I threw him into a canyon-"

Sarutobi face purpled in anger, and he unintentionally let out a spike of killing intent powerful enough to knock civilians unconscious (had there been any present).

"WHAT! How in the hell would that help!"

Jiraiya puffed out his chest defensively, "I was hoping he would borrow some of the demon's chakra and perform Kuchiyose no Jutsu! But instead, he just fell for a few seconds before… disappearing and reappearing beside me. I didn't know what to think of it, until I saw his eyes. At first I wasn't sure, but looking back on it… There is no doubt, he awakened the Sharingan. And not just your normal, run of the mill, three tomo one either. It looked… strange. Sort of like a twisted shuriken or something. I think…I think he used it to teleport out of the canyon somehow."

Silenced reigned throughout, Jiraiya and Sarutobi arguing with their eyes. Sarutobi knew what Jiraiya wanted to hear. He wanted to know who the boy's parents were, to have his long held suspicions confirmed. And with the news of Naruto's eyes activating, Sarutobi would be hard pressed to keep it under wraps.

"I have the Sharingan?" Sensei and Sannin looked towards Naruto. He was lying on his back staring at the ceiling. A foreign look carved into his sharp features; a look that screamed pain and loss.

How didn't I notice he woke up?

"That means I'm an Uchiha, right?" Naruto whispered it more as a statement than a question. Instead of the excitement they would have expected in the boy, the look of sadness only seemed to grow deeper into his features.

"Naruto…" Sarutobi whispered; a soft utterance filled only with the sadness of what could not be changed.

Naruto's thoughts were rushing through his head faster than he could process them. It could have all been avoided, this throbbing pain in his chest. The abuse, the hate the village harbored towards him, but most importantly, this feeling of complete isolation, of being alone.

Naruto's bright eyes dulled as he muttered, barely above a whisper, "They didn't want me did they? Because of this demon in me, my family didn't want me…" his voice trailed off. His blue eyes were starting to moisten.

Sarutobi shook his head in denial, "No Naruto! Of course they wanted you, but they died in the attack. With their death, I felt it best to make your heritage an S-class secret. Only my advisers and I know who they were." Sarutobi words were sad, regretful. But the confession only seemed to turn Naruto' sadness into anger.

"Why? Why did you keep it a secret? If people had known, I might have had a family!" Naruto almost screamed. "I wouldn't have been so alone…" He whispered.

"You have to understand, after the attack everything changed!" Sarutobi's voice was shaking as he held back tears, trying to plead with the child before him, to help him understand. "People, good people, were corrupted by fear and hate! The council already wanted you dead Naruto, the Kyuubi saw to that. Could you imagine how scared they would be of a jinchuuriki wielding the Sharingan?

"You'd be too dangerous! Too powerful in their eyes! Even the political might of the Uchiha wouldn't be able to protect you, not with both of your parents dead."

Naruto just laid there, only half listening as Sarutobi tried to explain his actions. Only one thing mattered to Naruto now. He wasn't abandoned like he always feared. His parents wanted him. His parents they…

"Who were they?" Naruto's voice was strong, demanding. He had to know, and refused to be turned away. Not this time.

Sarutobi was silent for a moment, not sure how to say what had to be said. After a moment his shoulders sagged in defeat. Raising his pipe to his lips, he took a long, slow hit before closing his eyes and breathing out. The smoke billowed around his aged face, thick and grey.

It was time for the truth.

"Your mother was Uchiha Hitomi."

"Uchiha... Hitomi..." Naruto repeated the name reverently, committing her name to memory.

A small smile set into Sarutobi's face as he heard Naruto speak her name for the first time. Perhaps finally letting out the truth would be good for his ragged, tired mind.

"She was beautiful. Hair blacker than I've ever seen, with eyes to match. While you look very little like her, you have the same love for life she did. The same energy. I see so much of her little brother Obito in you. Your eyes, they hold the same fire, the same adamantine will his did." Sarutobi stopped to take another drag off his pipe, breathing the smoke out slowly to calm his nerves.

"I suppose you might want to know a bit about her ninja career? It was her genjutsu that made her famous, or infamous depending on where you are from. She was Konoha's first Genjutsu Mistress. And Kami was she good. Compared to her, Kurenai looks like a toddler playing with finger paints." Sarutobi's smile grew at that, remembering the first time Hitomi managed to trap him in one of her Genjutsu.

Naruto grinned. His mother sounded so strong! He absent-mindedly wondered if she would be proud of him as he was now. Would he be strong enough to live up to her reputation? Thoughts turning back to the present, he stood up, to full of nervous energy to stay sitting down. Steeling himself, he turned back towards the Hokage.

"And my father?"

Sarutobi smiled sadly. Of everything Naruto learned today, he knew this would be that one piece of information that would change him the most; he just hoped it was for the best

"His name was Namikaze Minato. I'm surprised with how much you look like him; it's almost like looking into the past." Sarutobi set his pipe down, tapping the remaining Tabaco and ash out and into a dirty ash tray.

"I've never seen a ninja move like he did. I swear the boy was born with a kunai in one hand and an explosive note in the other. He was one the strongest ninja I ever knew." Sarutobi smiled fondly in memory of the man he had come to love as a grandson. "He loved this village and your mother more than anything else, and when he found out she was pregnant… He was happier than he had ever been-"

Jiraiya tuned Sarutobi out, closing his eyes to hide his regret. So it was true then? That made Naruto was his godson. He had always suspected, but never pushed the matter, trusting in the Hokage to keep the boy safe. He knew now, knew that he had made a mistake and shirked his duty. The boy had been left alone, to rot in a village that hated him.

Back to the Third's monologue.

"-you may know him as the Yellow Flash, or the Forth Hokage."

Naruto's eyes widened to the size of dinner plates.

"Huh?"

"Okay Naruto, I want you to push your chakra out of both hands into the leaves. If you do it right then they will stick to the palm of your hand. If you push too much chakra into it then the leaf will be torn apart, while if you push to little chakra into it, the leaf will simply fall off."

Naruto was sitting with his legs crossed, and hands palm-up, propped up against his knees — a leaf rested in each hand. Jiraiya said that this was supposed to be a chakra control exercise that medic-nins used to help them master their amount of chakra output. That was the reason it was chosen. Naruto had horrible chakra control, and this was a perfect technique for drastically increasing his.

"But Jiraiya, isn't it the same basic idea as tree climbing? I can do that no problem." Naruto asked in a questioning tone.

"In a way, yes. The difference is that tree climbing takes considerably more chakra. You have to master using less chakra at a constant pace."

The Chuunin exam was in less than three weeks. So naturally the Hokage sent him to the middle of nowhere to train with the same pervert who had the gall to throw him off a cliff. At least jii-san had been nice enough to send a few scrolls of fire jutsu with them. Not that Naruto had seen hide or tail of the scrolls since they left.

"But before we start, I want to test out a theory of mine." Naruto jumped to his feet without a moment's pause, excited to try something aside from chakra control training.

"First things first, create a Kage Bushin."

Naruto gave him a curious look before forming the ram seal. One poof of smoke later and a carbon copy of the boy was standing next to him.

"You stay here and have your clone follow me, alright?" Naruto nodded, and his clone followed Jiraiya into the nearby forest. Naruto absentmindedly rocked on the balls of his feet as he waited for his new 'sensei' to return. A second later Jiraiya emerged from the trees, followed by a sour looking Naruto-clone.

"What was the point of all that?" Naruto asked curiously.

Jiraiya smirked, he hoped this worked. It would save him a great deal of time in training the boy if it did. "You'll see." And with that he gave the clone a good smack in the back of the head, hard enough to dissipate it into smoke.

Naruto's face scrunched up in displeasure before groaning unhappily. "Whatdoya mean we'll be doing nothing but chakra exercises all week?"

Jiraiya smiled innocently. "What? Who told you that?"

Naruto crossed his arms angrily. "You did! Right after we walked into the woods!"

"No, I never told you anything. You stayed right here remember?" Jiraiya finished, waiting for his point to get across.

"No, we-!" Naruto stopped mid-sentence, dropping the finger he had been pointing accusatorily at the older man. Technically he hadn't followed Jiraiya into the woods, his clone had.

"The point of this little exercise was to show you the secondary function of the Kage Bunshin no Jutsu, memory transference. Everything your clones learn, you will remember when they dispel." Naruto continued to give him a blank stare. Jiraiya sighed, seeing Naruto hadn't quite grasped what he was getting at.

"Okay, let's say you create a shadow clone and you both train on a chakra control exercise for an hour. When you dispel that clone, you remember everything it did, which means you have finished two hours of training in one hour."

Naruto's face slowly morphed into one of understanding. "So I can cut how long it takes me to learn that leaf exercise in half by training with a Kage Bunshin?"

If anything, Jiraiya's smile only got bigger, "Why stop there? I know you can create hundreds of clones. If you train with, 500 clones for example, training that could take you weeks or months can be completed in a few hours."

Understanding settled over Naruto's mind. That meant he'd have this leaf exercise done before the day was over. Who knows what else he could learn in three weeks if he trained with all the clones he could summon? Flashing a foxy grin, Naruto formed the ram seal and-

"Hey, don't rush things just yet. First I want you to activate your Sharingan."

Naruto nodded, breaking the ram seal and letting his arms fall to his sides. Focusing on his chakra, he began channeling more into his eyes. At first there was nothing, but then it happened. He didn't feel a change so much as he saw it. An accelerated perception of time, how he picked out details that before he overlooked, and the clarity! It was like a film had been pulled back from his eyes.

"Everything looks so… beautiful." Naruto whispered, slightly awed at how differently he could see the world.

"I can only imagine." Jiraiya muttered, only half listening to Naruto. A frown scarred his face as he studied Naruto's eyes. "But you only have the normal, three-tomo Sharingan activated. When you first used your eyes they looked more like a four-pronged shuriken (AN: think Uchiha Shisui's advanced Sharingan eye)

"Huh? What's the difference?"

"If I'm correct, it was the other form of your eyes that allowed you to teleport out of the canyon. I need you to activate them so we can figure out how they work."

Naruto's face lit up. "I can teleport?! Awesome! Only, erm, how do I do I activate them?"

Jiraiya's scratched his chin, variables turning over in his head. "To be honest? I'm not entirely sure. But I have a few theories. First things first, how many clones can you make?"

Naruto scrunched up his face as he counted in his head. "The most I've ever made at once was like 600 or something."

"Ok, I want to make as many as you can. Push as much chakra as you can into the technique, we need to figure out your limits before we proceed."

Nodding, Naruto threw his hands up in the ram seal. Blue chakra started to rise from his body, billowing out like smoke.

Naruto squeezed his eyes shut in concentration. More and more chakra surrounded him, forming a blue, semi-translucent cloud.

More… Naruto dug deeper into his reserves, drawing out as much chakra as he could muster. His silhouette could barely be made out through dense, ever growing cloak of chakra.

Is this all I have? Naruto wondered. He had never been in a situation where he needed to draw out ALL of his chakra. Basically he had no idea what his limitations were, or even what chakra exhaustion felt like.

Naruto smirked. There. He had found more, a spark of power not yet drawn upon. Red chakra bubbled from his flesh, mixing with the blue to form an opaque purple. Oblivious to the fact he was drawing upon the Kyuubi's chakra, Naruto only strained harder to coax more and more of it out.

This feels weird. This chakra… The scent of blood filled his nose, and he could taste copper on his tongue. It's just like when I used Kyuubi's chakra on the bridge in wave!

Realization dawned upon Naruto. Quickly he pushed all the chakra he had drawn upon into his Kage Bunshin no Jutsu.

The sound of hundreds of clones popping into existence filled the air and the dense shroud of chakra that encircled Naruto disappeared into the technique.

Naruto fell to his hands and knees panting. His exhaustion was momentary, as the Kyuubi's chakra quickly flooded his body once more, coursing through his coils like a tidal wave.

Naruto's eyes shot open, the tomo in his Sharingan blending together in one fluid moment. In their place sat a black, twisted, four-pronged star amid a red iris.

"2350." Naruto's voice was deeper, more guttural. "2350 clones. But I'm not sure how many were made from the Kyuubi's chakra. I didn't mean to use it, I just felt the spark and…" he trailed off.

"I see. I think I figured it out."

"Huh? Figured what out?"

"It seems, at least for now, that you need to use the power of the Kyuubi to fully awaken your eyes. I'm sure threw training we can learn to overcome that limitation, but for now it will work. Divide your clones up into two groups; it's time for the real training to begin."

Author's notes: Just in case someone didn't know, Obito was Kakashi's teammate. He is the one that gave Kakashi his Sharingan-eye.

Vote for pairings. Tell me what you like and dislike. Peace.