(AN) on to chapter 3. This chapter most will be able to see which direction I plan to take this story in. I do apologize for the previous two for being quite short, I hope the rate at which I update would offset this fact. However, I ask my reviewers if they would prefer longer chapters, which will be somewhere in the 8K-10K range and will take me about two to three weeks two post, or shorter ones such as these which will take around a week.

I was also asked about Naruto's chakra capacity, and it will be explained in this chapter, keep in mind it will continue to grow exponentially from this point on.

Chapter 3: All is not as it should be.

Sarutobi Hiruzen was currently sitting in his office, to anyone who should venture in, it would seem as though he was doing the paperwork spread throughout his desk. However he was currently deep in thought. Pondering the situation the two vessels find themselves in. The villagers and shinobi alike were in a state of panic, and he couldn't really blame them. The chakra that the boy released was unlike any he had ever felt before.

Those nearest to the epicenter of the blast were reportedly forced to their knees fighting their own fear for the simple task of drawing breath, there were 24 civilians who could not handle the pressure and simply blacked out. And in the case of one elderly man, dropped to the floor and suffered from a mild heart attack. The man survived, luckily enough, he would have to take measures he did not want to if this was not the case.

How a mere child possessed such powerful chakra was the predominant thought running through his mind, Jinchuuriki or not.

And then there was Mito, he could not for the life of him understand how she was still conscious when the ANBU arrived. For even him, one of the best ANBU under his command was given pause by the chakra emitted from the boy. And that was just another matter to ponder, how did the child unlock his chakra? It was a difficult process that usually takes up to a month to accomplish and in very special cases around two weeks. Had the boy been told about chakra by somebody and proceeded to practice on his own?

And what of Mito, he knew from experience that the Kyuubis chakra should have healed her in less than an hour. The last time she had hurt herself, he had rushed her to the hospital with a broken wrist, the first doctor he approached refused to heal 'The demon' as he so eloquently put it. So he had proceeded to the nearest empty room, laid Mito on one of the beds and calmly walked up to the man. And in a flash faster than lightning, he fell dead with a kunai lodged deep between his eyes.

If you account for the time it took for Naruto to get her to the tower, and the refusal of the doctor to treat her, it was somewhere in the range of a mere half hour, and by that time, there was nothing to indicate she ever had a broken wrist in the first place. But after 2 hours of waiting at the hospital and no improvements to either, he had to return to his office to complete his work. A village cannot run itself after all.

There was a sudden burst of chakra as Tiger shunshined into the room, breaking Hiruzen from his thoughts.

"Report on Uzumaki Naruto and Uzumaki Mito." The ANBU said as he kneeled before the Hokage.

"Continue" the Sandaime said in the most neutral voice he could, he might have emotional attachments to the two children, but he could not let that show in the current situation.

"Currently the boy's condition has not changed at all, doctors have still not been able to successfully use any techniques nor penetrate farther than his skin." He replied.

"What of the girl? The Hokage asked.

"Uzumaki Mito's condition has stabilized, it also seems the Kyuubis chakra has healed her broken arm, the burn marks she received from the unknown chakra have lessened, however they have yet to completely fade. She has to be kept under constant sedation as the pain from the wound seems to be too much for her to handle."

"How is that possible" The Hokage asked, "It has already been six hours since the incident occurred. The chakra from the Kyuubi should have healed her hours ago."

The ANBU nodded "That is the assumption I had as well. However, given how much time has already passed. I have come to a very… worrisome conclusion."

"And what would that be?" The Hokage asked with narrowed eyes.

"That the chakra expelled from the boy is stronger than that of the Kyuubis, as it is the only foreseeable way the beast's chakra could be negated in such a way." The ANBU replied without a shred of doubt in his voice and posture.

"Impossible!" The Hokage barked as he stood up "There is nothing with greater power in this world!" The KI being radiated from the aged leader was immense, but highly focused and refined, and it was all being directed towards the ANBU agent.

Tiger, knowing that an explanation was in order did his very best to speak under the stern gaze of Hiruzen, "Hokage-sama, given the corrosive properties of a Bijuu's chakra the girls wounds are to be expected, however. The kyuubi is the most powerful of the nine and as such should have little to no problem healing the wounds inflicted upon the girl, even if only half of it was sealed into her, the kyuubi is said to be incomparably stronger than the other eight, which leads me to believe that we are dealing with something we cannot as of yet comprehend."

The Hokage was standing as still as a statue as he tried his upmost to understand what Tiger was telling him, it made sense. However frightening that was to consider.

"I understand what you are trying to say Tiger, but you are implying that a human child possesses more powerful chakra than the strongest entity humanity has ever come across." Spoke Hiruzen in a tired and weary voice, it is not often so much happens in a single day after all.

"I have heard enough theories for today Tiger." Spoke the Sandaime "Especially ones such as these. Return to the hospital and notify me as soon as one regains consciousness, hopefully we can find an explanation to all that has happened."

"Hai, Hokage-sama!" Tiger said before disappearing.

Hospital: same day. 7;00 pm.

As Naruto slowly awoke, he became aware of two things. The first, he felt amazing, truly his body had never felt so unrestrained and powerful before. The second, he was not alone. Slowly opening his eyes so that they may adjust to the light, he noticed two figures standing by his bed and conversing quietly.

"Hokage-sama" Came the harsh whisper of his voice, trying to draw the attention of the man. Almost instantly, they were by his side. The Hokage had an expression of relief on his old wrinkly face, he could not see the other mans, as it was hidden by an animal themed mask.

"Naruto-kun" He began slowly, giving the boy a chance to adjust before continuing "How are you feeling my boy?"

"W-What happened?" he managed to choke out, even though he felt amazing, his body was very fatigued. Why and how, he didn't know.

"Do you not remember?" The Hokage asked with confusion etched on his face "You drew upon your chakra, and the results were very surprising."

Now it was Naruto who was confused "Chakra?" He asked, "I am afraid I do not know what that is Hokage-sama." He was quite sure he had heard the term being used before, but he had no clue as to what it could possibly mean.

The Hokages face faded from the relieved and confused expression it held before, only to set itself into a very neutral and unreadable one.

"Do not play games with me boy." He said in a very sharp tone "What has happened because you decided to get a 'head start' or other such nonsense is a very series matter."

Naruto was quite surprised at the tone of voice the Hokage was using, but decided defending himself was the only course of action open to him at the moment.

"Hokage-sama, I can honestly say I have no idea what happened."

"What happened?" the Sandaime basically shouted "Damn near half the orphanage is nothing but rubble is what happened!" The Hokage was angry now, Tigers theory made far too much sense, and he needed answers to put his mind at ease.

Knowing that shouting would get him nowhere with the boy, he tried his very best to calm himself as much as possible and spoke in the friendliest tone he could "Naruto, you need to listen to me now, I need to know the name of the person who told you about chakra and how to unlock it. You also need to explain what happened when you did so."

But he wasn't listening, his mind was stuck on two words 'orphanage' 'rubble.'

"Where is Mito!?" he suddenly shouted, surprising himself and the others in the room at the forcefulness in his voice.

The Hokages face softened slightly at his question "She is in the room next to this one." He replied hoping to get this out of the way so he could get the information he needed from the boy.

Jumping of the bed and running towards the door as fast as he could, surprising both the ANBU and the Hokage at just how quickly he was moving.

'He was never this fast!' the Hokage thought in wonder.

'How is a five year old child moving at low chuunin speed!?' The ANBU questioned himself silently.

The slight pause was enough for Naruto to bolt out the door and into the next room. He stopped dead in his tracks when he saw Mito lying on the bed motionless, slowly approaching the bed he noticed a faint mark on her right arm, eyes widening slightly 'Was that because of me?' He questioned himself.

"She is fine. Her body is just resting from her recovery." He heard a voice say from behind him.

Turning, he saw the Hokage staring at him intently, although it was hard to tell with the ANBU.

"Did I do that?" he asked quietly.

The Hokage nodded, he wasn't going to sugarcoat the situation. He needed answers from the boy and if that meant breaking down a few emotional barriers then so be it.

"Naruto, you need to tell me what happened. Half of the orphanage has been destroyed and your sister was injured, what exactly happened, I want to know everything."

Naruto slowly nodded his head, taking a few moments to get his thoughts in order he began.

"Mito and I were both alone in the orphanage, she was reading a book and I was thinking." Here he hesitated slightly "Thinking about why we are treated differently to the other children who live there" At this, the Hokage flinched. "But I couldn't figure it out, it's like the answer was right in front me but I just couldn't grasp it. I remembered reading something about meditation and how it helps clear your mind."

It was at this point the Hokage started piecing together what exactly had happened. And it wasn't exactly helping to ease his mind.

"But when I attempted it, something else drew my attention." He stopped to try and find words to describe what exactly it felt like.

"Like a tiny ball just behind your navel, correct?" The Hokage tried.

Naruto nodded "Sort of, it actually felt really big, as big as my stomach."

The Hokage looked towards the ANBU member, who was staring at the boy with what he assumed was shock behind his mask. What the boy was describing should be impossible, chakra should not be so dense or concentrated, even when he felt out his own chakra, it was only around half the size the boy just described, even considering the difference in their size and mass. But considering the damages done to the orphanage and the state of panic the village was in, he could do nothing but believe the boy.

"That is the energy we call chakra." Hiruzen explained. "And you are sure no one explained chakra and the way to unlock it beforehand?" The Hokage questioned him.

A simple shake of the head was his answer.

"It actually felt like there were two different kinds." The boy suddenly stated, causing the ANBU to tense. The Hokages face returned to the neutral expression from earlier.

"Explain!" He ordered

"Well, after I let the first one move around freely I felt a second one. It was even larger and" he paused searching for the right words "It felt more uncontrolled and… Thicker than the first one did."

The Hokage was almost afraid to ask, but he did so anyway. "How much larger?"

"I don't really know Hokage-sama, while it was larger than the first it also felt different. It's like comparing the ocean to a lake."

There was a sharp intake of breath and the Hokage turned to see Tiger standing as stiff as a board. Only through years of dealing with situations and seeing things that would break any other man, was he able to stay relatively calm. On the outside at least, it was the first time dealing with a situation such as this after all. And as such, his thoughts were traveling a mile a minute, doing his best to comprehend what exactly this child was telling him.

"I see." he said. With a little more force than he had intended. "You may wait here for your sister to wake up, when she does I expect both of you in my office Immediately."

"Come Tiger, we have much to discuss." And with no further exchange of words, both disappeared from the room.

Underground base: several hours after the incident.

As he walked along the dark hallways where he spent most of his days, his cane cracking against the ground every time he took a step, a small smile made its way onto his bandaged face. Today was the day he would get something he had been craving for a long time. After years of waiting, his patience had finally paid off.

Reaching his destination, a large hall with a single thrown like pedestal at the very back, situated at the top of a short flight of stairs. As he made his way towards it a single man dropped down in front of him.

"My lord, your guest has arrived and wishes to speak with you." The man in an ANBU uniform with a tipples tanto and blank Wight mask spoke.

"Excellent." The man with the cane replied "Send him in immediately."

The man disappeared with no further exchange of words.

As he made himself comfortable on his thrown, he couldn't help but feel excited. He had been waiting so long for this day, and it had finally arrived.

He watched silently as a man clad in a black uniform with a few lines of red thrown in walked towards him, diligently followed by the blank masked ANBU, eyes of red and black glowing as he did so.

"I see you have finally arrived." Spoke the bandaged man "Do you have it?"

The man with the red eyes nodded slightly, showing him the sealing scroll he held in his hand, with a flourish he unsealed its contents. A single jar with two eyes, exactly like the man's own.

"I have the eyes as promised, if you fulfill your end of the bargain you shall receive the rest of them as we have agreed"

The bandaged man smirked as he gazed onto his prize with his single eye 'not for much longer' he thought. But he had one more thing to confirm.

"And you are sure these are the eyes if Shisui?" he asked.

The other man nodded "I would know, I removed them myself."

"Very well then." The one eyed man said "Although I am not complaining, rather curios as to why you approached me? I would have thought that you of all people would have attempted this sort of thing alone."

The other man spoke with slight disdain in his voice "While I am confident in both my clan and myself, I am not stupid. If we went up against an entire village we would surely be slaughtered, I came to you because I have heard very interesting whispers of your… expertise, pertaining to matters such as these."

A small smirk graced the other man's face "very well, until we meet again. Fugaku."

"To you as well, Danzo."

Mito's mindscape:

"Onii-san!" Mito called out once again, her voice echoing along the empty corridors she currently found herself in. For the past twenty minutes she had been aimlessly wondering through intersecting hallways that seemed to stretch on forever with no end in sight. She was currently pondering how she got in here, it appeared to be a prison, with cast iron doors around every corner and along every hallway. But what really drew her attention were the two pipes lined on each wall. The first was very large and seemed to be leaking a red acidic like liquid. Every time a drop touched the floor it would hiss and a small cloud of smoke would be released into the air, only for the ground to almost immediately seal over, the first five minutes she was here she simply watched the process repeat itself over and over.

Quickly becoming bored of the repeated phenomenon, she began to search for a way out. And more importantly, find her brother. She paid no attention to the much smaller pipe directly underneath the first, as it did not seem to be doing anything out of the ordinary.

She was quickly becoming bored of the endless walking, with no exit in sight and no idea where Naruto could possibly be, she slumped against one of the walls slowly sliding down to a sitting position.

The last thing she could remember was her brother radiating that powerful and frightening energy. She could recall how scared she was at that moment. But at the time that was just an insignificant thought at the very back of her mind, telling her to run while she still had the chance, to get away from the overpowering energy being released by her brother. But her mind was overcome with the concern she had for him, if she had felt the way she did, she didn't want to think what it was like right in the middle of it all.

But thinking of the smile that had made its way onto his face truly put her on edge, it was almost like he was enjoying it. But that couldn't be the case, could it? The energy and the feelings that had accompanied it were terrifying. All she had wanted to do was latch on to her brother and beg him to stop, but she was unable to at the time, she had been rooted to the spot in fear and the instinctual desire to flee.

Broken from her thoughts as a warm gust of air hit her in the face, she immediately stood. That was the first current of air she had felt since waking up, quickly deducing that it must be a way out she started rushing towards the source, turning down random corridors and following the warmth the air provided. Although she did feel that something wasn't right, the air came in precisely timed bursts that did not seem completely natural.

Turning another comer she saw a bright light at the very end, smirking as she thought she had found a way out she picked up as much speed as she could.

Only to come to a grinding halt as a feeling of pure evil and terror washed over her. In front of her stood massive bars, stretching farther up then her eyesight allowed her to see, each bar seemed to be as thick as a fully grown man, and right in the middle of it all was a single slip of paper with the kanji 'seal' on it.

As she was staring, completely transfixed by the scale of such a thing, two blood red eyes slowly opened behind their cage.

"So it seems my container has finally decided to grace me with her presence. Tell me mortal, how long has it been in the outside world?"

Mito could only stand there in shock as she gazed into the eyes of the terrifying beast, unmoving and unable to form a coherent sentence as her mind drew a blank.

"Speak mortal! For you are trying my patience" The beast spoke in an agitated voice, as it did so light seemed to flood in from behind it, allowing Mito to see the head of a fox, and nine tails flickering behind it, each one thicker and more intimidating than the bars that bound it.

" I-I uhm, w-what are y-you?" Was the only thing she could say at the moment.

The beast's eyes narrowed as she asked the question, almost expecting it to lunge and tear her apart. So she was genuinely surprised when it answered.

"I am the strongest of the nine Bijuu" It said in a loud and booming voice purveying the sheer size and magnitude of the entity "The one you humans saw fit to call the nine-tails"

Mito's eyes widened at the implications and she took a step back in fear. If this was truly the nine-tails, why was it here?

Wherever here is.

She decide to ask just that "W-Why are you here? The Y-Yondaime Hokage killed you five years ago!"

"So it has been five years" he beast said under its breath, but to her, it might as well have shouted for all the difference it made.

As it turned its attention back to Mito, there was a glint in its eye.

"Very well mortal, since I have nothing else to do and no way out of this cage, I shall tell you about that night. And perhaps we can even come to some sort of… agreement."

At this, its face twisted into an ugly mockery of a smile, a truly evil and terrifying sight to behold.

"Just know this, all is not as it should be."

Hospital: soon after Hiruzen left.

Naruto had been patiently waiting for his sister to regain consciousness, resting his head next to her on the bed whispering silent apologies. It had only been a couple of minutes since the Hokage had left him with her.

"I did not think you would be so close to her" a voice suddenly rang out directly behind him.

He jumped, quickly spinning around to assess the threat the person who spoke posed to his welfare. Only to be given pause, for standing directly in front of him was the strangest man he had ever seen.

He was garbed in a pitch black cloak with what seemed to be a plant growing out of either side of his neck, stopping just passed the top of his head and green colored hair. But the strangest thing was the man had two very distinct colors of skin, splitting his body perfectly in half, one side pitch black, and the other a pure wight.

"My my, so jumpy" he spoke with two very distinct tones of voice.

"Who the hell are you?" Naruto spoke with fear in his voice. This man could have easily killed him if he so wished.

"Me? Well, I suppose you could say I am a close family friend" he said with a smile on his face.

"The only family I have is Mito" Naruto responded with an edge to his voice.

The man looked confused "She did not tell you? I suppose it does not truly matter. But still, I wonder why?"

"Who are you!?" Naruto asked with much more force and venom in his voice this time.

"Who, Me?" The plant man answered innocently "You can just call me Zetsu." He stated.

"What do you mean by family friend?" Naruto asked.

"You shall find out later, when she deems you ready." Spoke Zetsu

"Who is it you are talking about?" Said Naruto narrowing his eyes.

An amused smile spread across Zetsu's face, just imagining what Naruto's own would look like after his next statement.

"Why, the woman who spoke to you after your little episode of course"

He was not disappointed, the look of shock that spread across his face was priceless.

"How do you know about that?" Naruto shouted, "I haven't told anybody anything about that!"

"How I know does not matter, if she chose not to tell you than it is not my place, but I am her will that has been given life. And you are the one who will bring her dreams to fruition."

Before Naruto could reply or ask any more questions the man threw a scroll at him before sinking into the ground leaving behind no evidence that he had ever been there.

Glancing down he saw the single word that was printed on the very front of said scroll.

Shikotsumyaku.

Chapter 3: end.

(AN) As I said in the beginning of the chapter, please let me know how long you want me to make them in future. I hope this chapter was up to standard.

Next chapter will feature a three year time skip, all loose ends will be explained in flashbacks or in the story itself.