Conundrum

Disclaimer: I do not own Naruto.

Summary: Naruto is no longer a part of the Leaf. Where has he gone to all these years? No one heard of him for quite some time. What happens when he returns for a visit and bearing a few 'gifts'. Life is just a series of questions that need answering.

Formats:

"...Speech..."

'...Thoughts..'

"…Disembodied Voices…"

Chapter 3: Excogitation

Still Two Years Ago

Urrgh, his aching head. Jiraiya is accustomed to being clobbered; being a ninja of his caliber he was always given difficult and dangerous missions and got beat up real bad. But they were always for a good reason. All those time when he was trampled by angry women at the bath, the reason was also there, even if it wasn't a good one. When dealing with Tsunade however, he never knew the reason, he got his butt handed to him anyhow. Now of all times, he can't vent on his student as he lay unconscious on the bed before him.

Tsunade took a few deep breaths to calm herself down. Trust the old pervert to be cryptic at a time like this. How can he be so cavalier about this when the seal might be the reason Naruto is in this induced coma and Kyuubi's chakra not regenerating him as it did before. "Now will you tell me what this stage two is all about? Give me a cryptic answer again and I'll make sure your readers will receive bits and pieces of you included in the next volume of your book."

"Okay, Okay, calm down will you? Sheesh, you and your monstrous strength is going to be the death of me." Jiraiya promptly picked himself up from the floor dusting his clothes all the way up. Seeing Tsunade's eyebrow twitch dangerously, he quickly settled into his 'serious' explanation mode. "Well, contrary to popular belief, the seal that Yondaime used was more than just one level. It's entirely different from what Sarutobi-sensei used against Orochimaru. The seal that holds Kyuubi have three levels that 'upgrades', so to speak, when certain conditions are met. Even if the seal does not go into later stages, Naruto will still take Kyuubi to the other side when he dies."

"So you're saying that this is all planned even this induced coma of his and the absence of Kyuubi's excess chakra. That can't be right, Yondaime would never do something to endanger Naruto. And what did you mean when you said Kyuubi was put to rest."

"No, no I don't think the seal is the cause of the coma, at least I hope not. You see, when the conditions are met, and the seal goes into transition from stage one to stage two, it cut off the connection between the sealed and its host. Then the seal attempts to eject the Kyuubi's soul and consciousness, leaving its essence and powers behind in the seal. This ultimately kills Kyuubi but leave its chakra behind. In theory, even if Kyuubi died with Naruto, he would still be able to resurface in this world in a few centuries because its powers still bound to it and goes with it when it dies. Stage two attempts to separate them, which again in theory would render Kyuubi powerless when it pass on and would take many millennia before it can return to this world, if it ever does again that is."

"So this means that Kyuubi is really gone for good or at least for long time anyway. But why does it cut off the chakra from Naruto. The chakra could have healed Naruto and if the condition for the stage two to activate is to have Naruto go through a life threatening ordeal then it would have been a more logical to give Naruto access to Kyuubi's chakra so that he can heal faster." Tsunade was relieved to hear the Kyuubi's demise but at the cost of having Naruto so close to death is not a pleasant thought.

"No, I don't think that his injuries are what activated the transition. Honestly, I don't really know what the condition is. The restriction to Kyuubi's chakra was there as to not only make the separation easier, but also to ensure it does not flare out of control and burn Naruto to a crisp. Once the third stage is achieved he will once again able to access the chakra. I don't really understand the mechanics of the third stage but Naruto would be able to use the chakra as his own. But when will that be I don't know for sure. My best guess is when he comes out of this coma, whenever that is." Jiraiya bend over to take a look at the seal again. "By the looks of it, the seal is in the final form of the second stage, which means Kyuubi is already gone. His coma is possibly caused solely by his injuries and exhaustion or there might be some other functions of this stage that Arashi had failed to mention to me."

"Hmmm, I don't think there's much we can do but wait for him to wake up on his own then. I'm going to place him in a private room in the new ICU wing so that I can keep him closely monitored. And the new ICU have chakra buffer that prevents chakra detection from the outside. If he flares up with Kyuubi's chakra, it wouldn't cause too much of a panic."

"So what are you going to tell the village now that Kyuubi is most likely gone? If nothing else it will give Naruto an easier time."

"We tell them nothing." When Jiraiya looked enraged, she quickly tries to clarify. "You know that most of the villagers, even most of the clan council, believed that Naruto is the Kyuubi. They didn't believe that the seal could contain such demon and must have surely taken over Naruto the moment it was sealed. Some of them had gone as far as saying that Naruto is the human form of Kyuubi. I've read Sarutobi-sensei's journal, if it wasn't for the Hyuuga, the Uchiha and the Aburame's support, the third would never have been able to keep Naruto alive when he was a baby. Even then the villagers have tried on many occasions to have Naruto executed. Now if we said that Kyuubi is gone, they would simply rationalize what they said in the beginning were true. Even your word won't be able to stay their hands this time. We must tread lightly over this matter; it could turn into a disaster."

Jiraiya sighs dejectedly knowing what she said was true. It's sad to realize that even the village he always hailed as one of the greatest ninja villages ever existed have such fault. "You're right. I just wished that Naruto could have a better life than he has now."

"I know, I wished for the very same thing. He saved me, more than just my life; he saved my heart. He brought me back from my self-imposed hell and willingly placed me in the circle of those he calls his precious person and let me do the same for him." She looks at Naruto fondly, watching her little brother sleep a sleep he couldn't wake from for quite awhile. 'Hope your life will be easier from now on little brother, without the weight of the world holding you down.'

xxxxxXXXXxxxxx

Naruto blinked. It was bright, but not too bright as to hurt his eyes. He wondered where he was, the last thing he remembered was grumbling saying Kiba should go on a diet and take a long shower. Now he's nowhere around him. He finds himself on a grassy slope overlooking a lake. He didn't recognize the place and was sure that Konoha don't have plains like this. Could he be dreaming or worst yet, did he die and went to heaven. He couldn't imagine heaven being so empty. And a dream wouldn't be this vivid; it's like the time when he appeared at Kyuubi's cage but with a more beautiful view.

"Naruto…."

What the. Whose voice was that? Certainly not the Kyuubi's, at least it's not what he remembered Kyuubi's was like. It always growled and snarled more and it never calls him by his name. He looked around and saw no one. "Who are you? What do you want?"

"You have done well…"

"All right, enough with the hiding. Show yourself." He jumped to his feet still looking around him for the source of the voice. Suddenly the air in front of shimmered and glistened, taking form slowly like the air itself molding, condensing into a shape of a man walking towards him. The man walked until he was a few feet in front of him, now fully formed, Naruto recognize him immediately. "What the hell are you doing here!"

xxxxxXXXXxxxxx

Morning had come at last. Shikamaru is really not a morning person, especially not when sleeping in an uncomfortable couch with the incessant beeping noises keeping him awake for the better part of the night. After the troublesome mission yesterday and waiting for news on Naruto and Kiba all day afterwards, Shikamaru had felt like retiring from active shinobi duty early. He settled for retiring to bed early, so he slept in Chouji and Neji's room at the hospital only to be awaken a few hours later when they moved Kiba into the room. Hearing the news that both Naruto and Kiba were fine had brought him great relief, so he snuggled back onto the couch and slept cursing the additional beeping noise added to the already annoying orchestra.

The only reason he's awake now is because of the commotion in the room from families coming in to fuss over their children. He quickly slips out of the room to get some fresh air. As he went out the front door of the hospital, he stumbled upon Ino and Sakura. He sighs, another round of twenty questions, how troublesome.

"Hey Shikamaru, we heard that they found Kiba and Naruto. Are they both okay?" Ino looked cheerful but her voiced were laced with worry. Sakura on the other hand looked depressed, probably because of the failed mission.

"Yeah they're fine, though Naruto is in a coma, Tsunade-sama don't really know when he'll wake up. I'm not surprised though, with the hole through his chest he was barely alive when they brought him in, I've heard." Shikamaru immediately regretted blurting out that way, seeing Sakura becoming more distressed at her teammate's condition. Without a word she quickly rushed into the hospital. Shikamaru threw an apologetic glance towards Ino but she just looked at the direction Sakura had gone looking a bit sad.

"So how are the others?" Ino finally asked.

"When I left, Chouji was playing tug-of-war with the nurse using a bag of chips in place of a rope. Neji's awake but still delirious probably because of the painkillers. Kiba was still sleeping and I don't know where Akamaru is probably with Kiba's family. Haven't seen Naruto yet." Shikamaru answered simply. Ino smirked slightly thinking about Chouji's fixation on potato chips. While she was glad that the others were on their way towards recovery, she was also saddened for Sakura with one teammate gone and another laid out in a coma.

xxxxxXXXXxxxxx

"What the hell are you doing here!" Right in front of Naruto stood the Yondaime Hokage of Konoha, Kazama Arashi looking exactly as he did in the picture on the Hokage's office wall. Here stood the man who sacrificed himself to protect the whole village from the demon Kyuubi. The very same man who had sealed the said demon in his belly. The man he both admired and despised for he had done to him. "Isn't it enough screwing my life once already, you're coming back for a sequel or something?"

"Nothing of the sort, Naruto. I'm truly sorry it turned out like this, but it was not my intention to ruin your life. What kind of man would I be if I truly intend that upon anyone, even more so upon you … my own son."

Naruto's brain stopped working at that moment. All those time he wished he had a family, wondered why no one was willing to adopt him and his constant attempt to pester the information about his parents from old man Sarutobi, never in a million years would he even consider the scenario that he is the fourth Hokage's son. He tried to get a word out but couldn't decide what to say; what can he say to the man that cursed him with the life of misery and loneliness. Even less when the man had claimed to be his father. No matter how much he wants to deny it all, he can see it in his eyes. The brutal truth is laid out to him. "Y-you're my father? That can't be right, Sarutobi-jiisan or Ero-sennin would've told me, wouldn't they?"

"No, I made them promise not to tell you. I wasn't sure if I could manage it but telling you all of this is my responsibility; as your father and as the one who sealed Kyuubi in you."

"B-b-but why did you chose me? No father would do something like this to his own son."

"What choice do I have, Naruto. I was in a lose-lose situation. If I didn't seal the demon everyone including you would die and if I seal the demon within you, you will be put in a precarious position. At least with the lesser of two evils, your chances of survival would be higher." Arashi took a deep breath (not that he needed any). He could see that Naruto is still not convinced, still saddened by the fact that he had to carry the burden all his life and that only now he had some sort of an explanation. "You don't know how much I wanted to avoid all this, but I can't seal it in an adult, they would be killed immediately and Kyuubi would be loose once again. I can't ask anyone else to sacrifice their own children. I'm the Hokage of Konoha, and even if I'm not as a human being how can I ask someone to sacrifice what I myself was unwilling to sacrifice. And I….I believed that you can do it, you can endure and become a better man because of it."

Naruto slumped to the ground. He didn't think he can stand properly with all the information being unraveled to him for the first time in his life. He's hopelessly confused torn between being happy he finally found out about his family and being mad that his own father put him in the twelve years of hell everybody but him called life. Arashi took pity on him by not saying any more and just sat down beside him and wait for him to calm down. They both sat in silence for what seemed like hours, quietly digesting the information.

"So…what are you doing here anyway? Don't tell me I'm dead."

"No, you're not dead. I'm not really here exactly. You see when I sealed the Kyuubi, I also sealed a copy of my memories and personality matrix into you set to be activated once the seal reached stage two. I am a facsimile of my real self intended to guide you while undergoing this transition."

"What transition? Am I going to be sprouting tails now or grow fur all over my body?"

Arashi chuckled a bit at his son's overactive imagination. "You do realize do that Kyuubi is gone now. All those changes to your body whenever you used its chakra won't appear anymore. After twelve years you're finally free of the burden of being a demon vessel."

"What! How did that happened. I mean how could a powerful demon suddenly up and disappear and why couldn't have done this the moment you sealed him away? Could've at least saved me the trouble." Naruto's face goes through every facial expression known to man during his outburst. Somehow, while he always cursed the ancient fox for tormenting his life, he has gotten used to its presence and a little sad that now he is truly alone.

"That's the main purpose of the seal. To get rid of Kyuubi for good or at least a very long while before it can re-manifest into this world, I have to render it powerless before killing it. Thus the seal that I used on you, a complex three stage multiple layered seal which I must say my greatest accomplishment to date." Arashi had a proud look on his face at which Naruto rolled his eyes with a snort. Arashi just ignored it and went on. "To which still overshadowed by my involvement in bringing you into this world. My seal may have imprisoned the Kyuubi but it was you that made it possible for the seal to destroy the Kyuubi. I'm proud of you son."

Naruto turned to face Arashi, his face slowly break out into a goofy grin. A few drops of tears can be seen trickling from the corner of his eyes. "You don't know how long I've wanted to hear that, and coming from my father made it even more special, even if you're just a copy."

Arashi returned the grin. "So we're cool now?"

"No we're not…" Arashi grin faltered at Naruto's words. Was what he did so terribly cruel and unforgivable? He let his head droop towards the ground. "Not until you teach me some of your jutsus."

Arashi's head shot up at the statement. "That's blackmail!"

xxxxxXXXXxxxxx

Sakura had been sitting beside Naruto's bed for hours. When she first got into the hospital asking for Naruto's room, the staff had declined and said the Hokage disallow any visitation for the boy who is still in serious condition. Sakura did not take that very well and went as far as demanded with the Hokage to allow her to visit her teammate. After fifteen minutes of full-blown argument between the two (which she couldn't believe she did that, god what was she thinking yelling at her superior), Tsunade relented only to have Sakura nearly fainted at the sight of her badly injured teammate. After Tsunade assured her that he will be fine with time and rest, she calmed down a little and sat near the bed.

Sakura almost yelped in surprised when a hand landed on her shoulder, so lost in her thoughts. She looked over her shoulder to see Kakashi standing behind her with a sad smile hidden by his mask but she could tell anyway. Sakura turned back to face her teammate, resigning to the fact there is nothing they can do but wait. She sighs sadly. Why does it have to be her team that was so messed up? They were great when they first started. She could easily say that their team is the strongest among the rookies even though she individually was among the weakest. Now Sasuke is gone in search for more power abandoning his friends, not without first rendering her other teammate bedridden. She was confused, as much as she liked to believe that she loved Sasuke wholeheartedly but can she truly love someone who would kill her in an instant when tempted with power.

Her parents didn't make it any easier for her. When they heard of the incident, they quickly cast the blame on Naruto just like everybody else in the village. So quick to judge even when they don't even know the real story. That had confused her, why did everyone that don't really know Naruto personally, so quick to blame him for whatever bad happened to the village.

She was like that once too, but mostly because he acted the fool during the times at the academy. After being with him and Sasuke doing missions as a team, her outlook on him began to change, though somewhat slowly. Now her thoughts on him had completely changed, he is the most dependable person anyone could hope for in a teammate, it didn't matter if he failed to bring back Sasuke for she knew he did no less than his best. He now had only needs to do his best to recover, so she can finally say thank you.

xxxxxXXXXxxxxx

"So, what's the deal with this place?" said Naruto as he motioned at the plains they were at. It's still confusing to Naruto as the last thing he remembered was dragging Kiba towards the general direction of Konoha.

"Ahh, this is your dreamscape induced by a space/time jutsu ingrained into the seal. Actually this was your mother's jutsu that she taught me, I just modified it a bit for the use with the seal."

"My mother…can you tell me about her? Was she a ninja?"

"She was not originally from Konoha. Came here with two of her friends a few years before you were born. She's a retired ninja because of some complications with her chakra system. I'll tell you more about her after we've done some significant progress with your 'training'. We have a lot of time to for reminiscing later."

"My training? If this is a dream world how can training does any good here, it's not like it affects my real body."

"Didn't I say that this dreamscape is a result of a jutsu? This jutsu is known as Yume Ryouiki no Jutsu, a space/time jutsu that create and place you in a virtual world while your real self is put into a temporary coma. This world reacts to the same physical laws as the real world but lies on a different timescale. You can spend years here but only a few weeks will pass by in the real world. Also whatever you do here, you real body will take into account and adapt accordingly, some fully and some to a certain degree. The only thing the jutsu does not affect is your age as it still follows the normal timescale."

"Okay…but why do I need this training other than for you to teach me some cool jutsus?"

"To explain that I need to tell you about the seal. Okay as I said before the seal is a complex three stage multiple layered seal that upgrades between stages when certain conditions are met."

"So I'm in this stage two thingy? What was the condition, I don't remember doing anything to the seal."

"Your resolve. While your chakra maintains the seal, your will empowers it. From your dream to become Hokage, to your willingness to fight for the village that shuns you and to the determination to save your friends even in the face of insurmountable adversity. That is the key; that is the trigger that sparked the moment you walked on the path to be a ninja and comes to full power just a few days ago. Quite an amazing feat considering your mother and I weren't there to guide you through life."

"I did that?" For the first time in his life he felt true pride. So this is how it felt to be praised by parents. He had never known such feeling.

"Yes you did. Now, as the seal goes into transition into the second stage, it cut you off from Kyuubi and its chakra, and then went ahead to separate Kyuubi's soul and consciousness from its essence and chakra. As you know no living being can survive without chakra, not even a powerful demon like Kyuubi. This 'kills' Kyuubi, if that is the right term and send it back to wherever it came from. Without access to its powers, it will not be able to rejuvenate fast enough to resurface upon the land until the next several millennia."

"And why is that? If the Kyuubi is so powerful, what's to stop him to regenerate and come back in the next couple of days? I always needed only a night's sleep just to recover from exhaustion."

"They really don't teach you much about chakra regeneration process in the academy, do they? Quite understandable as it is more of a Medic-nin level knowledge. Chakra regeneration process is kind of feedback system. Imagine your chakra reservoir as a water tank. The water tank uses a pressure pump, where you need to flow water through it to force more water from outside sources into the tank. To fill the tank with water you need the water already inside the tank to pump more water into it. Thus the more water the tank already has the faster it will be filled up. Do you get the picture so far?"

"Uhuh…" muttered Naruto while scratching his head.

"In simpler terms, you need chakra to produce more chakra. That is why people who suffers from chakra depletion takes quite a long time to recover fully as compared to people who lost only half of their chakra. Chakra regeneration is always exponential, the more you have the faster you regenerate." There is an exception to that statement as everyone has a limit as to how much chakra they can reproduce at any given feedback cycle. Although chakra regeneration rate usually goes up exponentially there is a point where it reaches constant regeneration rate.

"And people who have no chakra at all will never regain their chakra because there is nothing to feed upon itself."

"Exactly! You're really not as dumb as you pretend to be. In the case of Kyuubi, it may seem like it has almost limitless chakra, in reality its chakra reservoir is so large that the regeneration process is almost instantaneous, even when you use its chakra to do kage level jutsus the whole day. With the seal separating its chakra as it goes on to the afterlife, it will have no access to its chakra to regenerate. Kyuubi will still regenerate by some other means but it will take a very long time to replenish its chakra reservoir enough to breach the barrier between realities to get back to our world."

"That still doesn't explain why I need training."

"I'm getting to that. If the seal did not cut you off from Kyuubi in the process of killing it, you would've experienced chakra overload. The Kyuubi may be gone but its chakra is still kept within the seal, and without the consciousness of Kyuubi to keep it in check, you could burn to a crisp when the chakra flare out of control. Once the third stage is achieved you would regain access to its chakra, so to avoid from killing yourself I will train you to hone your chakra control. But remember, chakra control is also susceptible to emotional outburst, so you need to be taught how to keep calm and in control at all times. From what I can gather you're not a very patient young man, we will change that in your training."

"Hey, I resent that. I'm so very patient."

"Really, this is coming from a guy who yelled at a cup ramen for taking so long to cook."

"That's my stomach that's impatient not me!"

"I'm sure. Well you need to be more patient than that to control the chakra. A lot more. There is a difference between controlling yourself when standing still and when in full-blown fight. You could end up doing more damage to yourself rather than your opponent."

"So how long is this going to take? I mean, I can't stay in a coma forever, I still have to find a way to get Sasuke back from Orochimaru."

"Naruto, you have to realize that right now there is nothing you can do for Sasuke. You're not strong enough to take on Orochimaru. Even if you can, if Sasuke himself refused to return to Konoha, what will you do, force him to come back? You'll be the same as Orochimaru."

"He's being influenced because of the cursed seal! I know him, the real Sasuke would never abandon his friends, and he showed that already when we faced Gaara."

"Then train with me. Train to master your new chakra. You must realize your priorities; you cannot save everyone, or at least in Sasuke's case not immediately. You must know what is important and what is urgent. You showed that once already when you decide to save Kiba rather than charge head first to get Sasuke back."

"Okay, but you're still going to teach me some cool jutsus." Arashi fell flat on his face at that. He still didn't forget about those, did he?

xxxxxXXXXxxxxx

Elsewhere, a gathering was taking place discussing on none other than the vessel of the demon Kyuubi. A gathering kept from the prying eyes of others.

"He's in a coma. According to reports it will be weeks before he'll wake up."

"Do we grab him now or wait until he's up and around?"

"Trying to capture him now will only cause too much unwanted attention. We will wait until he comes to and preferably alone."

Author's Notes:

This came out a little late than I had hoped. It's been a busy week. Although late I do feel it was kind of rushed. There are some parts that I wish could have been better, maybe I'll update it when I got some time to re-edit it.

As always, the title is a bit obscure to some people I bet. 'Excogitation' means 'thinking something out with care in order to achieve complete understanding of it'.

Naruto will go through training with yondaime in between chapters, I won't go much into it as it will be revealed in later chapters what cool new jutsus he had learned. He won't come of the coma to become all powerful and as much as the Kyuubi chakra remaining inside of him becomes a trump card for him, it is also his biggest handicap.

I'm keeping a datasheet on the jutsus and stuff, some what is already common with my own interpretations to it but mostly are original. Do you think I should put it somewhere when the time comes as there is no combat scene as of yet?

Reader's Review:

One Azn Dragon Thanks for both the approval and the criticism. There won't be pairings that you hate so much (i.e. NaruHina or Yaoi) but there may be a twist to NaruHina but they won't go into any relationship. Sorry for the boring back story, just hold on for one more next chapter and then we will go ahead with the correct timeframe.

darkdragon24 Thanks for the offer to be a beta reader but I now have one. Who happens to be living in my neighborhood. Boy was I surprised someone that close read up my fic.

Madnarutofan Let me guess, you really hate history don't you. Bear with me, just another one next chapter and then we can Jedi duel to the death. Hope you don't hand-to-head combat, somebody threw his lighsaber at me and now it's stuck to my head.

Nakora-chan Kankurou didn't find Kiba because the time frame is a bit different from the anime or manga. In the anime by the time reinforcement came Kiba is already in the second leg of his fight with Sakon and Ukon, here he was still hiding until he came across Naruto floating in the river. I don't think Kankurou is that good of a tracker. About Naruto getting Kiba to Konoha, I want Naruto to learn to discern priorities. He must begin to learn what is more important, he can't afford to charge on to save Sasuke at the cost of someone else's life. I know the paragraph seems a bit long, I just often ramble on without knowing when to stop. Anyway thanks for the review.

Ninofchaos I was thinking of more towards NaruTem or NaruTen or some other obscure pairings, but not really sure which yet. I really don't like easy relationship, boy meets girl, girl likes boy, boy gets girl and live happily ever after. No, it will be a rough sailing.

DSecret eheh…that I am, evil that is. The clashing of Id, Ego, and Superego always has Id coming out on top.

Citan The chakra is still there, but right now, it'll most likely to kill Naruto if he doesn't learn to control it. He will become powerful but not immediately, there's a lot more to learn, but from what we see in the manga and anime if he keeps up the rate in which he is growing he will become quite powerful so why not in this story.

LbcLostKid, JohnnyG, ffgirl-07, Hunter Hatake, jpthug12, shina-lim, Hiei Girl 003 Thanks for the encouragement, hope you like this one and continue reading in the future.