Disclaimer: I don't own Naruto, go figure.

Posted: 8/30/08

A/N: Now that the intro chapters are out of the way, we can move into the nitty-gritty of the story. I hope that I didn't take too long in getting there.

As always, reviews are appreciated and help motivate me to continue writing in a (moderately) timely manner.

So far I haven't gotten any critical reviews. I'm not sure if that's a good thing or if everyone is just being too nice. Don't be nice. I can take it.

Chapter Title: Have You Ever Seen the Rain? by CCR.

It was Kyuubi, he was sure.

It had only taken him a few minutes to deduce that the strangeness that he was sensing was caused by a sealed bijuu, and the young Uzumaki boy was the only jinchuuriki that Konan would have encountered.

What puzzled him was why Konan had decided to bring the boy back with her. He had made it very clear that Akatsuki would not be ready to move for a good deal of time – possibly more than a decade – and that their main concern at this point was staying below the notice of the shinobi world.

Akatsuki was still new and still searching for worthy members. Though Madara had made it clear that he would not participate in the organization directly, he had provided a number of contacts that were beginning to turn into valuable associates. The elusive Zetsu. Kakuzu the Hunter. Akasuna no Sasori the great puppeteer of the desert. The Monster of the Hidden Mist – Hoshigaki Kisame. Even the traitorous Snake Sannin, Orochimaru, had been approached and expressed an interest in membership. They were some of the greatest criminals in history, and they were dangerous.

Pain would use them.

His thoughts shifted back to the problem at hand as he glanced down at the mountains of notes on his desk before him. Having the Kyuubi jinchuuriki here could not possibly help them. The technique he was developing to seal the bijuu was years away from completion, and on top of it all of his calculations showed that the Kyuubi - due to it's unprecedented strength – would have to be sealed last of all or the technique would almost surely become unstable. It's sealing was at least a decade away from Pain's perspective.

No matter. He would find out Konan's reasoning soon enough.

He began to meticulously clean his desk of the old sealing scrolls and newer notebooks containing his research, carefully placing them on the shelves covering the rock walls of this room, his study.

Konan would be there in short order with the boy and all would be explained.

"…Outside while I go let him know that you are here. Please be quiet and do not wander. I'll come out to get you in a few minutes, Naruto."

The Kyuubi for certain, then.

"What if someone else comes while I'm waiting?" The voice was that of young child, not yet five years old if Pain's intelligence was correct. It always was.

"No one knows about this place but us. Don't worry, you'll be safe."

The door opened and Konan's cloaked figure backed in through the door before closing it again and running her hand over the doorway, activating the seals placed into the wooden frame. She turned around and found Pain studying her from behind his desk with the intense scrutiny that she found only he possessed, as if he was peeling away her many layers of subterfuge with his eyes.

She had learned long ago that it was pointless to try to hide even the smallest things from him. He could see right through her. Then again, there wasn't much of importance that she ever did try to hide from him.

"Well?"

She averted her eyes slightly as the anxiety that she had been suppressing came back full force. "The mission was a success. Our new partners in Konoha have agreed to our terms and will begin delivery next month. I was also successful in tying up our loose ends. Takahashi was…"

"Konan." He pulled her eyes back up to his own. "You know what I meant."

She swallowed nervously. If there was ever a time before now that she had felt like a disobedient child being scolded by her parents, she certainly couldn't remember it. Yet here she was, caught with her hands in the figurative cookie jar, and by her best and only friend no less.

Pain sighed. "What could you have possibly been thinking? What purpose does bringing a defenseless child here serve? You know that we won't be able to extract the bijuu for many years yet, more than a decade most likely. It will take me that long just to complete the jutsu."

Konan looked up quickly, an almost angry expression on her face. It startled Pain a bit. He wasn't used to her showing him negative emotion. "I didn't bring him here to kill him," she practically hissed.

Pain's eyes narrowed at that. "And for what other purpose would you risk our organization's secrecy other than to obtain the power of the Kyuubi?" He asked it slowly, almost daring her to give another reason.

Konan straightened up impressively, not wishing to show any weakness even to her friend. "That boy's whole life was a despicable farce! No one deserves to live like he did in Konoha. You didn't see how the people looked at him, spat on him. He was living far worse than we ever did, Pain. I couldn't leave him there to suffer that."

"So you kidnapped him to what? Give him a better life?" Pain scoffed at that. "You knew what sorts of lives jinchuurikis lead. I didn't think you the type to cave in over one sniveling little brat. Perhaps you would rather open an orphanage to help disadvantaged children instead of trying to prevent the very wars that create those orphans to begin with?"

Konan was angry now. Angry and thankful that she had activated the privacy seals on the doorway. "Don't speak to me as if I don't understand what our purpose is, as if I haven't given everything for our cause! Naruto can be useful to us if we raise him to be our ally."

"That boy is going to die, and we are going to kill him. Or have you already forgotten that, Konan?" Pain was as calm and collected as ever - and it only served to anger Konan more.

"If we train him properly he can become more useful to us alive than dead."

Pain contemplated that for a moment. "We have no knowledge of how to train a jinchuuriki to properly utilize its powers. In any event, Madara would not stand for it. He seems obsessed with recovering the Kyuubi from within the boy for his own purposes."

"Then we won't train him as a jinchuuriki. We'll train him as a ninja. We can do that at least." Konan paused here and gave Pain her own piercing look. "And when did you start caring what Uchiha Madara wanted?"

Pain looked at Konan sternly. "I do not, but that does not change the fact that if we keep the boy here Madara will undoubtedly discover his presence and become overly curious. I wish to avoid conflict with that man if at all possible - especially this early in our campaign. Besides, he is a valuable ally to us." Pain's countenance softened a bit and he exhaled loudly before looking at Konan again. "What are we to do now? We cannot return him to Konoha without raising suspicions about ourselves. We cannot kill him without dispersing the Kyuubi. I have no way of knowing how long it will take to re-manifest itself. We could all be long dead by then."

Konan cut in quickly. "We will have to keep him here then - hidden away so that no one can find him - and create a story to give to Madara should he come calling. We may as well train him as a ninja if he is to be here for the next decade or more."

Pain frowned. "It seems you've planned this out carefully. Did you intend to corner me like this?" He shook his head slowly while trying to find another solution. Seeing none, he looked up again. "I have trouble believing that you took him simply because you saw a kindred spirit, especially when you seem so intent on giving the boy training. What makes you think he will make a formidable ninja? The boy is simply the final survivor the Uzumaki clan, is he not? A powerful history there, to be sure, but not nearly enough to catch your notice."

Konan grinned for the first time since entering the room and summoned her Bingo Book from up her sleeve. Quickly rifling through it, she found the desired page and handed the open book across the desk to a puzzled looking Pain.

"Namikaze Minato? The Fourth Hokage - SS-ranked ninja of Konohagakure, also known as the Yellow Flash. Hero of the Third Great Secret World War. Sealer of the Nine-Tailed Fox into its current container, Uzumaki Naruto. Hero of the Village Hidden in the Leaves. I know all of this already, Konan."

"His son."

Pain looked up from the book. "Pardon?"

"He sealed the Kyuubi into Uzumaki Naruto, his son."

Pain blinked, then cocked his head to the side. "You are sure of this? I wasn't aware that he had children."

"Naruto would have been his first I believe, and given the circumstances he would have been born on the day of his father's death. As the son of a Hokage he would have had many enemies."

"And so they gave him a false name and covered up his lineage to protect him, interesting." He closed the book and set it down on the desk.

"It's possible that he really is an Uzumaki and simply took his mother's maiden name."

"Indeed." Pain took on a thoughtful expression for a moment as he pondered this new development. "If what you say is true then he very well could become a powerful ally, and a loyal one. How do you know of his identity?"

Konan smiled conspiratorially. "Why don't I just show you?"

Pain quirked an eyebrow as Konan turned to the door and opened it. "Please come in now, Naruto. There's someone here that I'd like you to meet."

Naruto spun his head to look up at the doorway from his seated position against the wall of the corridor to meet Blue's smiling face. She beckoned him in with a few words of encouragement and Naruto followed cautiously through the door. He hoped that Blue's friend would like him.

Entering the room he came face to face with one of the strangest yet most imposing characters he had ever seen. The man was neither particularly short nor tall, but had a bearing that spoke of endless power and authority. Like Blue, he wore a black cloak decorated with blood red clouds that he kept buttoned from his waist to the collar. He had spiked, unruly hair much like Naruto's own, but instead of a golden blond his was a light red - almost orange - shade. The severe countenance on the rather youthful face was enhanced by a myriad of black piercings that occupied his nose, lower lip, and ears many times over. Most of all, Naruto was drawn to the piercing, ethereal, steel blue eyes that had no whites in them. Instead the entire eye was occupied by increasingly larger concentric circles that gave the appearance of someone having dropped a small stone into a puddle of mercury. They were unnerving.

The man studied him closely even as Naruto took in his appearance, a small smile gracing his lips, as though he were giving approval of Naruto.

"Naruto." The boy finally broke his fixation on the strange man and his attention found Blue once again. "I'd like to introduce you to my friend and partner. This is Pain," she indicated, gesturing to the man. "Oh, and I nearly forgot. Now that we're here, I can tell you that my name is Konan."

Naruto smiled at the woman he now knew as Konan and replied. "That's a very pretty name, Konan." He turned back to the man. "It's nice to meet you Pain. Will you be helping me train to become a ninja?"

Pain began to walk around the desk, picked up the Bingo Book Konan had given him and tossed it back to her. "That remains to be seen." His mesmerizing gaze still studied Naruto with intense scrutiny. "Take off your shirt."

Naruto was momentarily taken off guard by the strange request. "Wh-what?"

The next thing Naruto knew he was staring into the cold eyes of Pain, glaring mere inches in front of his nose. He gasped - or tried to - and it was then that he realized that he was suspended three feet off of the ground, grasped at the neck by the man called Pain. There wasn't even enough time for him to be afraid before the man spoke in his calm, steady, and deep voice. "Child." Naruto found that though he wished it, he could not tear his eyes away from those metallic pools before him. "You will do precisely as I say, precisely as I say it, or I will lock you in a small, dark cell and never let you out until the day you die." He paused for a moment to let his words sink in. "Do you understand?"

Naruto nearly panicked at his situation, but managed to compose himself just enough to answer. Though he was held by the throat, he found that the grip was not particularly tight or painful, and rasped out his answer fairly quickly and intelligibly, given the circumstances. "Yes, sir."

He was carefully lowered down to the ground, and as his feet touched the floor the tension in his body released just a bit. When he finally regained his bearings he looked back to his cloaked companions who he found were simply staring at him. He blinked back at them for a moment, before Konan gave her collar an exaggerated tug.

He scrambled as he remembered what he was supposed to be doing. Quickly tearing his dirty shirt from over his shoulders, he quickly placed it in Konan's outstretched hand. Pain nodded. "Now get up on the desk and lay down on your back."

Naruto turned to the desk - which his spiky hair barely reached the surface of - then looked back to Pain in confusion.

Konan giggled. Pain glanced at her and grumbled something unintelligible, then stepped forward to pick Naruto up underneath his arms and set him on the edge of the desk. "Lay on your back."

Naruto did as he was told, though he was quite nervous about what was going to be done to him. He watched the redhead's eyes narrow in concentration as they bore into his stomach and forced himself to remain still as Pain placed the fingertips of each of his hands on the sides of Naruto's belly, the bellybutton directly between them.

Pain glanced to Naruto's face for a moment before he spoke. "This will be uncomfortable."

And it was. Naruto's face scrunched up painfully as Pain started flowing his chakra into the seal. It didn't hurt so much as conveyed a feeling of wrongness to Naruto – as if something slimy and alive was creeping through his gut. Despite the discomfort, Naruto raised his head to look down at what was occurring. He was surprised to see dark tattoos appearing on his stomach centered on his navel that had never been there before. From his position he couldn't make out the designs well, but they looked to be in a strange language and drawn in a circle.

Having failed to determine what was happening, he looked back up to Pain who was studying the designs with a frown. As the minutes dragged on and nothing seemed to be happening, Naruto couldn't help but fidget slightly, drawing Pain's attention away from the seal. He released the pressure on Naruto's belly and stepped back while keeping his eyes fixed on Naruto.

"This is wrong."

Konan looked shocked for a moment before replying with a flustered "what?"

"This is the most complex seal I have ever seen - much different from any of the others that I've studied. It's not a simple jinchuuriki seal though. I'm just not sure what its purpose is…"

"But he is the one we're looking for, right?"

Pain glanced at the woman beside him and then back to the small child now sitting on the edge of his desk. "Naruto, you will need to go back outside for a few minutes."

"Alright." The golden-haired child held his arms out to the man before him who looked at him strangely for a moment, before again grabbing the boy underneath his arms and letting him down. Konan helped put the grimy shirt back on and the child scampered out the door, closing it quietly behind him. She hastily refreshed the seals on the doorframe and turned back to her friend, who was leaning comfortably on the edge of his desk.

"I've never heard of a seal like this one before, but it's a certainty that what's left of the Kyuubi resides in that boy."

"What's left?"

Pain crossed his arms and adopted a pensive expression. "Yes, the Kyuubi's chakra within the seal is incredibly unbalanced, as though part of it has been torn away. I would have to determine the exact jutsu used to seal the beast in order to find out why, but the fact stands." He sighed almost inaudibly. "Whatever it is that Namikaze did will make it incredibly difficult to extract the Kyuubi from the boy in any state. If what I fear is true then the Kyuubi truly will be destroyed upon Naruto's death. The seal itself is so complex and specialized that I'm not sure it can be undone. In any case, my jutsu will not be able to break it."

"I suppose it's a good thing that I brought him here then, is it not?" She gave him a slight smile of encouragement.

Pain nodded back, still in deep contemplation. "Yes, very fortuitous. Especially if we cannot recover the Kyuubi. If that's the case then our only options are to destroy the boy or recruit him. Having such a powerful influence working against us is unacceptable."

"And what will we tell Madara?"

"Simple. We'll tell him that I needed a proper jinchuuriki seal to study and that Naruto was the easiest to acquire. Madara is still operating under the belief that Kyuubi must be sealed last into my technique, which would have been true if the technique could extract the Kyuubi. We have plenty of time."

A hopeful expression grew on Konan's face. "Does this mean that you will agree to help train Naruto?"

Pain refocused on his close friend and frowned. "Are you really so close to the boy after so little time that you care about his well-being to such an extent?" He closed his eyes and shook his head. "Don't grow too soft Konan. If I agree to help you train him I will not go easy on him, and neither should you - for his sake as well as our own. You know what growing up in this country means."

"A childhood in the Weeping Country is nothing to envy."

"Precisely. He will have to prove his worth to us, and quickly. I will not waste my time on him."

Konan nodded. "Very well."

"Also, we cannot afford to shirk our own responsibilities in favor of a child who holds no worth to us now. Our plans must stay on track if we are to succeed."

"Of course."

Pain stood up off of the desk and walked around it, opening a drawer and removing a strange kunai as he did so. Konan's eyes followed it closely as he set it point down on the desktop, holding it in place with his hand. As he began to speak he slowly spun it, drilling lightly into the wooden surface. "Contact the quartermaster discreetly and have him supply Naruto with proper attire. We can have Naruto stay in the library so long as he does not ruin anything. I'll set up a cot for him."

"Do we have equipment for a child so young in our stores?"

"I ordered our raid groups to recover everything from the Rain supply depots we've assaulted. They have been thorough so far. I imagine that there is quite a lot of gear there that Naruto can use, considering he is our only young compatriot. It shouldn't be an issue."

"Very well." Konan's gaze was drawn to Pain's fiddling with the strange kunai. "I haven't seen you look at that in quite some time, did Naruto remind you that you still had it?"

Pain glanced up from the weapon to meet Konan's eyes. "I'm going to give it to him."

"What?" Konan had a look of disbelief on her face. "You can't be serious."

Pain smiled. "It's nothing more than an odd kunai now. The seals are damaged enough that they can't be used or deciphered. That's the reason why it wasn't recovered in the first place, after all." His smile shifted to a thoughtful look for a moment. "Every child wants something to remember his parents by, even if no such thing exists. Naruto may make good use of it in any case."

"Don't you want to study it more, to see what it does?"

"I know what it does, Konan. I just can't understand how it does it. There should be no way to reverse summon oneself, but somehow Namikaze managed to discover the secret. This kunai is of no use to me any longer."

"I just can't believe that you'd give away a legendary weapon like that," Konan replied, a petulant scowl on her face. She looked up after a moment and turned to the door. "I'll get Naruto settled in. Goodbye."

"Konan." At the sound of his voice the blue-haired woman turned back to listen. "No one, absolutely no one, can know that he is here outside of ourselves and Madara. I'd prefer it to just be us two, but there's just no way to keep this from him. Zetsu as well, in all likelihood. As of right now Naruto is our most closely guarded secret. Only the four of us are permitted to know. I will make sure that Madara and Zetsu understand this."

She nodded and gracefully exited the room.

Pain watched her leave and remained staring at the door for a moment, deep in thought. The famous tri-pronged kunai still dug slowly into the wooden desktop as it turned in his hand. It was nearly twenty minutes later that he finally spoke again, this time quietly and to himself.

"It wasn't the kunai that was legendary, Konan. It was the one who wielded it. Now we'll simply have to forge our own legendary weapon, greater than the last."

Konan led Naruto down a dimly lit hallway cut from the living rock of the hill they had entered before meeting Pain. It was only a minute before they reached an unassuming door, identical to the one leading to Pain's study and the few they had passed on the way here. Naruto resolved that he would learn to keep his directions straight while inside the bunker.

Inside the room - which was a fairly passable rectangle despite being hewn from solid stone - sat four long bookshelves jutting out from the back wall and filled from floor to ceiling with scrolls of all sizes. Next to the door was a small writing desk with a very utilitarian reading lamp and a rather plain cot.

"This will be your room for the foreseeable future. We don't have much extra space at the moment, but you won't be doing much other than sleeping in here anyways."

Naruto looked the room over carefully, spending extra time studying the bookshelves. "I've never had my own room before. This should be nice." He walked over and sat on the edge of the low cot and bounced slightly. It didn't have much give to it, but Naruto determined that it was as good as - if not better than - the lumpy bed he had slept on in Konoha. "How did you find this place?"

"Pain and I built it some years ago. Our own secret hideaway."

"Straight through the rocks? It must have taken a long time to dig it out."

Konan laughed lightly at this. "Yes, digging certainly would have taken quite a long time, but that's not what we did. We used our ninjutsu to tunnel into this hillside. We used skills similar to the fireball technique I used in River Country, but with earth instead."

Naruto's face shifted into a picture of awe. "Ninjas can use the earth too? You can do that?"

"I'm not particularly good at it, especially when dealing with bedrock like this. It takes a very powerful ninja with an earth affinity to manipulate dense stone in any large quantity. I usually just helped move the rocks and dirt out."

"Does that mean that Pain has a strong, um, earth affinity?"

Konan quirked her head to the side in amusement. "Something like that."

Naruto nodded slowly, but clearly wanted more of an explanation. He decided to hold off until later since Konan didn't seem willing to spill the beans just yet. "There are lots of scrolls in here. What are they about?"

"Hm… Pain spent a good deal of time collecting historical scrolls about the ancient clans, their histories, and rare abilities when we were a bit younger. Most of what you see here are those scrolls. I think there may be some on basic chakra theory and sealing somewhere around here as well." She turned to look Naruto in the eye. "Now Naruto, Pain has said that he will let you read any of these scrolls that you like so long as you do not damage them or misplace them. They are ordered carefully, so if you take any down to read you'll have to be able to replace them properly. Understand?"

"Yes, Konan," the small boy chirped with a smile on his face. It appeared as though he wanted to do some reading.

"Either Pain or I will be waking you up tomorrow morning, early. I expect you to get some sleep and be ready to begin your training in earnest. We will not be going easy on you at all Naruto. Remember that you told me that you would try your very hardest to become a great ninja. We will hold you to that. Now get to sleep."

Konan turned to leave the boy to his rest and moved swiftly to the door. Just before she closed the portal she was stopped once again by a voice. "Goodnight, Konan."

She reopened the door a bit and looked back inside to see Naruto already flopped on his cot. "Goodnight, Naruto."

Konan closed the door and placed her hand over a subtle seal on the wall next to the door and used a small burst of chakra to extinguish the lights inside the young boy's new room. She turned and moved down the corridor with a light-hearted smile and a barely perceptible bounce to her step. Tomorrow would be an interesting day.

"Wake up."

Naruto grimaced and covered his eyes as the lights flashed on around him. A loud complaint nearly escaped his lips before he clapped his hands over his mouth and frantically rolled off of his cot, thumping loudly to the ground. He scrambled to his feet and faced the voice, still trying to protect his sensitive eyes from the rude intrusion of the overhead lighting.

As his eyes adjusted they fell upon the face of Pain, the corners of his mouth quirked up in a small smirk. It was his voice Naruto had registered in the nick of time. Naruto wondered if he really would have been locked up had he retorted to Pain's command as he rubbed his eyes with the backs of his hands - one at a time, of course, so that he could keep the stern man in sight.

"I see you remember our conversation. That's very good." Pain turned to walk out the door and spoke without pausing. "Follow me."

Naruto wasted no time in complying, and followed the dark figure up the corridor in the direction that they had entered the tunnel complex from. They stopped again at another nondescript wooden door near where Naruto thought Pain's study had been. The tunnels were truly confusing.

"So that intruders are hindered."

Naruto's head snapped up towards Pain, who again sported a slight smirk. Naruto was about to ask how the man had known what he was thinking when Pain spoke again.

"Inside you will find a bucket of water, a cloth, soap, and fresh clothes. You will wash yourself, dress, and then meet me here. You have five minutes." Pain turned and started off down the corridor without a second glance.

Once the words had registered in Naruto's head, he quickly opened the door to find himself in a small, bare room. It couldn't have been more than eight feet to a side, and had only a small wooden bench as furniture. A wooden bucket sat on the floor filled with clean water and the soap and linens could be found on the edge of the bench. Naruto quickly stripped and began scrubbing himself thoroughly. He hadn't had a bath in two days and was truly grateful for the opportunity to rinse the grime of his journey off of himself. As he scrubbed, he noticed that the water ran down the imperceptible incline of the floor to a small gutter along one side of the room, where the water then flowed through a grated hole in the wall. He rushed to finish washing himself before Pain returned.

Ten minutes later - in which Naruto was introduced to a makeshift bathroom similar in design to the shower room and a room that he assumed was the kitchen based on the food he was supplied with there - found the small boy staring in awe at a massive cavern. He was dressed in a sturdy, long-sleeved shirt, pants, and a fresh pair of ninja sandals, all colored dark gray. The ceiling of the cavern - covered in the same mysterious lights Naruto had seen in the other rooms of the complex - towered high above the boulder-strewn floor. It was clear to Naruto that this room was all natural as there were no sharp corners or truly flat surfaces. The walls were smooth and slick with moisture while the ceiling and floor sported fearsomely sharp rock formations in the likeness of the maw of some ferocious beast. Naruto found that the light reflecting from the glossy surfaces gave off an ephemeral beauty that added to the otherworldliness of the cavern. It was a foreboding and wondrous place.

"Before you ask, no, Konan will not be joining us today. She is on a mission and will not return until sometime tomorrow." Pain paced a few steps into the cavern and surveyed it slowly. "This is our training room. No elemental ninjutsu may be used in this place under any circumstances. Is that clear?"

"Elemental ninjutsu… Is that like Konan's fireball and your, um, digging moves?"

Pain blinked and mentally berated himself for assuming that Naruto understood what he was talking about while simultaneously thanking the gods that the boy had picked up on his meaning already. "Correct. You cannot use such jutsus as of yet, but when you can remember this rule. It would be much too easy to cause unnecessary damage to this place if such skills were attempted here. We wouldn't want the ceiling caving in on you, now would we?"

Naruto gulped and shook his head.

"Good. Now, the first thing a ninja-in-training must do is learn to access his chakra. Do you know what chakra is?"

"I know that it's in everything and that we need it to live and that ninjas use it to do special ninja moves."

"Did Konan tell you this?"

"Um, a little, yes."

"Very well. Sit."

Naruto crossed his legs and plopped down with his back to a stalagmite to listen. Pain remained standing to begin what would be the first of many lectures.

"Chakra is the life energy that all living organisms produce. It consists of the spiritual energy found in all life combined with the physical energy of the creature's form. In our case, the body's health is a good indicator of physical energy. By combining both spiritual and physical energy, a ninja can create and mold chakra to perform a nearly unlimited number of feats that most beings have no hope of achieving. What separates ninjas and nin-animals from most creatures is the ability to perform this manipulation to produce a desired result."

Pain stopped when he noticed a puzzled look on Naruto's face. "Nin-animals are sentient creatures that occasionally form cooperative partnerships with ninjas. We will discuss them in depth further into your training."

Naruto's expression softened at that and he responded with a short nod.

"Ninjas must be conscious of not only their chakra as a whole but also their spiritual and physical states separately. A strong control of one's chakra is essential to being an effective ninja, and a strong control of chakra can only be achieved through a balance of both spirit and body. Neglecting one aspect of your chakra can result in poor or inefficient performance and low power.

"Because each person's body and spirit are unique, each person's chakra is similarly unique…"

It took nearly two hours of explanation before Pain was content with Naruto's understanding of chakra and its uses. Despite his fidgeting, the small boy was immensely happy that someone had spent the time to explain something in detail to him. He was even more elated that his questions were answered, and thoroughly, instead of simply being dismissed.

Pain was equally pleased. In his more than twenty years of life as a ninja he had never considered taking on a student of his own. Though he was a bit miffed that this one had been more or less forced upon him, the child was truly willing to learn.

Pain had learned long ago that many ninja didn't truly understand the fundamentals of what they did or the power they controlled. Perhaps it was a curse of his bloodline to see the intricacies of the ninja arts, but the man had become a perfectionist in every sense of the word where his chosen profession was concerned. And his student listened attentively to his complicated explanations. They were long-winded, he knew, but it would be worth it in the long run to make sure that Naruto understood the fundamentals thoroughly in order to prevent any damaging misconceptions.

Most of all, speaking with Naruto gave him an outlet for his thoughts and a slight distraction from the ongoing war that he was ferociously waging. Truth be told, Pain was a lonely man. He only ever spoke to Konan – who despite their closeness was often away on missions for extended periods of time – and his most trusted lieutenants – whom he forced himself to keep aloof from. It was a sad truth that Pain had only ever trusted three people in his life after the loss of his family. One had abandoned him and one had been killed thanks to his own foolishness.

So he no longer trusted.

Reluctantly he admitted to himself that the small boy before him could very well be his fourth trusted person.

"Stand up."

Naruto rolled onto his feet and stood up shakily. Hours of sitting on the hard rock floor had put his legs to sleep, so he found himself stretching and bouncing from one foot to another in order to get the blood circulating through his body once again.

"You're going to draw out your chakra now. Form the ram seal as I am doing."

Naruto watched as Pain brought his hands together palm to palm with the ring and little finger of his right hand curled over those of his left while his index and middle fingers remained extended. The boy then brought his hands together in the same position, paying careful attention to his fingers, then looked back to Pain's hands to check his work.

"Good. The ram seal aids in the circulation and molding of raw chakra, which can then be put to use in a multitude of ways. The seal on its own, however, does nothing. In order for it to serve its purpose you must consciously initiate the flow of chakra within you. This is done by first feeling the chakra within your body.

"To access your chakra you must feel within yourself for the natural flow of your energy and draw it out. Luckily you possess an incredibly high chakra capacity for your age, so this should be much simpler for you than for others."

Naruto seemed surprised by this. "Um, how do you know I have lots of chakra? Is that good?"

"I know for a number of reasons, which I don't wish to address today. Suffice it to say that I am well informed. As to your second question, a large chakra capacity is an exceptionally good thing for full-fledged ninja. It allows them to use more and stronger abilities in battle and contributes to a ninjas stamina – that determines the length of time a ninja can fight without becoming fatigued." He paused as Naruto's eyes furrowed and he unconsciously mouthed Pain's last word. He sighed. "It means to become tired."

Naruto's face brightened up at that. "Oh, I get it! So I'll be able to fight longer!"

Pain nodded. "Correct. Now, close your eyes and feel within yourself for the flow of your energy. I will bring you lunch in a bit. When you finish, I will be in my study. Come and find me when you accomplish this."

Naruto looked at him expectantly. "Third door to the right." The boy nodded and resumed his seated position on the ground as Pain turned to leave. He had more research to do if he ever intended to break Naruto's seal successfully. He found himself hoping that he wouldn't have the inclination to.

Pain cursed as he was interrupted from his work by a quiet knock on his door. It was late afternoon and the boy had only been working by himself for around four hours. He strode quickly to the door and opened it swiftly, gazing impassively down at the small golden-haired boy before him. "I have nothing else to tell you until you finish your exercises. Do not disturb me again." He began to close the door when Naruto spoke.

"I did finish, I think. I can feel my chakra now!" The boy was rather indignant, and it caused Pain to raise an eyebrow.

"Come in." He moved inside and around his desk to sit once more. Naruto followed and stood next to his chair quietly. Opening a drawer Pain pulled out a sheet of blank, white paper and drew a circle - only a bit larger than a golf ball - in the middle with his fingertip. The circle fell away from the rest of the sheet and he quickly picked it up off of the desk, stuffing the excess paper back into the drawer.

He turned to study the boy for a moment, taking in his curious gaze and determined posture. Naruto's forehead was beaded with sweat, as though he had been concentrating too intensely for a period of time. He leaned forward and wiped the moisture from the boy's brow with his sleeve, studiously ignoring the small flinch of the whiskered child.

"Draw on your chakra and focus it to your forehead, I'm going to perform a test."

Naruto nodded and placed his hands in the ram seal before closing his eyes tightly. "I'm ready."

"Very well, remember to focus your chakra to your forehead." Pain placed the circle of paper on the boy's brow and let go. The paper immediately popped off of the skin nearly an inch and fell to the floor. "Continue." He recovered the paper and placed it on Naruto's forehead once again, and once again the paper popped off before falling to the floor. "You may stop."

Pain was honestly surprised at the result. Even with Naruto's large chakra he hadn't expected the boy to succeed in finding his chakra so quickly – nearly as quickly as he had when he was twice this boy's age. Naruto's chakra was strong enough to push the paper away from him - which was the expected result of such an uncontrolled molding of energy. Sticking the paper to his forehead would be the next exercise – one taught to Pain by his old master – and would require Naruto to mold his chakra precisely so as to not push it away or lose his "grip" on it.

This spoke well of Naruto's talent. To grasp his chakra so quickly was extraordinarily rare. Still, his massive chakra capacity would cause him to be plagued by control issues for a great deal of time to come.

No matter. It was an excellent starting point in Pain's opinion. Naruto would be a worthwhile student.

"Naruto."

"Yes?"

"I am not sure how much Konan told you about our situation here, but if you are to be my apprentice then this information is important to you." Naruto straightened up and looked Pain in his steely eyes. "Konan and I currently lead a rebel army against the leader of this nation and his pawns. They wish nothing more than to destroy us completely. By joining us you too will become their enemy. Konan and I have no desire to see you harmed or placed into a dangerous situation until you are prepared to handle it. Therefore, you will remain inside this compound at all times unless accompanied by one of us."

Naruto nodded, wide eyed.

"You are here, Naruto, to learn, but do not expect me to accommodate you more than is necessary. My goals are already set and my time is precious. I will agree to train you so long as you show the ability and inclination to become a powerful ninja capable of helping me achieve my aims. If you fail in this then I have no desire to assist you - or tolerate you - in any form. I will give you the same consideration that my master gave me." Pain studied Naruto closely and was pleased to see that he still drew the boy's undivided attention.

"Three years. That is the amount of time I will give you to train and prepare you to serve in our cause. If your conviction is strong enough then it should be plenty of time for you to become proficient in the ninja arts. If not…"

The boy seemed to puff up as Pain spoke, causing him to gaze warily at the child. "I won't disappoint you, Pain. I promised Konan that I will be a great ninja, maybe the greatest ever, and I don't go back on my word!"

The older man stared at Naruto's proud and determined smile and gave a small nod. "That is good, Naruto. I would not want to be disappointed." He glanced around the room quickly, seemingly looking for something, before standing abruptly and turning to Naruto.

"Stay here." Pain left the room quickly and returned a few moments later with a simple wooden stool, which he placed in front of his desk. "Take a seat, we'll move on now to the basics of the ninja arts. Training is over for today, but pay close attention to what I tell you now because this information will be essential to you throughout your ninja career."

Naruto moved around the desk and clambered onto the tall stool. Sitting atop it he could easily see over the edge of the desk to Pain, who had retaken his seat behind the wooden fixture.

"Ninja abilities are divided into three basic groups, known as taijutsu, genjutsu, and ninjutsu. Each branch constitutes a different set of skills used for different situations and performed in different ways. What ties the three together is the use of chakra in each of the branches to achieve a desired effect. Believe me when I tell you that a thorough understanding of each of these three branches is essential to surviving as a ninja. A weakness in any one area could spell your death against a cunning adversary.

"Taijutsu is the branch which deals with physical attacks – generally hand to hand. Ninjas utilize taijutsu by channeling chakra to their limbs and body to enhance their strength, speed, and durability. Some ninjas learn extensive forms of taijutsu. We will not be doing this. I will teach you basic forms, strategies, and techniques in the usage of taijutsu and leave it up to you to develop a style that most suits your own body. Any ninja can learn to copy the instructions of another but only great ninjas can successfully create a style that suits them perfectly. Just as every ninja is different, every ninja's ideal taijutsu style is also different, even if only slightly.

"You will not be training to become a good shinobi, Naruto. I already have plenty of those under my command. You will be training to become an exceptional one. This means that you will have to influence your own training and style to a great degree. I could teach you everything I know and you would not be my match simply because my style would not be ideal for you, among other things. I expect you to put effort and creativity into developing your own style."

Naruto nodded in agreement. "Will I be using weights to train my taijutsu, Pain? I heard ninjas in Konoha use them sometimes. They sound really cool and help you become really strong!"

Pain snorted. "No, absolutely not. As I said, you will be training to be exceptional. Weights are simply an implement to develop one aspect of a ninja's growth at the expense of others."

"Um, isn't being stronger a good thing?" Naruto couldn't comprehend how that could be bad, but Pain was the master and he was the student. He would do as he was told.

"It's true that weights apply extra strain to muscles while they are on and can assist in muscle growth and development. However, wearing excess weight often fools one's body into believing that it is heavier or bulkier than it actually is. When the weights are removed the body becomes confused. As a result, ninjas who train with weights often ruin their natural reflexes and reactions. They are forced into learning a rigid style of taijutsu due to their lack of adaptability. Against an enemy of similar or superior skill these ninja are doomed to lose, and badly. We will not limit your abilities in such a way. The speed and strength gained through weight training can be achieved through other training methods that do not create such limitations."

"I understand. Um, do all ninjas know this?"

"On some level they probably do, but not all ninjas have the capacity to achieve true greatness. They make up for this by focusing on one area of ability despite the risks. In truth, this strategy works well enough for the great majority of ninjas. Still, by taking such a stance they will always run the risk of being defeated by a ninja who exploits their weaknesses. I expect you to show no weaknesses, Naruto."

"Yes, Pain."

"Very good. The next branch of ninja arts is known as genjutsu. Most ninjas would describe genjutsu as techniques used to create an illusion against one's enemies in an effort to promote confusion and misdirection." Pain watched as Naruto nodded his head emphatically.

"This is wrong."

Naruto stopped his nodding and cocked his head to the side, awaiting an explanation. "I prefer to classify the branches by the method in which they are employed and not their effect. It makes them easier to understand and defeat in battle. Genjutsu, by my definition, refers to the school of abilities in which a ninja uses his own chakra to influence the chakra within the body of his target ninja in order to confuse or fool the sensory organs of the opponent. Allow me to demonstrate."

Naruto watched as Pain's hands came together and blurred quickly before drawing apart once again and settling into his lap. Naruto frowned, believing that nothing had happened, when Pain's voice spoke from behind him.

"This is a simple genjutsu that I have cast on you. To you it seems as though there are two of me within this room." The Pain behind Naruto walked to him and placed his hand on Naruto's shoulder. "You can feel this, yes?"

Naruto gasped in surprise when the Pain across the desk from him reached forward and grabbed his right hand. "You both feel real!"

"And yet only I truly exist," said the Pain still seated in the desk chair. The Pain behind Naruto moved around him and sat on the edge of the desk facing the boy. "I am only a figment of your imagination. If anyone else walked into this room right now they would see only you and the real me sitting silently."

"How do I stop genjutsu?"

The phantom Pain disappeared while the true version nodded. "It will be some time before I am able to teach you to dispel any but the simplest of illusions. Now, tell me what the difference is between my genjutsu and this illusion ninjutsu."

Naruto didn't see any hand movement this time, but thought that he may have just missed it. Standing next to Pain was another perfect copy of himself, who proceeded to walk around the desk and stand in front of Naruto. Naruto looked at it closely but couldn't see any difference from the cloaked man in the desk chair.

"Why don't I give you a hint?" The illusion Pain then leapt into the air around three feet and fell down to the floor gracefully. As he landed, Naruto's eyes widened in realization.

"He didn't make any noise!"

Illusion Pain nodded this time. "Touch him," came from across the desk.

Naruto leaned forward and gasped as his hand went through the illusion causing it to shimmer and disperse.

"As you can see, this jutsu is only meant to fool one sense – that of sight. It creates an illusion by lacing the air with chakra in order to form an incorporeal replica of the caster. Any disturbance in the chakra structure of the illusion will cause it to become unstable, dispelling the jutsu. This is known as the basic clone technique, and is generally one of the first that apprentice ninjas learn. While it is an illusion, I do not consider it a genjutsu because it does not act directly on the opponent's chakra - only on the air that the clone inhabits. Do you see the difference?"

"Yup, I think I get it. Genjutsu tricks your body into thinking something is real that isn't, but that clone was really there, it just wasn't what it looked like."

"Excellent. We can move on then to the final school of the ninja arts. Ninjutsu is by far the broadest school of the three and can be divided more thoroughly into smaller sub-categories. Elemental jutsus, such as the ones that we discussed earlier, can be considered one branch, while sealing techniques could be considered yet another branch."

"Sealing techniques… Is that what you were looking at yesterday? A seal? Where did it come from? Why do I have a seal on me?"

Pain paused for a moment and studied the boy across from him, who had now leaned forward and placed his small hands on the edge of the desk. He was practically coming off of his stool. Pain began his reply slowly and deliberately. "I have every intention of explaining it to you, but I feel that it would be prudent to wait until your training has progressed further. You are right to be curious though – that seal will become very important to you in the future and you will have to be taught about it extensively. At the moment you need not worry about it. There are other subjects that we must cover beforehand in order for me to properly explain it to you. Right now any focus on that seal will only serve as a distraction from your training."

Naruto decided that he could wait if Pain thought it was best. "Just please tell me as soon as you think you can. I don't like it when people keep things from me." Naruto continued in a small voice. "Like why nobody in Konoha liked me."

Pain narrowed his eyes briefly before replying. "Very well. I will tell you as soon as I believe you are ready, but for now, ninjutsu." Naruto straightened and wiped the melancholy look from his face.

"As I've already told you, ninjutsu is a very broad subject and covers all of the chakra manipulations that a ninja can perform by molding his internal chakra to affect either himself or creatures and objects outside of his body. In a sense, ninjutsu consists of all ninja abilities that do not fall within the scope of taijutsu and genjutsu."

"Um, how is ninjutsu different from taijutsu if both can work inside the body?"

"A good question. Taijutsu utilizes raw chakra to strengthen a ninja's physical form. In a sense it is rather unrefined. Internal ninjutsu can change the body's make up completely. You have seen Konan's paper abilities, correct?"

Naruto smiled and nodded. "Yeah, that was really cool."

"Konan has an excellent grasp of her yin/yang affinity – so much so that she can change various body parts into paper and allow them to operate independently of her natural form. Soon I expect that she will be able to turn into paper completely. As you can imagine, that would be an exceptionally useful ability for many reasons."

Naruto wrinkled up his nose in slight disgust. "So all of her clothes are actually made up of parts of her body?"

Pain smirked at the boy. "No, but they are made up of paper which she controls. Even a ninja as skilled as she is couldn't manipulate her body at all times to such an extent."

"Oh! What's a yin/yang affinity? Konan said that you had an earth affinity last night."

"Did she now? I suppose that's not technically incorrect. As far as affinities go, there are six in total. The five elements: water, earth, lightning, wind, and fire, as well as the yin/yang manipulation affinity make up the six. The five elements are considered the major affinities and every person has an affinity for one of these five elements. Some ninjas also have strong skill in the yin/yang affinity, which deals with manipulations outside of the elemental ones."

"So that means I have an elemental affinity. How do I know which one it is?"

"That will come later in your training. I should tell you though that most high-level ninjas train themselves in elements beyond their natural, primary affinity. By doing so they create secondary affinities that they can use in battle effectively. Any ninja can use basic skills of any element. However, to use powerful abilities efficiently a ninja must stick to those skills that are part of his affinity. Doing otherwise is wasteful and ineffective."

Naruto placed a hand over his mouth and furrowed his brow in deep concentration. "I think I get it. I'll find out my affinity later and then try to learn more."

"Yes." Pain stood from his seat and looked down upon his apprentice. "I think that's enough theory for today. I have work to do now. I will bring you dinner in a bit. If you feel up to it I would suggest practicing molding your chakra like you did earlier, but try focusing it to different parts of your body, hands first. That way you can turn the lights on and off. When you become tired you may make use of the library if you like. So long as you take care of my scrolls you will have access to it in your free time. Tomorrow I will begin assigning you reading and we will start your physical conditioning. Make sure you get plenty of sleep, I will be waking you early tomorrow."

"Alright Pain." Naruto hopped off the stool and headed towards the doorway before halting.

Pain smiled at his back. "Left. Sixth door."

The boy turned around and gave him wide grin. "Thanks a lot, Pain. For everything."

Pain hummed quietly to himself and made a decision. "Before you go, Naruto, I wanted to give you something." He pulled open the top drawer of his desk and pulled out a three-pronged kunai, the likes of which Naruto had never seen before in Konoha. "This is a very rare weapon that was created and used by the Fourth Hokage." Pain paused as the small boy's eyes widened and his mouth hung open in awe. "I thought you might like to have it since you were originally from Konoha. He's rather well-known there, is he not?" Pain enjoyed leading the blond on and sat back to observe his shocked expression. Naruto slowly walked forward and took the strange weapon from Pain's hand.

"R-really? You'd let me keep it? No one's ever given me anything like this before. Thank you so much!"

Pain nodded happily. The boy's demeanor was contagious. "Take care of it, Naruto."

"I will. Thanks again. This is so cool!"

With that the boy turned to leave his master to his notes, reverently holding the kunai to his chest as if it were some precious companion.

Pain was left alone with his thoughts. A kunai was certainly a better gift than a stuffed animal for a four and a half year old apprentice ninja, he was sure.

A/N: I'm not sure if I'll be doing endnotes too often, but here's one for you.

We've finally gotten to Rain Country and the story will start moving now. Expect a one to two year time skip next chapter, some training, some history, some revelations, and maybe some more character appearances (if we get that far).

I hope I didn't bore you with all of the technical explanation that Pain gave, but the man is meticulous if nothing else. Also, I'm sick of crappy clichés like gravity seals and the like. Where is that stuff in the manga?

My Naruto isn't going to have a million jutsus, much like in canon, but he will use his knowledge of the ninja arts to defeat his opponents instead of simply brute-forcing every situation. Don't worry, he will be strong, but as a member of a criminal organization he also has to be smart.

Again, reviews are appreciated and encouraged, especially if they contain constructive criticisms.