Title: ROOT

Summary: Fate doesn't intervene just for those who are pure of heart. Naruto, a ROOT operative, wakes the morning after completing the most heinous mission of his career in a place where creatures as deadly as shinobi stalk the lands and chakra is beyond the common man. But when returning home proves impossible, will the cold-hearted blond embrace this new chance or revert to his old ways?

Rating: Heavy T, Eventual M

Pairing: ? There's a poll for input.

Inspiration: "The Traveler" by The Straight Elf. By far the best Pokemon fic I've ever read. Thankfully he's been so kind as to lend his support and invaluable advice for this story, and has given his permission for me to draw ideas from his work. I can't stress it enough, if you've never read it, do yourself a favor and go bask in its greatness

AN: So, as you could probably glean from the summary, Naruto won't be the best person in the world. Really, he'll be quite the bastard. I can't stress that enough. How long this will last, I'm not entirely sure. To be honest, the part of him that was trained by Danzo will likely never completely fade. But in my own opinion, it's the broken ones who are the most fun to read and write about.

The story itself begins in Johto, but won't be contained to this region alone. The story will expand beyond its borders. Just how far is yet to be decided.

UPDATE: I know how much people hate Naruto, but he does change. Give it a few chapters.

Chapter One: A Boy and his… Cat?

"Professor Elm."

With a great deal of reluctance, said man tore his focus from the stream of information upon the monitor to hold twin pools of crisp, stoic sapphire with his own gaze.

"Mr. Uzumaki?" Elm glanced over the youth's shoulder to where the rest of the examinees resided, diligently pouring over the test that would determine whether they would become League recognized trainers or would spend the next year preparing for the same test once more. "Can I help you? Is there something you didn't understand?"

Extending the heavy booklet, the blond said in his scratchy drawl, "I'm done."

Elm arched a thin, dubious brow. Taking the exam from him, the professor flipped through its contents with a discerning eye. "I'm aware your situation is different from that of the others sitting this make-up exam, what with you being our youngest applicant and that this is your first time taking said exam at all. But to underestimate this test by not giving it your all or rushing to be the first one done is a folly that could cost you greatly."

"Look to your peers," Elm waved a hand at the rest of the examinees, teens ranging in age from a year or two older than the preteen himself to those on the cusp of adulthood. "This exam is not to be taken lightly. Though anyone your age is permitted to sit it, as you can no doubt see, a sizeable portion fail to achieve the required percental to pass. It would be wise to spend the remainder of the time you've been afforded revising."

The blond shrugged, unconcerned, a wide, unnerving smile that didn't touch his eyes slinking into place upon his lips. "I'm done."

The professor attempted to get a read on the young man, to discern something, be it false bravado or staggering arrogance, from the flat depths that were his gaze, but found only chilling nothingness. If nothing else, the kid had a hell of a poker face.

"Very well," Elm sighed, dropping the booklet onto his desk and opening it to the first page. "Since no one else is finished, and won't be for some time, I suspect, I'll grade yours personally. You may either return to your seat or tour the lab until I'm done."

The blond nodded his gratitude as he made for the door, turning a blind eye to the leering of the other test takers. To the outside observer, his movements were random, the wonderings of a too curious twelve-year-old. But his stride carried a purpose none save the blond himself knew. It was staggering how trusting and unobservant the people of this world were.

It had been akin to the dousing of a flame. One moment it had been there, an ever-constant presence flickering just upon the fringes of his senses. The next, someone or… something had snuffed it from existence.

A harsh breath that had ruthlessly and without remorse extinguished the world's life-force… chakra.

Or to be more accurate, as he had quickly come to learn as he investigated the land in which he woke, a gale born of fate's cruel lips that had spirted him away from his home. Not only Konohagakure, but the Elemental Nations as a whole.

By no means was he a sensor type. Despite his master's heavy handed tutelage, his charka was too potent and plentiful for the delicate control required to be anything more than a novice of the craft. Yet even he could sense its absence in the trees, its people, and every living thing around him. It was surreal, like waking to find one of his limbs or five senses had been severed.

For what felt like the thousandth time since waking in the sleepy little settlement known as New Bark Town, Naruto violently disrupted the flow of his chakra network. Yet no amount of genjutsu combating exercises could release him from the illusion that was his new reality.

It was this realization that saw him here today, in Professor Elm's research lab, sitting for an exam that would allow him to become a pokemon trainer. As Danzo-sama and his handlers in ROOT had always stressed, should one find themself taken unawares, they must be quick to adapt and conquer, or risk the integrity of your objective.

And the only sin known to the murderous little monsters that were Naruto and his brothers and sisters in ROOT was compromising the mission. And though there was no official mission to be completed, per say, he would do both. Adapt. And conquer.

With a lack of charka in the world and its people, status and one's influence was decided through battles between trainers, or more accurately, the pokemon trainers captured and trained.

It was all very similar to the ninja academy. One became eligible to become a trainer at the age of eleven—a year earlier than the average shinobi graduated from the academy—given that they proved themselves capable of handling the responsibilities and hardships synonymous with the day-to-day life of a trainer. Once this symbol of status was achieved—the equivalent of a forehead protector—from there on it was up to one's own skill how far they would go.

Before he knew it, Naruto found himself around back of the lab, perched on the fence in which the lab's younger and newborn pokemon were kept. Groups of rattata scampered about squeaking and hissing at one another. Green, spider-like pokemon with vaguely face-like marking on their abdomens skittered about, spinning elaborate webs and hanging from the very trees in which a large number of Hoothoot were taking up residence out of the mid-day sun and catching a bit of shut eye.

Pokemon, as he had come to know them, were not a form of wild summons as he had first suspected, but were, however, capable of posing just as much danger as the nin-animals shinobi signed contracts with. While these creatures were incapable of harnessing chakra like their human counterparts, they were not to be underestimated. Though rare in the extreme, even the youngest of hatchlings, if threatened or given great enough cause, could turn dangerous, if not outright deadly. The humans of this world, bar their incredible advances in technology, were no match for the threat a pokemon, any pokemon, could present with their natural capabilities.

And though he himself had yet to encounter any such pokemon, from what his investigating revealed, they could grow to be true forces of nature. As powerful as any shinobi from his world. Possibly even, if the tales of legendary and mythical pokemon carried any truth, as strong as a Kage.

"Mr. Uzumaki." Feigning surprise, the blond slid from the fence as the speaker, one of Elm's aids, approached. "The professor wishes to speak with you about your results."

Nodding, Naruto allowed the stern-faced woman to lead him back into the lab, pausing only long enough to cast a glance in the direction of the boy lurking just out of sight within the tree line encompassing the rear of the lab. With only a short trip, he found himself in a room different to that which the exam had been held. He deduced it was the professor's personal study as the man himself sat behind a large, handsome desk, looking quite at home, his focus ensnared by what he recognized as his exam.

"It's rare for someone to surprise me," Elm admitted. He wore a look of begrudging amazement as he once more glanced over the preteen's work. "And you say you didn't attend a trainer's school?"

Naruto shook his head. Unknown to the professor and his assistant, the remaining bunshin hidden away in the lab's library dispersed with a silent pop.

"Remarkable," the man awed. "It's a shame you didn't take the exam earlier. Had you done so and achieved the same score as you did today, you would have been a shoe in to receive one of Johto's elemental starters. As it is, however, the maximum number we can distribute each year has been reached. But on a positive note, your score more than qualifies you to receive a pokedex."

"Thank you, Professor." He accepted the scarlet handheld, feeling clunky and out of his element with the piece of tech in hand. While his world did have such things as radios and television, the technology displayed and utilized on a daily basis here was leaps and bounds beyond anything the Elemental Nations could ever hope to replicate. At least through technologically speaking. There wasn't much a true master of fuinjutsu couldn't achieve with their complicated seals. Fortunately, he was taking steps to rectify his ignorance, using the lab's computers, which were open to public use, and familiarizing himself with the pokegear he had "liberated" from an unsuspecting trainer he had happened upon in the woods surrounding New Bark Town.

"Normally, trainers who don't qualify to receive a chikorita, cyndaquil or totodile, are given one of the more common breeds that frequent the areas around town, such as rattata, caterpie, or the like. However, given your admirable showing, we've decided to break from tradition."

Withdrawing a nondescript pokeball from his desk, he presented the new trainer with the red and white sphere, which the blond took without hesitation. Without fanfare or a drawn out pause, Naruto tapped the button just as he had read to, expanding it to its full size and tossing it into the open space within the office in a single fluid motion. Instantly the room was illuminated with crisp, blue light that was quick to consolidate and take form. When the lightshow subsided and the dots had disappeared from his retina, Naruto was left staring at what could be best described as a cat.

While mostly cream-colored, its tail, which was mostly straight save for a tight, abrupt curl at the end, and hind paws ended in a shade of darker brown. But its most notable feature was the sizeable, golden coin upon its brow. For all intents and purposes, it appeared to be your typical feline, he noted, until it raised up from its haunches to stand on its hind legs in what was a very human-like manner, a likeness that was compounded when it began to stretch its front paws high overhead and yawning widely.

"You'll need to register it to your person," Elm cut in, pointing a finger at the palm sized computer he had given him. "But until you do, it will still function properly. All you need do is point it at the pokemon you wish to learn about and it will give you a brief description of its species," he added when Naruto didn't react right away.

Doing as he had been instructed, he directed the pokedex at the cat who had turned intelligent, listless eyes upon him.

"Meowth, the Scratch Cat Pokemon." The pokedex droned on in a stoic, mechanical voice. "Nocturnal in nature, Meowth withdraws its sharp claws into its paws to slink stealthily about in the night as it hunts for round, shiny objects."

"Meowth knows the moves: scratch, bite, screech and foul play. Its ability is Technician, which doubles the power of weaker attacks."

"Meowth are known to be frighteningly cunning and hold the compacity for human-like intelligence," Elm explained. "This one is no different."

Naruto nodded, surveying the normal-type with a critical eye. "Interesting."

ROOT

Stepping off into open air from up high, Naruto dropped noiselessly from a mighty oak into the same deserted meadow where he had originally found the trainer whose pokegear he stole. The crack of meowth's pokeball played in time with the displacement of air that signified the appearance of a kage bunshin.

Meowth's teal gaze danced back and forth between Naruto and the bunshin he had conjured. The normal-type looked burgeoningly curious at the appearance of her new master's clone. Though even this development wasn't enough to hold her evasive focus for long.

"Let's see what you're capable of," Naruto began in a commanding tone that brooked no room for disobedience. "It only takes a strike of moderate force to disperse my clone." To demonstrate, the blond backhanded his doppelganger, sending it from existence with an audible pop and a bit of lingering smoke as proof it had ever imitated life.

"I want you to use each of your attacks on it," he continued, earning a fleeting look of surprise from the feline as he created another clone to take the original's place. "Starting with screech. From what I gleaned from the pokedex, it's the only attack you know that doesn't do direct damage. After, you'll spar with one of my clones."

When meowth made no move to follow his instructions, Naruto gave his clone a silent signal to act. Before the normal-type knew what had happened, she found herself pinned to the ground by an unbudgening weight at the base of her skull.

Naruto walked around the struggling pokemon and his clone, who had pinned the feline to the ground with his foot, so the former could see him as he spoke.

"You can resent me if you like, but know you will obey me. In return, I will feed you, protect you, and nurture you into more than you could ever hope of becoming on your own. There is no room for negotiation. If this proves too much for you to accept, then grow strong enough to claim your freedom with my life's blood. Just know, each time you try to take my head or flee, I will make you pay for such impudence."

They were the same words Danzo had breathed into his ear as his private force conditioned him to recognize the old cripple as his master. Brutal as they were, Naruto himself could attest to how affective of a motivator they were.

Giving the same silent signal as before, the clone stepped away from meowth, allowing her to rise slowly onto all fours and glare up at him. The speed with which she lunged at him surprised the blond, but a moment later a frown crinkled his brow and thinned his lips.

From what he had read about the species from the pokedex, meowth would evolve into a larger, more powerful breed of cat, one that traversed on all fours. Yet meowth itself walked upright on its hind legs like a human being. A problem he would have to see that she ceased. There was a reason a normal human couldn't outrun most four legged creatures. Utilizing only its hind legs was a waste of its potential and was unknowingly impeding her speed.

Her claws were only inches from his unguarded face when his clone stepped in, grabbing the cat by its tail and slinging her bodily into a nearby tree. Before gravity could catch her and drag her back into the earth's cold, unfeeling embrace, Naruto appeared before her, pinning her to the tree's abrasive face with his foot. The soul of his sandal dug painfully into her narrow chest as the bark tore at her fur covered spine.

"Your speed is impressive, but there's room for improvement. There's always room for improvement."

ROOT

"That egg," the redhead jabbed an accusing finger at the large, melon-sized oval. The other boy, holder of said egg, a dark-haired preteen who sported a backwards cap, struggled as he attempted to stow it from sight in his backpack. "That's a pokemon egg, right?"

"And if it is?" The one to speak was neither of the boys, but a young girl, who stood protectively in front of the boy with the backwards cap, her arms folded across her nonexistent chest in a way that promised pain should he attempt anything.

"How in the hell did you two manage to get your hands on one?" The redheaded boy, the same youth Naruto had spotted lurking about Elm's lab almost a week half and a half prior, demanded. In a move that was meant to intimidate, but only Naruto caught on to, his hand fell to his side, his fingers grazing along the polished surface of the pokeball on his hip. "Pokemon eggs are rare. And neither of you have been a trainer for more than a few days."

From his perch up a nearby tree, Naruto arched a single sun kissed brow at this tidbit of information. Without giving his actions thought, he allowed years of conditioning at the hands of his former master to take control.

"If you must know, we're bringing it to Professor Elm's lab," the girl, Lyra if Naruto wasn't mistaken, growled as the boy at her side stood up, slinging his bag over his shoulder. From what he could discern from the trio's body language, Naruto knew the confrontation could end in only one manner. Conflict.

"Why don't you hand it over," the redhead cawed harshly. "I'll keep it safe for you."

Their answer came in the form of a chikorita and a cyndaquil, both starters tensed at the sight of the redhead, ready to pounce at a moment's notice. Mimicking them, the redhead sent out his own pokemon, a blue reptile that Naruto recognized as totodile, the final member of the elemental starters Elm had mentioned to him in passing.

"Two on one," Naruto mumbled loud enough for all to hear as he exited the woods halfway between the antagonistic redhead and the duo who were the subject of his game of cat and mouse. "Those odds seem a bit skewed, don't you think?"

"He started it," Lyra grumbled hotly, glaring at the redhead over his shoulder.

"I did," the redhead admitted nonchalantly. "And I'll finish it, too, as soon as you get out of the way!"

"Sorry, red. My pockets are a tad light at the moment. I'm in need of a bit of spending money. How 'bout it?" he inquired, directing his question at the fairest member of their mismatched foursome. "You up for a little one-on-one?"

Lyra looked momentarily taken aback by being addressed by the new arrival. But quickly regained her composure, her wide, doe-like eyes narrowing determinedly. "I'm game."

"Good," Naruto clapped his hands jovially, causing the other boys, who had been too busy glaring at one another to pay attention to his antics, to jump in surprise. Rule number one, always keep the opposition off balance. "Think you can handle him with a type advantage?" Naruto asked patronizingly, giving the redhead's water-type a lingering glance.

"You just worry about not losing," the redhead sneered.

With a nonplussed shrug, Naruto tossed meowth's pokeball, releasing the normal-type a few feet from totodile. From next to him, the redhead snorted.

"A meowth?" he goaded.

"At least I didn't steal mine," Naruto shot back, low enough that only the redhead, Silver, as Naruto knew him, could hear.

Waving off the beginnings of what was a stuttered denial, Naruto turned his attention upon the grass-type. "Focus," he growled, partially to Silver, but more so meowth, who eyed the grass-type with something akin to disinterest. The normal-type, realizing her folly, tensed upon all fours, ready to obey any command imparted.

"Chikorita, use razor leaf!" Lyra cried out.

"Dodge it," Naruto ordered quietly. "Use your speed to get in close and use scratch and bite."

Doing as she was commanded, meowth slinked close to the ground, well beneath the barrage of flora, and quickly closed the dived between her and the grass pokemon. Without hesitating, she threw herself at the slightly heavier pokemon, bringing both fang and claw to bear upon its unprotected face and neck. With its canine-like yips spurring her on, meowth didn't relent for even a second.

"Quick, Ivory. Use vine whip to toss it away!"

"Retreat," Naruto ordered at hearing the lass's exuberant command. "If any of its vines get too close, cut them down."

Using the grass-type as a launching pad, meowth sprang away, dancing back before its opponent could retaliate. Out of habit, meowth rose up on to her hind legs, a mistake a sharp hiss from her trainer corrected.

"One more slip up like that and there will be consequences." Naruto warned under his breath.

Using its vines to upright itself, chikorita sent them high into the air overhead before bringing them crashing downward with a grunt of effort. Meowth, as he had commanded her to, sidestepped the heavily telegraphed attack, moving in close before chikorita could reel them back in and severing the tiny, harden nubs at the end of each appendage with her razor-sharp claws.

Lyra cried out in concern with chikorita, who gave a pained yip at the loss of her vines.

"Ivory!?" Lyra almost sobbed, taking a few steps forward before a hand on her shoulder, belonging to her traveling companion, stopped her in her tracks. Both Silver, the other boy, and even their pokemon had stopped to watch the battle between meowth and chikorita playout.

"Are you alright? Can you still battle?" In confirmation, Ivory barked as she returned her vines into the folds of her neck. Making it clear she could no longer use them in their current battle. They would take at least a week to grow back and properly heal. "Good girl," called a relieved Lyra, who looked on the verge of tears. "Use tackle!"

Naruto shook his head, a motion that wasn't wasted on either boy, though Lyra herself missed it, focused as she was on the wellbeing of her starter. "Finish this with foul play," he commanded under his breath.

Foul play was a dark-type move. A technique capable of harming ghost-types and that turned the opponent's power against them. And while it was useless against something like razor leaf, it was the perfect choice against physical attacks.

To Lyra and chikorita it appeared as if meowth had sudden decided to stop fighting, resting on her hind haunches in the middle of the dirt road. But as the grass-type launched itself recklessly at meowth, the normal-type rose onto her hind paws, as she was only allowed to do when using said attack. Using her momentum against her, meowth slammed the grass-type over her shoulder and straight onto her skull, rendering her unconscious instantly.

"Still not done, red?" Naruto taunted as he recalled meowth. Not waiting for an answer, he strolled up to Lyra, who had rushed forward to kneel next to a prone and unconscious chikorita, holding his hand out expectantly to her. Clearing his throat when she failed to produce his winnings, he waved his open palm in her face. "Come on," he urged impatiently.

He made an aggravated sound as she fumbled with her bag, searching for her purse. When he had his fist full of pokedollars in hand, the blond didn't waste any time standing about, quickly brushing past the still reeling girl and her traveling companion on his way to the pokemon center, eager to investigate the additional weight his rucksack now bore.

"All of you need to train more," he called over his shoulder, "I expected more of a challenge from someone who scored high enough on the trainer exam to receive a chikorita.

ROOT

Ethan fiddled nervously with his cap as he waited for his call to be answered. When finally his outdated PokeGear connected, giving a telltale crackle followed by the sound of someone absently clearing their throat, he couldn't hold back the stream of babbled apologies and pleas for forgiveness that spewed forth from his mouth.

"Slow down," Professor Elm sighed, his brow furrowing grimly at the lack of video. It was rare in this day and age, and more than a little disconcerting he would readily admit, to receive a call without a live feed of the person on the other end of the line. "Now who is this?"

"It's me, Professor. Ethan."

"Ethan? Are you alright? You sound upset."

Ethan wasn't sure what inspired the thought, but couldn't escape the same suspicion about the Professor. The man sounded uncharacteristically cross, as if someone had succeeded in ruffling the normally composed man's feathers. "I'm sorry, Professor. It's the egg Mr. Pokemon gave us. It's gone. Someone stole it." The teen couldn't hold back a wince at the long string of obscenities that greeted this revelation.

"Not another one," Professor Elm hissed to himself in a manner that was very unlike the cheery, albeit forgetful persona he normally displayed to the public.

"Another one?" Ethan parroted, his confusion momentarily overwhelming the guilt that had plagued him since his discovery that he had lost the egg.

Professor Elm sighed, the sound a harsh, weary one. "Yes. Unfortunately, a pokemon was stolen from the lab earlier this week. The only lead we have is a sighting. Nothing concert mind you. Only a youth with hair a vibrant shade of red. A boy about your age, or so I'm told, that one of the aids spotted hanging about the lab in the days preceding the theft."

"A redhead?" Ethan mumbled distractedly, his mind going back to the trainer he had battled, and defeated, just before the egg was discovered missing. "The pokemon that went missing? Was it a totodile?" he clarified. Across from him, Lyra, who had been fidgeting as nervously as if she were the one responsible for telling the professor that the priceless egg they had been charged with transporting had been stolen, perked up.

Elm stuttered, understandably bewildered, before finally coughing out, "Yes, yes it was. How could you know that?"

"Because I battled a redheaded trainer just before the egg went missing. He had a totodile and was really interested in the egg." Ethan clicked his tongue in time with the professor's knowing "oh".

"There was a..." Ethan hesitated, casting an uncertain glance at Lyra. "There was also a blond with a meowth. He battled Lyra and Ivory, her chikorita, while I faced the redhead. It fought like it was possessed. It almost felt like staring down a wild animal."

"A blond with a meowth, you say. Did this trainer happen to have any distinctive scars, or a notable birthmark?"

"Yeah, they looked like… whiskers." A chuckle bubbled at Ethan's lips at the faint dusting of red that appeared on Lyra's cheeks at the mention of the trainer that had defeated her, but smothered the reflex as he doubted the professor would take very well to his laughter at a time like this.

"That would be Naruto Uzumaki. An impressive young trainer who quite randomly showed up on the lab's doorstep about a week or so ago and aced the trainer exam. His results were some of the most promising I've seen in some time. While certainly not the most outgoing or winning of personalities, I certainly wouldn't think of him as the type to steal a pokemon." Ethan waited patiently as the sounds of the Professor's fingers gliding across a keyboard drifted through the receiver. "I've just looked at his trainer information, Naruto Uzumaki has only one pokemon registered. The previously mentioned demon meowth."

Clearing his throat, Elm continued. "We only give out twelve elemental starters at the beginning of each conference season, only four of which are totodile. I'll search our records and find out if any of the four match the redhead's description. Unfortunately, even if there isn't such a trainer on file, that doesn't prove he's our culprit."

"Why not?!" Lyra nearly fell off the stump she was perched upon, so random and indignant was Ethan's yell.

"Because it's quite possible, however unlikely the odds may be, that the trainer you battled received his totodile as a gift, either from a parent or some other individual, or captured it himself. All my research will yield is a possibility of clearing him of suspicion, nothing more."

"You should have seen him, sir! He just gave off this vibe that screamed 'I'm up to no good!' And his friend, Naruto, he was just as bad!"

"Pardon my asking, Ethan," Elm began, a bit of wry humor and exasperation entering his voice. "But what exactly is your problem with Mr. Uzumaki? Did he perhaps win his battle with Lyra?"

Ethan stuttered indignantly, "He did. But I don't see-"

"Has it ever crossed your mind that it might be resentment that has you categorizing him along with the young man you suspect stole the egg?"

"Of course not," he denied, shame burning his cheeks.

"All I'm saying is don't be so quick to pass judgement on others. Especially those you don't know. It's quite easy to mistake one's own bitterness for the stirrings of suspicion."

"Yes, sir," Ethan sounded thoroughly chastised. Though both Lyra and a burgeoningly amused Elm could still detect a hint of resentment in his voice.

"About the egg," Elm continued. "There's nothing we can do about it now. It was unfair of me to have asked so much of you and Lyra. And I can't very well fault you for a theft when my own personal lab was burglarized while I was here. We'll call it even for now. Someday when I need a favor, I call upon you two, again."

ROOT

"Not too impressive to look at, is it?" In the privacy of their room in the Cherrygrove Pokemon Center, Naruto studied the egg he had snatched from Lyra's friend. The mostly pink egg rested motionlessly upon a cradle of pillows and mismatched blankets he had tossed together. "Are all pokemon born of eggs?" he asked absently, not expecting any sort of answer from the normal-type. As intelligent as she had proved to be thus far, he didn't expect her to start spouting off answers in human tongue anytime soon. Or ever.

Withdrawing his pokedex, which was rapidly becoming his most invaluable asset in his quest for dominance over Johto, Naruto set to work looking for the answer to his own question. He was surprised with what he found. While not all pokemon were hatched, a large majority were, in fact, oviparous.

With his excitement once more rekindled, he glanced over the egg at the feline who had spent the past half an hour sending it resentful, unimpressed glances. Only a warning glance from the blond kept her from batting at it with her paw. Bored with their current setting, meowth slinked forward, a pleasant rumble in her chest as she attempted to side up to him, seeking an affectionate touch or any form of contact at all. Meowth were very social creatures, after all.

"You should be working on learning pay day." Naruto pinned her where she stood with a stern look, his narrowed gaze daring her to brush against his side. "Tomorrow we set out for Violet city. It'll be a week's travel at a normal pace. Your slip up today aside, continue to battle as you did against chikorita, and you'll have nothing to fear from me."

Creating a bunshin, the clone made its way over to the lone window, which it proceeded to wrench open. "I promised to feed you, and I intend to keep my word. However, you will need to learn to how to hunt for your own food as well." With a curt nod, Naruto motioned for the normal-type to follow his clone out the second story window. "Don't return until you've captured your dinner," he called out as she disappeared from sight. Once more alone, Naruto returned to pouring over his pokedex and the entry on pokemon eggs, which, funnily enough, was penned by none other than one Professor Elm.

ROOT

The most exotic creatures populating the road bridging Cherrygrove and Violet City weren't the pokemon, but the droves of trainers who insisted upon ladening their teams with the all but useless bug-types that polluted the area. Left baffled by their strides toward mediocrity, he continued to push meowth as harshly as Danzo and his handlers had him.

"Again."

Sitting upon the edge of a creek, her mammalian features twisted into a rictus of grim resolve, meowth poured all of her focus into creating the tiny spheres of energy the pokedex described in its entry on pay day. But just as all of her previous attempts over the past five days had ended, this session too had proved to be fruitless.

"Damn it!"

Meowth had only enough time to turn rigid with fear before she was sent crashing into the creek. Hacking up water as she shakily pushed herself upright, her master's ill-boding shadow fell across her in time with his sandaled foot catching her round the chin and lifting her up and out of the water and across the clearing. She landed in a tangle of limbs, her momentum having yet to slow before he had once more kicked her, this time back into the water.

"I warned you," Naruto shook his head, disgusted. "If you're not going to give me your best, I'll force you to go above and beyond the limitations you've set for yourself."

"Now then, run!" In helping her build up the proper muscle memory to make the transition from two legs to four more natural, Naruto had been forcing her to make a portion of the journey each day at a full-on sprint. As a result, not once since their battle against Lyra had she slipped up and returned to her hind paws during battle.

Meowth scampered from the creek as quickly as if death itself were on her heels, her undercoat soaked through and her already filthy paws sinking deeply into the muddy bank. Naruto stayed close on her tail the entire way, his pace little more than mild jog. It was in this manner that they reached their destination.

Violet City was by far the largest settlement he had ever laid eyes upon. There were countless glimmering buildings, the sun catching their reflective surfaces and alighting the air like fire, each as mighty and as tall as Konohagakure's Kage monument. Their pointed, heaven piercing spires scraping against Kami's heels like a bed of kunai lying in wait. From the crest of a hill overlooking the city, the blond could make out structures more akin to those found in his world, sturdy, traditional, and constructed from the bones of mighty trees, dotted throughout the forest of twisted iron and sleek, polished metal that was the home of his first gym battle, Violet City.

Next to him, meowth spared the human settlement an apathetic look before pursuing more pressing concerns. Mainly, attempting to rid her once luxurious coat of the filth marring it. Rare were the occasions, when outside her pokeball, that she wasn't being put through the ringer by her temperamental human. While she could indeed rest inside, it was essentially a form of stasis or suspended animation, akin to being trapped in a continuous moment, the same restless second again and again. While free of its confines and her master proved to be too caught up in his own musings to bother with her, as fleeting and rare as these moments were, she could at least stretch her legs and, thankfully, try to bathe.

"Come," Naruto ordered, taking the first of many such steps that would lead them to the heart of Violet City. "I want to challenge Falkner and his overgrown birds before nightfall. But first we need to locate a pokemon center."

At his words, meowth tensed, prepared to once more cross a distance that should have taken hours in a fraction of the time. Yet was surprised, pleasantly so, when his pace proved to be sedated, if only by his own insane standards. To anyone who hadn't been subjected to traveling with him over the past two weeks, he would have been the perfect image of a rookie trainer only hours away from challenging their first gym, all except for the rigidness of his smile that is. No matter how often he showed challenging trainers or passersby on the road that same tilt of the lips, it failed to warm the sharp, frozen depths of his sapphire-shaded gaze.

Luckily, like most metropolises, Violet City possessed multiple pokemon centers. One to the north, south, west, and where Naruto and meowth entered, the east. It took only a few minutes to get registered for a room, and only a handful more to have meowth given a quick once over by a cheery, if a touch harried Nurse Joy. The youthful healer gave the retreating blond and his filthy pokemon a weary glance as they disappeared upstairs.

Having dropped off his belongings, including the egg, which had been returned to its throne of blankets and pillows, he pulled out his pokegear, flipping through its features to the section with detailed maps of the region. He ignored the laughter of a passing couple, the fairer half of the duo needlessly pointing out that "his" pokegear was pink, whereas her boyfriend's only remark was to comment on how dated the piece of tech was. Locating the Violet Gym on the map, he took a roundabout route, going out of his way to stop at one of the city's pokemarts. Using the funds he had won battling and snagged from the pockets of the inattentive, he purchased a few potions, antidotes, a book on some of the more common plants, herbs and berries found in Johto, and finally a couple of spare pokeballs.

"I need to see some ID." The clerk behind the counter barely looked up from a watch-like device he wore, on which he was talking with someone else.

Naruto nodded impatiently as he withdrew his pokedex, which doubled as an ID, his gaze lingering upon the expensive looking device strapped to the man's wrist. The need for verification was one of the reasons—really, the only reason—why he hadn't just stolen someone else's pokeballs. Until the sphere was registered to a trainer, a pokeball was little more than a pricy paperweight. It was how the league and people like Professor Elm were able to determine which pokemon a trainer had captured and avoided confusing one trainer's pokemon with another's. Use a ball registered to another to catch a pokemon you defeated, it was then their pokemon in the eyes of the League. And there was no legal means to regain ownership of the pokemon, bar the owner of the ball willing transferring its ownership, and subsequently the pokemon within.

With a grunt, the clerk verified he was who he said he was and registered them to his trainer card. The entire process took less than five minutes, but the blond was left annoyed by the process. Grumbling his discontent as he exited the mart, casting a final glance at the watch, he absently followed the directions to the gym he had memorized as he pursued the book on the properties of local flora and berries.

Medical ninjutsu was just another branch of jutsu that had been lost to him thanks to his abundance of chakra and the beast that had once upon a time called his gut home, prison, and hell. As such, Danzo had seen to it that he was well versed in other healing crafts, such as potions and elixirs, binding wounds and broken limbs, and even the crafting of poisons. Call it his inner cynic, or the overly cautious tendencies of someone who had been a part of one too many missions that had gone sideways in the worst possible way, but he believed in being prepared. It just seemed the epitome of idiocy to go off into the wilderness, often for weeks or more at a time, where pokemon centers and hospitals were as scarce as danger was plentiful, without a bit of knowledge on your side.

It was only about mid-afternoon when Naruto found himself standing before the Violet Gym. Plenty of time to challenge Falkner before the gym hours ended. What he hadn't expected, however, was a wait. There was a sizeable group loitering about outside the gym, all trainers given their varying states of worn and dirty clothing and row of pokeballs resting low on their hips. Near the entrance stood a teenager, more of a man than a child, with a ridiculous haircut that fell in a way that obscured a portion of his face, attempting, rather unsuccessfully, to calm the discontent of so many restless trainers.

"Everyone will get a chance to battle leader Falkner. However, there will be a wait. Unless you're willing to battle one of the gym's trainers, you'll need to return tomorrow."

Naruto stepped forward while many others grumbled about not getting to battle the gym leader immediately. "I'll battle anyone, as long as I get a shot at the gym leader tonight."

Nodding, the gym affiliated trainer pulled out a pad and pen as he asked, "Name and number of pokemon on your person?"

"Naruto Uzumaki, and only the one." The blond stared blankly at the teen taking his information, who had chuckled obnoxiously at his answer before abruptly sobering when catching his mirthless gaze.

"Alright," he coughed, uncomfortable with the weight of the youth's intense eyes resting with him. "How many badges do you have currently and, if you've competed in a conference in the past, what's the highest you've ever placed?"

"No badges," Naruto shook his head. Behind him, another trainer, a girl who had been there before he arrived, lined up behind him. "This is my first year registering for a league."

The boy nodded as if expecting such an answer. "Go stand over there. Someone will come find you when we have your opponent ready. Next!" As Naruto moved toward where the lad had gestured, he caught the goofy smile to appear on the information taker's face as the girl behind him gave her name. "Hilda."

To pass the time, as he had taken to doing in the two, almost three weeks since receiving it, Naruto poured over his pokedex, devouring the abundance of information it had to offer with zeal. He had never been what one would call studious, but early on he had learned the importance of being well-read, as he was shown by the un-repentant and unwavering hand of his ROOT handlers. So it came as a bit of a surprise, even to the blond himself, the fever with which he had taken to all things pokemon, including the purely academic portions. Perhaps it was the novelty of it all which saw him take such an interest in it, or perhaps after taking beatings all his life, he finally realized reading and having a bit of smarts wasn't all bad. Either way, he had systematically devoured every bit of information on pokemon and the world he found himself in that the pokedex had to offer, and showed no sign of slowing anytime soon.

It was like this, with his nose buried in the crimson handheld, that the same teen as before approached him.

Looking bored, and casting not so subtle glances in the female trainer's direction, he motioned for the blond to follow him. "Uzumaki, let's go. You're up first."

Sliding his pokedex into his back pocket, he followed him inside without comment. The structure itself, a massive cylinder design, was a testament to the tasteful architecture favored by Violet City. It was apparent from the high, vaulting ceilings that each floor had been constructed with flying-types and their aerial acrobatics in mind. High up in the rafters roosted a wide verity of flying-types, most of which Naruto had never seen. There were even large, powerful looking avains as large as himself, whose feathers and plumage shined and clinked like segmented steel as they shuffled minutely, their soulless black eyes tracing his every movement as only the eyes of a predator could.

"You'll be facing one of our newer trainers," Naruto's guide informed him as he led him to one of the four battlefields on the second floor. "He's only been with us for a little more than six months now, but what he lacks in experience, he more than makes up for with enthusiasm."

Said trainer looked to be only a year or two older than Naruto's own twelve years, sporting a simply graphic tee and shorts, and a backwards cap that looked two sizes too big for his head. Beaming proudly, he clutched a pokeball, the only one on his person Naruto could make out, tightly in his fist as Naruto approached.

The blond was slightly taken aback by the audience crowded around the field in which his battle would take place. It looked as if all of the gym's trainers and students were there to watch. Catching sight of his surprise, his guide explained as he jogged off to the side to watch the coming match with the others.

"This time of year is always exciting for us. At the start of each new League season, there's always a mad dash by trainers who want to collect their badges earlier rather than later. It's when we get to battle the most." Naruto nodded as he stepped into the challenger's box, opposite his opponent.

"You ready!?" his opponent called to him. Naruto gave a curt nod and a predatory smile, unclipping meowth's ball from his hip as a member of the crowd made their way to the middle of the field to officiate the match. Calling out the rules, which even Naruto now knew by heart, and declaring the match a simple one-on-one battle, the official returned to the sidelines just as the psychic shields that protected both trainers and bystanders from any stray attacks or debris snapped into existence around the field. As one, Naruto and the other trainer, whose name he never quite caught, released their chosen.

Meowth appeared in a flash of blue opposite a black bird of comparable size. The crow-like avian gave a harsh caw before rising into the air with a rhythmic pounding of its inky black wings.

"Come on, Murkrow! Get high up." Flowing its trainer's command, the dual type drifted above meowth in lazy, taunting circles, well beyond her reach. The look in its coal-shaded gaze was enough for Naruto and meowth to know that the dark/flying-type didn't consider them to be a threat.

"Go for it," the other trainer bellowed much to the watching crowd's enthusiasm. "Night shade!"

Naruto's gut lurched when the air about murkrow visibly distorted and turned an otherworldly crimson as a wave of ghostly, sinister energy raced toward a patiently waiting meowth. The normal-type turned rigid at the rapidly approaching attack, but knew her master well enough that if she began without waiting for a command it would spell repercussions for her later. There was something about the attack that reminded him of his last night in his own world and the massacre in which he had participated.

"Move," Naruto hissed. It was a peculiar choice in opening volley. He didn't know if his opponent realized meowth's immunity to ghost-type attacks would protect her from it or if he was really so ignorant as to not know about typing advantages. Unlikely given that one of Johto's premier gyms had chosen to take him on as one of their own. Either that or he was a very fortunate idiot who had yet to encounter a bad typing or a battle in which he couldn't spam night shade. "Don't stop."

"Let's go," barked murkrow's trainer. "Haze! Blind it!"

Inky black smoke poured from the avian's beak, laying heavily upon the field and slowly making visibility all but an impossibility. Meowth cast him a questioning glance as she skittered along the edges of the encroaching smoke, careful not to come into contact with the unknown element.

"Dive in," Naruto ordered. "Stay low and hidden. Force it to come to you." Meowth's leaping ability was as impressive as its speed, which was above average from what he had seen, but she was outclassed in both speed and mobility by murkrow. Luckily for them, the dark-type had yet to display any ranged abilities that would make it all but impossible for them to win.

Quick as a shadow, meowth slinked into the rolling wave of smoke, disappearing from sight.

"Use your perspective to locate it. Then use wing attack!"

Naruto could just make out a vague form belonging to meowth in the cloud of dense smoke, doing as she was told, spidering close to the ground in wait for his next command or a chance to strike at her opponent. This moment came as murkrow, whose sharp gaze picked out the same discoloration upon the backdrop of blackness Naruto was using to follow meowth's movements, descended upon the outline, her wings rigid and ready to punish the normal-type.

"Screech directly overhead! Then stand and use foul play!" Naruto grunted, burning a hole through the avian's feathered form with his gaze.

Smoke clung to meowth's slight form as she did as they had practiced during her spars with his clones, following a command that she herself didn't completely understand, but trusting him enough, if only in the heat of battle, to know he wouldn't lead her astray. A piercing, air distorting cry tore from her throat, dispersing a bit of the smoke cloaking her and causing murkrow to flinch, its sensitive hearing being punished by the auditory attack. It was enough to make a difference. Partially blinded by the dense smoke, it was instinct which allowed meowth to turn her opponent's impressive momentum against it. Murkrow made a pitiful sound as it crashed beak first into the field's unforgiving floor, the tide of its built-up speed only adding to the force of the feline's attack. The dark-type stilled for only a second, smoke billowing from the site of its impact, before it gave a pained lurch as it awkwardly attempted to stand using its ruffled wings and smarting beak.

"Don't let it up, Naruto ordered ruthlessly. The crowd by now had gone silent, their cheers and cries of encouragement for their fellow trainer dying on their tongue's as meowth pounced upon the downed murkrow.

"Peck! Shake it off!"

"Pin it by its neck, if it moves, punish it." With its nape clenched between her teeth, meowth pressed her needle-like claws against its vulnerable wings. All it would take was a moderate amount of pressure from her to "clip" them.

"Call it," Naruto snapped at the referee. Showing mercy went against everything he had ever been taught. It was like saying "wait till my back is turned and guard is down to kill me." But in pokemon battles it was frowned upon to permanently harm one's pokemon, let alone finishing the job. So he would let his opponent forfeit the match, but if they refused his kindness, he'd show no mercy. From her position, anything meowth did would be devastating.

The referee was surprised by being addressed. He looked to murkrow's trainer, who looked stunned by the abrupt turn the battle had taken.

"Forfeit," Naruto ordered coolly, his icy tone like a slap to the face. He had expected more from someone who had been a trainer for at least six months. But like all things in life, he expected there were just those who would excel where others faltered.

Cap askew and mouth agape, the trainer looked pained into silence at the sight of his helpless pokemon. Though Naruto could see it, read it in his warm brown eyes, there was still fight in him. Fight which he was more than willing to crush.

The order formed on his lips, turning them rigid and crooked with an angry sneer. Yet before the command could be voiced, the crack of a pokeball and a tan streak on the air blew them all back, including Naruto and meowth. The blond used meowth's pokeball to recall her before her momentum could carry her into the psychic shields encasing the field.

Returning her ball to his hip, Naruto straightened from the defensive crouch he had fallen into. Standing off to the side, another group of trainers at his back, was the one Naruto was willing to bet was the inspiration for his guide's choice in hairstyle. Hovering on the air before him was the beforementioned tan blur. The massive avian, with its glossy, colorfully plumage and cream-colored underbody, floated in place, its majestic wings, the span of which was easily as wide as Naruto was tall, beat downward in a sedated, rhythmic pattern that dispersed any remaining smoke and created a gentle breeze.

"Matty, this loss is yours," the new arrival declared in a haughty, self-important voice. It was enough for Naruto to know instantly they wouldn't be getting along.

Extensive conditioning to be emotionless to all things aside, which had never been quite as effective on Naruto as it had others, there were still those who he tended to dislike on principal. That his handler had been a Hyuga, the pinnacle and very definition of blustering, opinionated, and full of undeserved pride, he tended to carry a rather intense dislike for any who exhibited any of these qualities.

"You lost the moment he turned your advantage against you." Dressed in clothes that wouldn't have been uncommon in Naruto's own world, but that stuck out like a sore thumb in this new society, the trainer sauntered forward, recalling the magnificent flying-type as he went.

"Leader Falkner," Matty gasped, hastily recalling murkrow, who had only just begun to rise now that the weight, meowth, had been removed from its back.

"Go," Falkner snapped, refusing to look at the teen. His focus lay with Naruto, an unimpressed look lurking in his eyes. "We will speak at length about your failures once I'm finished with… this."

"Challenger," Falkner continued as he turned toward a grand set of stairs that would lead them higher into the gym and eventually to the roof. "Are you prepared to challenge me for the Zephyr Badge?"

Naruto's lips thinned, displeased, as he shook his head. "No, I'm not."

The crowd, which had been making their way toward the stairs, paused, giving off stirrings of surprise and discontent. Falkner also came to a stop, a knowing, shit-eating grin affixed to his face.

"And why not? Your meowth appeared no worse for wear after your battle. From what I heard, you were the most eager to challenge me."

He was correct of course. Meowth hadn't been harmed at all during the match. But aside from screech, which had been more effective than he had realized it would, he had no way to close the insurmountable dived between meowth and his sky bound flying-types. Unlike "Matty," who had been all about close quarters combat. Naruto was sure Falkner wouldn't be hindered by any such flaw. His pidgeot had blown meowth away with just the strength of its incredibly powerful wings, no wind attacks necessary. And while he was sure they wouldn't be facing it or anything remotely as powerful as the avian, he knew a lost cause when he faced one. Falkner was looking forward to thrashing meowth for its win against his student. Naruto wouldn't give him the satisfaction…yet.

"Because unlike your trainee, I know when to fight and when to retreat."

Giving a genuine smile, a dark, antagonistic twist of the lips at the affronted look his words earned, he turned to leave, but stopped as he almost walked into the female trainer from before. Sporting a black and pink cap, a simple vest over a tight white tee, and a pair of cutoffs that displayed miles of toned, well defined legs, she silently regarded him with crisp blue eyes that drifted between his own blues and meowth's pokeball. How long she and her guide had been there, he wasn't sure, which bothered him more than he would admit.

The moment lasted all of a second before she moved on, following her guide toward the field next to the one his battle had taken place upon. Without waiting for an opponent to appear or the ref to step forward, she released a flying-type of her own.

The avian was easily as large as Flakner's pidgeot and just as impressive to behold. Its wings were made up of shades of red, white, and dark blue. In spite of himself, Naruto withdrew his pokedex and directed it at the bird. But when its name was revealed, it wasn't his pokedex which spoke.

"A braviary," Falkner observed, sounding impressed, if only mildly. Forgetting the one who had insulted him and his gym, the admittedly handsome twenty-something year old strutted up to the obviously foreign trainer, a hungry look warming his eyes as he gave her a slow once over.

Scowling down at his pokedex and the "seek national pokedex upgrade" message, Naruto shoved it roughly in his pocket as he strode back downstairs and out of the gym. There was training to be done.

AN: This story is very much a study in what a trained killer—a real assassin—would be like as pokemon trainer. I hope I've at least caught a bit of what I was going for.

As I hope will be clear by next chapter, Naruto's selection in pokemon won't be what you normally find in such stories. No, he won't have any legendries nor pseudo legendries. Though just because his choice in pokemon isn't the same as what's normally spammed by other such stories, doesn't mean they won't be powerful.

As for the egg, it's not the same pokemon as you get in the games or hatched from Ash's and Misty's egg. Though I kind wish it was. Have you seen the stats for togekiss, togepi's final evolution? It's a beast.

And finally, if you're interested in doing beta work on this please contact me through my PM.