Project Naruto: Shinobi X.

Disclaimer: I do not own the Naruto world or characters. Those are the property of Masashi Kishimoto. The challenge I answer here is from devilzxknight86, with all due credit for the basic concept. Let's see how well I can do this.

Basic Premise: Naruto is transformed into a Weapon-X project. This is not an X-men cross-over, the basic 'Weapon-X' idea is the only thing that transfers over.

First Seal: Assault.

The pain was fading... That was certain enough, but it was fading slowly. As the boy, bruised and beaten, cut in several places by sheer impact trauma, forced his one good eye open, and that only halfway from the swelling on his face, he could feel the slight burn as his body healed... again. Every year this happened. Every October tenth a mob came looking for him, and the beatings were getting worse. Especially as he continued to recover. He was lifted gently by a pair of arms belonging to an ANBU in a dog mask, and the familiar jolt-and-bounce of a shinobi running as fast as he could began. He was heading to the hospital again, he knew. The Hokage would be there, as soon as he found out, but why couldn't he stop it from happening in the first place?

The blond boy didn't know who was doing this to him, and the people who did get caught somehow mysteriously walked free within hours with all charges dropped. He was in so much pain sometimes that he almost wished it would all stop. But then he'd hear a vague and somewhat shy giggle in the back of his mind, a soft voice that he could never quite place saying something he could never remember, and he would drag himself back up and fight for his life. Even now, when his very blood was leaving a clear trail showing the ANBU's progress, as the boy slipped into unconsciousness, he'd recall vaguely the girl (that much he was sure of) and his attacking the bullies who'd cornered her. He'd lost of course, but he'd fought them hard, drawing their attention, and luring them, away from their first target... Some days, he wished he could remember who she was, but the five boys had beaten him harshly, even if he'd given well nigh as good as he got. The girl's minder had shown up and bought the bullies' story that Naruto had been bothering the girl, and delivered a strike to the boy's head, ignoring the protest of the girl. As she'd knelt beside him that day, he'd heard her apologising, thanking him for saving her, before being dragged away...

The doctors and nurses at the hospital were indifferent to the boy. As long as the ANBU was watching they did their jobs, but the second he left to report to the Hokage, they left him in a room alone, to die... or live, as he had a distressing tendency to survive. The boy had heard the hate-filled epithets they muttered at him before, and though they puzzled him, he had long since grown inured to them. It was not living he was doing now, it was surviving. He'd made up his mind that he would be Hokage one day, and he would manage it... if only for her.

The white-haired young medic-nin looked at the boy's chart. The way this Uzumaki brat was healing was incredibly rapid, almost unnatural. Maybe he could use that to find a cure for his Master's disciple. It would take a lot of planning, but if it worked...

Naruto opened his sapphire blue eyes to see a ceiling that had been spattered with something brown, almost black in some places. To one side, he could see a table with silvery instruments arrayed upon it, and two men discussing some kind of notes. He was firmly secured to the table, and to the other side, if he twisted his eyes far enough, he could make out another table with someone strapped to it. Even as he watched, he saw the taller and skinnier man, who had strange yellow eyes, collect a shard of what looked like bone from the other person's chest. Since there were no screams, the other person must have been unconscious. As the two upright figures stood over him, the taller one spoke in a voice that seemed designed to give people the creeps.

"Oh, good, you're awake..." he said, smiling sadistically. "This experiment is most likely going to hurt a little." The searing pain as the shorter man opened the flesh of Naruto's chest with a scalpel and quickly cracked the sternum caused the boy to scream in agony... and he hadn't screamed when the mob had come for him. The taller man inserted the shard of bone into the fracture in Naruto's breastbone, and the two men then sewed the wound shut.

"Over the next few days, this is going to hurt a little more," the snake-eyed man explained. "Either you'll survive, in which case you might be useful, or you'll die, and we can disect you to see what went wrong. It's a win-win situation... for me..."

As the blond boy, barely nine years old, drifted into the oblivion of unconsciousness once more, the 'experiment' began...

The shinobi of Konoha were mobilized by the order of the Hokage, and sent out to find Naruto within minutes of the boy being reported missing. Since that didn't happen until the ANBU in the dog mask stopped by the hospital at noon the next day, the chances of finding him were significantly reduced. A great many ninja didn't put much effort into the search, wanting nothing to do with the 'demon child', not that they said it in as many words, of course. But if an Inuzuka 'overlooked' a scent here until the trail was cold, or a Hyuga or Uchiha 'forgot' to activate their doujutsu there, who could prove otherwise? And as for the few who actively concealed evidence... well, the ROOT program had been shut down, so they couldn't possibly exist, could they?

The boy had lost track of so much time. As bone shards were inserted all over his body, one at a time, he was hurt more and more, he got weaker, his senses shut down... in short, he was dying. The snake-eyed man, called Orochimaru-sama by his subordinates, watched. The experiment was failing. Kimmimaro could no longer afford to donate bone shards. If it hadn't been for the blond brat's marrow, injected directly into his bones, Kimmimaro would have been useless long ago. These reports had the brat healing well for the first few weeks, but then his bones had begun their breakdown. At this point, the boy was a burden on their resources. Ironically, much like the Konoha medics, the researchers here relegated the boy to some out-of-the-way corner to die.

Naruto knew he was dying. It was hard not to as his hearing dulled, his eyesight dimmed and his sense of smell and taste shut down. The very act of moving too fast was enough to break bones now, and too fast was any motion quicker than a slow, time-consuming crawl. Since he was of little other use, the researchers had attempted to strengthen his failing bones with that silvery, chakra-conductive metal, but with little effect. In fact, the malaise that seemed to be breaking the boy down was corroding the metal implants, breaking them down and whisking them away through his bloodstream. Now all he could do was wait for death...

As he closed his eyes one more time, uncertain if they'd ever open again, he saw that vague silhouette of that girl, and wished he at least knew who she was.

It had been three months since Naruto disappeared. No-one was looking anymore, except the white-haired old spymaster Jiraiya. He'd even given up writing to search, a fact that depressed the former ANBU called Hatake Kakashi. But he was the only one allowed to look, by order of the council. It hadn't been a unanimous vote, but for some reason the edict had gone out. The Toad Sage had spent a week lamenting the fact that his information network in his home village was... underdeveloped (say rather, non-existent), and had then thrown himself into both building it up and investigating the disappearance. In a move uncharacteristic for him, the 'Legendary Super-Pervert' even eschewed his 'research' in favour of these tasks, and did not like the results... or rather, the lack of them. Someone was sabotaging his efforts...

The Academy took in its next class in another three months, and most of the prospective students couldn't care less about this whole mess. A number of them were even glad that the incorrigible prankster was gone. But there was one little girl who looked around shyly, searching for him with her pale, moon-like eyes and quietly crying at his absence. Every day, in the corner of her garden, she would open a bento-box and put out enough lunch for a person to eat... remembering a boy who had saved her.

It was ironic, in a way, that the very neglect that threatened Naruto's life, the wasting of his bones, led to his salvation. Deep inside the seal on his belly, a seal none had seen for the boy could not channel chakra yet, nor mould it to any purpose, the Kyuubi no Yoko took note of its jailer's plight. In the boy's weakened state it was easy to see the seal that trapped the biju within him, at least from here in Naruto's mindscape, and the effects were going to carry both boy and beast into the afterlife. Spiteful as he could be, the demon-fox wanted to live a lot more than he wanted revenge on his prison. Of course, he couldn't reach past the seal to do much without the damn thing triggering. All he could do was send out his chakra in a blind attempt to heal the boy, and he didn't know enough about humans for it to do any good. On top of that were the several shards of foreign bone in the boy, and the tissue rejection issues they were causing, as well as the boy's general shutdown.

Fortunately, perhaps, the Kyuubi could feel he wasn't alone in here. The Seal held two more segments of chakra, suppressed and contained for specific triggers. He could feel these triggers, and knew how to set them off, and those chakra signatures wouldn't trip the seal's failsafes. He just had to do this right...

Stretching out with the thickest strand of his demonic chakra he could manage without tripping the seal, the fox gently eased the boy into his mindscape, a vast, sewer-like construction with a single incongruous ray of sunlight. Usually, the thing was overflowing with stagnant water, but in Naruto's current state of mind, it was blood, thick and black. Although Naruto was shocked and scared when he saw the Kyuubi, he was truly beyond caring what happened to him.

[Wake up, boy,] the demon rumbled, its words appearing in Naruto's strained mind without passing through his ears, [or don't you want to find out who the girl is?]

Struggling to stand, the blond boy leaned against the bars. "I'm dying. Looks like I go to Jigoku if I'm seeing the Fox that the Yondaime Hokage killed..." He was too hurt to flinch as the Killing Intent of the Kyuubi washed through him.

[KILL ME!?] he roared. [That man barely had the power to seal me! And he was the strongest leader your village had ever seen.] Shaking his head, the demon fox pushed his temper aside. Living was more important at the moment. [Boy, if you want to live, you're going to have to pull down that seal. That will release what you need to survive.]

It seemed a simple enough proposition, even to Naruto, but the very simplicity made it suspect. "And if I don't?"

[Then we both die and your village will probably fall in as little as five years,] the Kyuubi replied, pulling a wild guess from thin air. His eyes narrowed as he went for the weak spot. [Including that cute little vixen you can never quite recall...]

That did the trick. Naruto reached up with the full intent to shred that seal... and found his wrist caught by a man who greatly resembled the Yondaime. The demon fox didn't even pause for breath or to let the man speak as he extended a tendril of his power towards the boy, commanding as he did so. [Master it, boy, take it inside you and claim it!]

Without thinking, Naruto attempted that very thing, even as a confused looking Yondaime glared at the fox. The effort smashed the boy's conscious mind deeper into oblivion, even as a red-haired woman appeared. The last he knew of anything was the fox's 'voice'.

[We don't have time, he and by extension that means me as well... we're dying. I have the power to fix it, but can't reach beyond the seal, and don't know how. The two of you can, and may just know enough...]

Had anyone thought to check, they might have noticed the boy sweating and curling into a ball, wracked with pain as red chakra surged through him in a curiously controlled manner, super-charging his immune system and laying hold of any material it could use to rebuild him. His senses were rebuilt, sharper than ever, more potent, sight and sound and scent... His bones were strengthened and healed, stronger than ever, shifted around as Kimmimaro's kekkei genkai was assimilated in a unique manner, as claws, blades of bone stronger than tempered steel, grew within his arms, and the muscles and nerves surrounding them shifted to facilitate their use... The bones were further strengthened as the remnants of the chakra conductive metal were retrieved from within his system, and plated onto and tempered with his bones. The last and possibly most essential phase was the enhancement of the kekkei genkai of the Uzumaki line, the unknown factor that allowed them to heal quickly, and resist diseases and poisons, as well as maintain a lifespan at least half again that of others. This would mean his wounds would heal impossibly fast, and his immune system would vastly increase, rendering him almost immune to toxins and illness.

As the chakra infusions that were all that was left of Namikaze Minato and Uzumaki Kushina faded, the Yondaime's echo turned to the demon fox. "You've only got three hours, use them well, and get him to somewhere or someone safe if you can." He then suppressed the seal as he faded away, smiling at Kushina, sacrificing themselves for their son a second time.

It was perhaps fortunate for Orochimaru that he, Kimmimaro and his top spy from Konoha were not present when this happened. Over the course of two hours, every living creature in the base that was not a prisoner was used to paint the walls a most horrific shade of red, and then, leaving a number of dazed and terrified former experiments and prisoners behind (although in Orochimaru's strongholds the difference was negligible), the creature that had slaughtered so many tore across the countryside at top speed.

Senju Tsunade glared at the dice before her. The hard sixes. Six times, she'd rolled, asking the proprietor if someone might have swapped out her dice for loaded ones. No-one else who'd rolled them had managed to score the highest 'hand' in the game. One more time she picked the dice up, all six of them, dropping them one by one into the cup, rattling it hard, and casting them. Again, the six dice all showed the same face... the circle of six dots representing a crown. Pushing her winnings across the table, along with her case of IOUs, she asked a favour of the house.

"Could you see that these debts get paid off, please?" she requested, slightly shocking her apprentice Shizune. "If my luck is holding true to form, I may not live to." Gathering the rest of her things, including a purse containing a modest sum (as compared to the massive pile of ryo she'd left inside), she immediately began to leave town, with Shizune pushing herself to keep up, with no idea what was about to happen.

The savage creature that was, to all outward appearances, a nine-year-old boy, raced through the forest and the storm as though the very hounds of the Hells were at his heels. Where he could, he simply forced his way through, and where he was blocked... his new claws made sure that he was not blocked for long. The fox that was riding his mind, guiding him through instinct, could feel the seal beginning to close, and had little desire to collapse for what would be years to him and wake up as a pile of wild animal droppings. So he pushed the boy's body harder, as if by sheer will he could get him some where safe, heading by instinct closer to Konohagakure no Sato.

When he burst out of the shrubbery onto the road, which he had not expected, he paused for a critical moment as he turned to assess where he was, and heard a pair of voices gasp in unison, and a pig squeal in fear. Focusing on the travelers he'd just startled (or terrorised, whatever word worked best) he saw a tall blonde woman with an oversized pair of breasts (she smelled older than she looked, for some reason) and a shorter black-haired woman with a more modest figure holding a panicking piglet. Then the seal slammed shut, and Naruto's face eased back from the savage snarl into a puzzled look, as he collapsed in the street.

Tsunade stared at the boy who'd leapt from the bushes at the roadside, far too exhausted to notice them until too late. She could see the scars fading as what remained of serious wounds healed before her very eyes, in seconds rather than weeks. His clothes, what remained of them, had once been hospital-issue, but were now little more than decorative ribbons. He looked familiar, too, as though she'd seen him somewhere before... She shook her head as she took in the last detail, the most surprising: the blades that emerged from his hands, three on each, each a good eight inches long and from what she could see, sharp as a razor. A kekkei genkai, perhaps? The blades seemed to be metal, too, that chakra sensitive alloy that some shinobi used for their weapons. Still, he was a boy, and unconscious. Sighing, she picked him up, and stroked the muscles of his arms like a cat's paws, hoping the blades would retract. They did, and the Queen of Slugs and Elixirs turned to her apprentice.

"We'd better set up camp for the night, Shizune. We're not going to get far now." As they stepped from the road, Tsunade increased the chakra flow to her muscles a fraction. From the weight of the boy, she'd guess that his entire skeleton was that bone-metal amalgam, and that his muscles were sturdier to handle the extra mass. The little gaki was heavy!

Naruto opened his eyes, and immediately regretted it. They were extremely sensitive, and the sunlight he stared up into was painfully bright until they adjusted. Rubbing at his eyes as he rolled to face away from the sky, he learned his muscles were incredibly sore. The pain was fading, almost completely gone in fact, but there was a residual ache that was slow to depart. He could hear breathing from nearby, and looked in that direction.

Over ten feet away, the two women (looking vaguely familiar; He didn't have much recall of how he got here) were sitting by a small fire, discussing something in some scroll they were looking at. As he lifted himself, absently noticing he was heavier than he remembered, they looked in his direction. Their voices were incredibly loud to his ears, and he covered both with his hands to filter the noises. The old one who didn't look it smelled overwhelmingly of sake, and the other had some rather acrid scents about her. It looked like this would be quite the challenge.

Jiraiya was following a lead. Somewhere out in this direction was one of Orochimaru's little strongholds, and it was in this direction that his meagre clues brought him. As he trudged along, he came to a gambling den where he overheard an interesting snippet of conversation.

"So there she was, all night, casting the worst hands possible at any given time, and she's about to chuck it in as a bad lot when Kudama eggs her into putting everything she's got left on the hard sixes. She goes him one better and calls hard sixes by seven, apparently figuring if she won she could clear her debts, but if she lost, it wasn't like she'd owe us any more." The speaker was a rough-looking gambler type with a case of IOUs and another filled with money, gradually dispensing the latter to the proper claims of the former as he spoke. "Please, bear in mind this is the Legendary Sucker."

As the other gamblers chuckled, Jiraiya frowned. Tsunade was out this way as well? That was quite a coincidence. He returned his attention to the gambler's story.

"So, yeah, Kudama covers it, figuring it's a sure thing, and puts his stake all in. Then she casts them, seven times. The hard sixes, the ring of crowns, whatever you want to call it. She frowns a bit, and casts twice more. Same thing, and Kudama's about to call her for cheating when she passes me the dice and asks if someone's switched them out! Beats him to it! So of course I send them round the table once, and they're just regular dice. Even Kudama gets them, and double checks them. So she gets the dice back and throws again and again and again. Now she's really staring at the dice, glaring at them almost, and she throws her last hand. Hard sixes. She's won, and asks me to see to her debts. Kudama insists she's got to be using loaded dice and points at her as she's leaving, and an extra set of dice falls out of his sleeve. Now everyone sees how suspicious that is, so I pick up the dice on the table and cast. Sure enough they're loaded... for all the ones. Seems Kudama switched them when he was looking them over. So we had Oniyama take him out back to... discuss things with him."

As the gamblers laughed riotously, the Toad Sage calmly walked away... at least to outward appearances. No-one knew better than he how Tsunade's luck ran. If she'd scored such a massive win, her life was most likely in danger...

Breaking into a run, he chased her rumoured path from the vilage.

Naruto stared at the claws that extended from his hand. After explaining where they'd found him... or rather, he'd found them, they had told him of what they'd seen. He'd always healed quickly, if not this fast, and he'd rapidly learned how to focus his senses, from self-defence if nothing else, but they'd had to help coax the three blades from his arm. There was a particular muscular twist to it, and a similar one to retract them, and of course, he had to want them to do so. A moment's testing was all they needed to determine that yes, his bones were all melded with the silvery chakra conductive metal that now laced them. It presented an interesting idea for a shinobi to have weapons that couldn't be taken away from them, but in most such cases rejection issues clouded what was possible.

As the three packed up their camp, the older lady, Tsunade, spoke. "I can't believe we forgot to ask, gaki," she apologised, sort of. "What's your name?"

"Naruto," he replied, handing Shizune the folded bedding to place in a storage seal. "Uzumaki Naruto." He realised, falsely, that these two nice women wouldn't want to travel with him anymore, and sighed as the Sannin lady stiffened, which to his young mind confirmed his guess. "If you could just point the way to Konoha, I'll get out of your hair... sorry to bother you..."

He lost what he was trying to say as Tsunade grabbed his shoulders and began investigating his face... yes, her features were there, a little harder at the edges, mixed with the father's... and with that blond mop, there was only one person that could be. Seeing the fear start to rise in his face she loosened her grip as she crouched, talking with him on an eye to eye level. "I'm sorry, I didn't mean to scare you, it's just... I knew your mother. When I heard she was killed, I was told her child, her son, didn't survive... that he'd been killed by the Kyuubi."

A vague image rose in Naruto's mind. The three figures he'd seen last night, working together... The Kyuubi providing the chakra, the redhead focusing it and the Yondaime directing it... into him. He didn't know who they were, but from what the Hokage had said to him... they were probably his parents. He couldn't picture anyone else, with a handful of exceptions including these two nice ladies, who cared enough to save him. He was about to speak when a suddden explosion of smoke burst in front of them and an old white-haired man in red and green, standing on the back of an outsized toad appeared, beginning to loudly proclaim himself, hurting the boy's ears.

Jiraiya had spotted the boy, and with the two women distracted, had decided on a fine prank to get back in the swing of his normal routine. As he appeared he began his speech, hoping to impress Naruto and tick off Tsunade, just a little. "Attend," he cried, striking a pose on the back of Gamatoro, one of the battle-toads of Mount Myoboku. "I am the mighty Toad... Sage..."

His planned speech was cut short as Naruto flicked his arms outward and his claws sprang forth with a meaty 'snikt'. By instinct, the boy crossed the blades across his chest, guarding his vitals as he watched the intruder. He was worried, but if these nice ladies were in trouble, he'd help them... Not that it seemed necessary as Tsunade gritted out the newcomer's name, in pieces...

"Ji-rai-ya," she said, almost sweetly if you could ignore the grinding teeth behind it. As he glanced in her direction, she hit him, driving him hard across the clearing until he hit a tree on the far side. "We just got him calmed down you old fool!" she hissed in the aftermath as Naruto put his claws away, making the mental note not to piss her off unless he really had to.