AN: Naruto belongs to Masashi Kishimoto and VIZ Media, with both COBRA and G.I. JOE being the property of Hasbro and the various animation studios and film companies they employ that have cooperated with them adapt, create, and release their many adventures. I hold no ownership rights to either of these franchises whatsoever, and I never will. I am simply writing this story as a leisurely past time, and because I am a humble fan of both these universes simply telling a story.

Okay, now that the legal bullsh!t is out of the way, let's get to what you guys came here for then. I originally wrote this a while back, but never really got around to posting it until now due to one thing or another getting in the way. To be completely honest, I haven't had any real interest in the Naruto-verse as a whole since high-school, and now that I've moved on to more interesting anime/manga/comics/etc, I can't even remember why I enjoyed it so much in the first place.

But enough about that, you're here for the story. This sort of came to me out of the blue one day, after watching some episodes of G.I. Joe: Renegades on Netflix. And then it hit me: The shinobi world of the Naruto-verse is incredibly corrupt, politically and morally, so what better way to fight a monster than with a monster? And what organization thought themselves the saviors of the world through criminal activities? That's right, none other than COBRA themselves. So, this story is basically my cutting off all the ridiculous parts of the Naruto-verse off at the knees, and rehauling the ninja world by force through the superior technological and militaristic might of a new COBRA, led by a much more serious, and way more ruthless, Naruto as COBRA Commander.

NOTE: Before we get into the story, I wish to make clear that I'm only posting these chapters to test the waters for this story, and that I'm still planning on updating AZO when I get the chance to work on it in-between my major projects I actually have to get done for college. My life and career comes first, with fanfiction and other such things coming in second as a luxury when I have free time. It's not that I don't appreciate you guys, it's just that life and a lack of inspiration tends to gunk of the creative gears from time to time. Asking when the next update is and asking/telling me to "update soon," is not helpful and will not make me go any faster. If anything, it makes me want to go slower, and makes me disenchanted with the story altogether.

Anyhow, now that we got that out of the way, on with the story!

Prologue.

"Never let your sense of morals prevent you from doing what is right."

- Salvor Hardin, Foundation.

Konohagakure no Sato, Hi no Kuni

Time: 8:45pm.

October 10th.

"... Ow." The throbbing sensation at his temple didn't to go away, pulsating steadily as his vision swam and the world came blearily into view once more. The cold, damp, hard floor beneath him was a small comfort to the pain, wet and clammy against his exposed skin, sending gooseflesh pimpling across his arms and neck. As his senses began to reawaken and the world reorient itself, the damp, musty stench of aged moss and stagnant water filled his nostrils, scrunching up his face in disgust.

All around him, the world was dark. Black as pitch, hollow as the grave. What little light he saw came through slats in the cobblestone ceiling overhead, signifying he was somewhere underground.

Wearily, the twelve-year-old Naruto Uzumaki pushed himself up to a sitting position, steadying himself with one hand while the other nursed the slowly bleeding wound on his forehead. The ringing in his ears began to subside as he tried to figure out what happened. All he know for certain, through the fog of what he hoped wasn't a concussion, was that he had been celebrating his birthday at Ramen Ichiraku with Teuchi and his daughter before heading home, stuffed to bursting with warm broth and noodles. A fitting birthday dinner in his mind.

However, just how he ended up here was a complete mystery.

Of course, the head wound, the underground setting, and the gaping hole in the boarded-up hole over his head seemed to suggest he had fallen through some long-forgotten well-site on his way home through the winding alleyways of Konohagakure no Sato. However, exactly where he had fallen through in that complex maze of concrete was uncertain.

Weakness washing over him, the blonde boy forced himself to his feet and steadied himself against the moss-covered wall, a twisted ankle adding a limp to his walk as he pressed further into the sewage tunnels. This place had to have some sort of maintenance entrance after all, and even with his injured leg he could climb out, or wait for repair crew to come by and help him out. But, given his reputation with the villagers outside of the Sandaime Hokage,- Hiruzen Sarutobi- the staff at Ramen Ichiraku, and his teacher, Umino Iruka, he hoped he could make it out on his own.

For a while, time seemed to slow to a crawl, even as he moved through the tunnels with as much speed as he could muster with his injuries. Vertigo overtook him more than once, and he nearly stumbled into the murky stream of sewage opposite the walls supporting him. Thankfully though, Naruto was a strong boy, and as he pressed on, he felt the pain of his wounds begin to lessen. Soon, the only thing weakening him was his own muscles, tired from the day's work at the Academy, and the energy he once had not mere hours ago being depleted from a lack of sleep.

Stumbling to his knees, Naruto felt as though it might be a good time to rest and reclaim some of his strength, slowly sinking down against the wall behind him for respite. Just then, something caught his eyes at the junction to his left, a small symbol inlaid into a single brick that stood out in the dim light of the moon that shone through the slats of a sewage grate.

It was a cobra. A crimson, stylized King Cobra, it's hood flared wide with intimidation and fangs bared, ready to strike.

Somehow, despite the tired sensation creeping into his bones, Naruto found the energy to rise to his feet and inspect the strange marking. It was finely crafted, and a quick look-over of it revealed that someone took incredible amounts of time in its creation. Curiosity gnawing at his otherwise dreary mind, Naruto reached out and touched the serpent's head.

click

whirrrrrrrr

Machinery that had slept for millennia suddenly found new life at his touch and sang with activation, causing the boy to start for a moment, before becoming instantly fascinated with the sight before him. Like magic, the seemingly solid stone wall began to spiral apart like a snake uncoiling it's body before his very eyes, the darkness beyond suddenly becoming alight as a series of overhead lamps sparked to life, illuminating a pathway that lead further onwards and down at a sharp angle. Far past the range of his sight, Naruto's ears caught the sounds of more machinery coming online, and the steady hum of a generator.

"What the Hell?" he wondered aloud, peering warily into the newly lit tunnel. What was this? Some kind of secret, underground bunker? Did the ANBU Black Ops know about this place? Was it theirs to begin with? It couldn't have been, he rationalized. That snake isn't the symbol of the ANBU, but they're the only ones in the village with a secret headquarters...

Right?

An unexpected tickle against his exposed ankle caused the boy to look down, only to meet the simple gaze of a sewer rat that had chosen to brush past him before looking up at the whisker-cheeked child in animalistic curiosity. Grimacing at the creature before watching it scamper off into the darkness, Naruto gave into the temptation and crossed the threshold, starting once more as the passage closed behind him with a sharp hiss! and locked shut.

"I guess it beats waiting around out there all night," he reasoned soundly to no one in particular, still grossed out at the encounter with the slime-covered vermin. "Bleugh!"

That gruesome reminder of what waited for him outside still fresh in this thoughts, Naruto continued further into the tunnel, this time following the neat metal guard-rail that ran along the wall instead of the walls themselves. Much to his surprise, the interior tunnel was far better preserved than the sewers that lay outside its doors. It looked like it had been cleaned just hours before, the tiled floors practically sparkling in the light! Descending down the staircase for what seemed like twenty minutes or so, Naruto finally exited and stepped squinting into a much brighter room. When his eyes finally adjusted though, what he saw made his jaw drop.

"WHAT THE FUCKING HELL?!"

All around him was a massive chamber, filled with all kinds of devices, machines, inventions, work-stations, staircases to other levels, doorways to other rooms or passages, and all sorts of odds and ends usually found in a military base. A small whirring sound drew his attentions to a series of small robots patrolling the area, each one running a small vacuum on its undercarriage to clean the facility like a fleet of dutiful little housemaids. It was almost amusing... If not for the massive room he was standing being far more impressive by comparison. There were technologies here that the shinobi world could only dream about, and writers of science-fiction could only fantasize about creating or seeing brought to life.

At the far back of the impressively huge chamber, sat a large, round, meeting table, ringed by ten high-backed dome-chairs, and emblazoned with the same blood-red cobra head as the brick outside had been. Against the back wall was a large screen display-monitor and a series of control panels, flanked by smaller monitors for less important operations no doubt. It was the sight of this table that finally snapped him out of his daze, as a sudden red light flickered into existence at its center, drawing him in like a moth to the flame as it grew and stretched upwards, taking the form of a human man, dressed in a military tunic, slacks, combat boots, gloves, a cloak that rested over his shoulders, and a high-tech, featureless helmet that obscured his face. At his hip, was a sheathed straight sword.

"Well, well, well," tutted the illusionary man in intrigue from his seated position, resting his cheek on his knuckles as he spoke. "What have we here? Either one of those foolish JOES come to plunder what remains of my Empire in this safehouse, or an ignorant bystander, lost in the tunnels of this pitiful city. Whatever the case may be, however, I commend you for your discovery, Interloper. Not many know the location of my secret bunkers, and yet, you manage to find the one that has all the things worth taking. That aside, if you are watching this recording, then my time in this world has undoubtedly come to its inevitable end, and my dreams and ambitions have been all for naught."

Now that got Naruto's attention. He knew a few things about dreams himself, and he whenever he did dream, he dreamt big. And, from the sound of things, this man did as well, but at the same time, he never got to see his dreams realized. Something about that just seemed... Wrong, to Naruto. The man had all this technology, all of these resources, and yet he never found what he was looking for.

Why?

"Regardless, your presence here means that, though the world may have undergone a few "cosmetic" changes, in my absence, at its core, the rot still remains." Naruto raised an eyebrow at that. "The government suppresses the governed, those in power pillage and rape the planet and its people without care for the damages they do, or the lives they ruin. The systems that should be there to protect the innocent from the corrupt is instead stacked against them in favor of those with all the power and all the money to make the world go 'round. Men make war over invisible lines in the dirt, over religion, over wealth, over resources, over a burning desire for more and more."

Almost instantly, Naruto's mind flashed back to his history lessons at the Academy, and what the man was saying could be seen clearly in them. All of the Great Shinobi Wars in the past had been fought for reasons such as these. And yet, the ruin they brought was not repaired, the world left in shambles as the powerful sat back and counted their blood money with glee. He remembered sitting in class as all of this was recounted to him, his mind racing with the consequences of the actions of these privileged few and of their role in it all as their hands and feet in accomplishing these tasks. After all, shinobi were mainly seen as tools of the military, the guard-dogs of the governing bodies of their respective nations, easily replaceable when the time came for them to die.

It made him sick.

"You see all of these atrocities, you experience them in your day to day life, and how they have impacted the people around you. They are angry, they are hateful, they resent those who go against the norm and try to change things. They fear what they do not understand, they fear change."

Naruto was taken aback at that, having known those reactions and emotions most of his life, as the villagers always regarded him in this manner. Aside from the old man, Iruka, and the people at Ramen Ichiraku, everyone shunned him and treated him like a pariah, brushing him off and looking at him sideways through judgmental eyes. All he wanted to do was live a normal life, to help people by becoming a ninja, and they looked down on him for it.

"And unless you are simply a treasure hunter or just one of those damn JOES sneaking about my last vestige of power, these sights and sensations disgust you to the core. This world needs to be pulled out of the darkness, brought back on track, and have the cancers plaguing it expunged with fearsome force unlike any seen in history. That, is what you see before you: the remnants of a movement bent on saving the world from itself, poised to strike like the serpent from which we take our namesake. We were COBRA."

"COBRA," echoed Naruto in awe, realizing the scale of what was before him, even at such a young age. Here was all that remained of a once great force that tried to save the world from the people who had driven it into the darkness, only be themselves, hunted down and destroyed by the guard-dogs of the very monsters they sought to kill. He knew the horrors of his world, the prejudice and the corruption, and it made him angry. So very, very angry. By himself, he was powerless to do anything to stop it, but if he had been a part of an organization like this...?

"And if your intentions in this place are counter-intuitive to our own, you will take all the wealth and riches you can carry in those greedy little hands of yours and leave without a second thought, returning only to pillage what remains for your own success. However..." A sudden hissing noise drew Naruto's attentions to the center of the table, where an egg-shaped metal device rose from the cobra's mouth, a hand print etched in red on its surface. "If you see what we have seen, if you feel as we have felt, and you would seek that which we had sought so long ago, then I leave you this place, as one who would carry on the legacy of COBRA, the heir of the Commander. Should you chose to take up my mantle, and shoulder my cause," the hand-print lit up, glowing an eerie red, "Then I leave you with the means to do so... But know that once this crucial step has been taken, that there is no going back. You will become the head of the serpent, the new COBRA Commander in my stead, and the power of COBRA shall be yours to wield. The burden of saving the world from itself shall be yours..."

Hesitantly, Naruto approached the table, his gaze locked with the hand-print as it seemed to urge him onwards. He had always wanted to change the world, to make it a better place for people like him, people who had been cast out and picked on for who they were. He had wanted to make the people who hurt others for selfish reasons pay, to show them that there was someone in this world willing to stand up for what was right. Now that the power to do so had been handed to him on a silver platter, could he really pass it up?

Climbing on to the table, he stretched out his hand to the metal oval, fitting his small palm and fingers into the much larger inlaid slot. For a moment, nothing happened, his hand simply resting there, bathed in the warm touch of the machine. And then?

Pain.

Mind-numbing pain, enough to send his brain alight as though every nerve-ending were ablaze with invisible fire. From his hand, blood flowed in a steady stream, and though his arm and torso went into convulsions, he remained rooted there. Whatever was digging into his skin just wouldn't let go!

"It will only hurt for a fraction of a second," lied the recording of COBRA Commander as Naruto shuddered and shook beneath this holographic visage, a darkness invading the corners of his eyes as unconsciousness took him. "What comes next? More so."

As he slipped painfully into the dark, Naruto swore he heard two final words from the Commander's lips before he lapsed into the blackness, the red-light that held his image blinking out.

"Hail COBRA."

Blackness behind his eyes, blackness when he awoke.

The first thing he noticed aside from that, was the warm, wet sensation that flooded over his entire body, lapping at the sides of his face gently as he gasped abruptly upon waking. The world around him was dark, and soundless. Blissfully soundless, wonderfully silent, beautifully quiet, as though for a moment, the world had gone completely still, just for him. He was in a coffin-like device, that was certain, one that was a bit too big for him, if the spaciousness of the interior was anything to go off of, he reasoned.

In a moment, a flash of recognition crossed his mind, causing his eyes to widen in realization at what was happening. He knew what this was, it was a sensory deprivation tank, designed to block out all sounds and sensations to give the user total immersion in themselves, a unique form of meditation used by those who could afford it to...

"Wait, how do I know all of this?" questioned the whiskered blonde aloud, his voice barely echoing within the casket, the only other sound being the sloshing of water around him as he moved slightly. Just then, the knowledge came to him as easily as before, and everything began to click. 'The Legacy Egg, a steady injection of nano-mite robots into the bloodstream, each one containing the knowledge, memories, and collective experience of the previous COBRA Commander, downloaded and converted into electrical data to be uploaded into a host willing to take up the cause of COBRA. Once circulated to the brain, they latch onto the portions dealing with memory, such as the hippocampus and amygdala, and distribute the knowledge directly to the host's subconscious mind. The initial shock from the upload caused me to black out, allowing the nano-mites to continue their work, and me to gradually adjust to the knowledge and tap into it once the process was complete."

With almost practiced ease, Naruto tapped the button beneath his right index finger and was greeted with a series of clicks and hisses as the tank's lid unlocked and steadily slid open. Squinting in the light of the ceiling flood-lamps, Naruto hauled himself out of the water and swung his legs over the side of the tank, seated on the edge. For a moment, he simply sat there, taking in what all he had learned and remembered about his predecessor's life over the duration of his unconscious episode. It was all there, years of experience, wisdom, learning, and training. He knew more now than any book could teach him, he knew how to work every bit of technology in this room as though he had built it from the ground up, how to use every weapon before him with practiced ease. Even his body felt stronger, better, more fit. He was more awake now that he had ever felt in his entire life!

And on the underside of his wrist, as if a badge of honor to signify the reality of his situation and his new cause, was a brilliantly red tattoo of the COBRA Organization's insignia.

He had it now, the power and the means to change the world for the better.

Slowly, a deeply pleased, and somehow ominously malicious grin spread across his face as he balled his hands into fists at his sides.

"Excellent."

A mechanical sound to his left drew his attentions, as a humanoid metallic shape came into view. Unlike the little Roombas milling about on the floor, this automaton was fully humanoid in design, with its steel-skin, visible joints, and slightly skeletal facial structure giving away its robotic nature. Dropping to one knee, the creature offered up a fluffy towel to the dripping wet pre-teen in a servile manner.

"My Commander," the robot intoned dully as Naruto took the towel and dried himself before returning it to his new butler. "Forgive my effrontery, but upon discovering you on the round table, this humble Trooper thought it best to isolate his Lord until the process was complete."

"You have my thanks, Trooper #559." That's right, he remembered creating these robots, these Battle Android Troopers, with the help of his subordinates during the prime of the COBRA Organization. After his predecessor's death, he had stationed them in various locales around the globe to gather intelligence and chronicle information and world-events in real-time for the COBRA Database, ensuring that nothing would be left to chance for the new Commander once he took his place as heir to the previous.

This would be an invaluable asset to him now, he mused as he collected his clothes from one of the nearby tables, noting how they had been recently washed and neatly folded. They had been somewhat ratty before, and now they were like new, and smelled just as great. He could definitely get used to this sort of treatment.

"Tell me, Trooper," he asked as he got dressed, "how long have I been unconscious?" A pause for thought before he cut off the B.A.T. abruptly. "Gross estimates, please. I am not really in the mood for lengthy figures at the moment."

"Approximately two days, Commander," was the monotone reply. "The current time is 11:47pm, on the day of October 12th."

'Perfect,' thought Naruto with a smile as he pulled his black shirt over his head and slid his arms through the sleeves. "The festival honoring the sacrifice of the Yondaime Hokage, Minato Namikaze, is probably still in full swing. No one would have noticed I was missing in all the commotion, especially since the Old Man and Iruka-sensei already celebrated my birthday two days ago. Then again,' he snorted in mock amusement as the thought crossed his mind, 'I doubt they really cared if I was around anyway. After all, I seem to get more dirty looks during these three days than the other three-hundred-sixty-two.'

"Very well," the blonde replied as he retrieved a shiny new pair of goggles from one of the workstations, continuing to instruct the Trooper as they returned to the main foyer. "Retrieve the files needed for COBRA Project #99741, codenamed, Project: Shed, then contact the Troopers stationed in around the Elemental Nations and any of the adjacent Hidden Villages. Their orders are to upload any and all data pertaining to any shinobi and/or individuals with unique and desirable skill-sets that would be of use to the Organization."

"At once, my Commander." Turning on its heel, the B.A.T. strode swiftly out of the room, leaving Naruto to his thoughts.

As he waited for the android's return, he stood beside the large round table as he had only two days prior, running his hand along its smooth edges and top nostalgically. After all, this was where he had been reborn. Through pain and bloodshed, he had been given a new life, a new path, and a new nindo to follow.

Within moments, the B.A.T. had returned, carrying a small, black, metal case in one hand, and a wicked-looking katana housed in a snow-white sheath in the other. The first steps towards rebuilding COBRA, though small, were the most important in the long run.

"The others have been made aware, my Commander," the B.A.T. reported as kneeled and offered the two objects to his new master, head inclined. "Data transmission should begin within the hour, and a full upload of all knowledge gathered shall be completed within two days time."

"Excellent," Naruto praised the robot as he took the objects, fitting the black case into the kunai pouch on his thigh. "You have my thanks, Trooper. Now, send out the activation codes to all Troopers assigned to Project: Rehabilitation, and let them know that they are to begin the moment they receive their orders. They are to approach their targets with extreme caution, and not to engage in open combat. They are to observe them, and wait for an opportune moment to intercept, and only then when out of the public eye. They are not to be seen by anyone but their intended target, and only then if they have ensured a proper assimilation."

"By Your command," was the reply.

Naruto couldn't help but smile at that, a pleased, Cheshire-like grin spreading across his face. Resting the katana across his shoulders, he proceeded toward the corridor on the second-level of the base, having given the Trooper instructions to continue upkeep of the facility until his return. With the previous Commander's knowledge now pulsating through his cortex, he knew all the secret entrances to his new home that were scattered about Konohagakure, and he could use any one of them to enter at any time.

Right now, however, he wanted to take the long way home. Reflection was good for the soul, after all, and he needed some time to think and plan for the initial stages of Project: Shed.

The ride on the express elevator was a smooth one. No jostling or noises from without that would give feelings of unease to the occupants, and the speed! It was little more than four minutes than he found himself at the top of its ascension, and stepped out into another dimly lit corridor. At the end of the tunnel was a series of metal rungs leading up to a hatch at the top. Once out, he took a deep breath, the cool, clean night air filling his lungs and prickling his exposed skin as he climbed out to take in the view, after replacing the camouflage of course.

The Hokage Monument at the far rear of Konohagakure was one of the village's most treasured and visible landmarks, towering over the city as if their leaders of old were still with them, watching over them, protecting them from harm. His new fortress was somewhere deep within the mountain's center, as it were, a relic of the long-forgotten past, keeping silent vigil behind the relics of the newly forged legends of the ninja world. Far below their watchful eyes, the city was alight and abuzz with activity, people milling about in happy celebration for the freedom and prosperity given to them by the sacrifice of the Yondaime Hokage, completely oblivious to the part they played in the horrors and injustices widespread across the ninja world.

But today, was the day that all would change.

An amused smirk played at the corners of Naruto's mouth as a memory came to mind, more specifically, a memory of a song. A set of lyrics had always been a favorite of the previous Commander, and now that he knew them, Naruto couldn't help but agree. Especially in light of things to come.

"There's a hole in the world, like a great black pit, and it's filled with people who are filled with shit, and the vermin of the world inhabit it..." The smirk grew into a wide, almost evil, grin. "But not for looooooooong!"

AN: (Sing-songing) "They all deserve to die. Tell you why, Msr. Lovett, tell you why? Because, in all of the whole human race, Mrs. Lovett, there are two types of men, and only two! There's the one staying put in his proper place, and the one with his foot, in the other one's face! Look at me, Mrs. Lovett, look at you!" … Ehem, sorry about that, kinda got caught up in the moment there. Anyhow, it looks like things are starting to move for the new and improved COBRA of the Shinobi World. Now that he has this power, what are Naruto's plans for rebuilding the organization? Why did he take that katana and metal case with him? Just what's in that case exactly? What are Projects Shed and Rehabilitation, and what do they mean for the future of both COBRA and the Shinobi World? All of these questions and more will be answered as the story develops, so stay tuned for more updates as time allows. Again, please do NOT bug me for updates, as- again- I only posted this fic to test the waters and see if there might be interest in this project. If there is, I MAY consider continuing it, but that will all hinge on my own investment in its progression and the allowed time of real life outside the 'net. Please remember to leave a review if you feel so inclined (constructive criticism is welcome, flames are doused, and trolls are crushed by their own bridges), and I'll see you guys next time. Take care out there! EXCELSIOR!