A/N: This story will be canon with the Naruto manga up to around chapter 440, where the Yondaime repairs the seal and sends Naruto back to fight with Pein. After this point the story will deviate pretty heavily from the manga.

Full Summary:

Konoha has fallen. In its moment of weakness, Rokudaime Hokage Shimura Danzo took control of the village and ordered the execution of one Uzumaki Naruto, believing the threat of the Kyuubi will die with its jinchuriki. Our heroes escape underground. Three years later, they revolt.

However… despite their preparations, the Konoha rebel army is driven back by the force of an unlikely alliance, and must turn to the seas for refuge. Alone and in unfamiliar territory, our heroes struggle to find their place in the New World, and resolve to one day take back their home. Unfortunately for them, nothing is quite what it seems, and they are all just mere pawns in a much larger game…

The main story takes place in the One Piece world two years after the rebellion. Assuming most of the Rookie Nine/Team Gai are 15/16 when the initial Pein invasion occurred, they would be 18/19 during the rebellion and so 20/21 during the current storyline. The story picks up at the Baratie arc, so Luffy will be 17, most of the others Straw hats will be 19, etc.

Sneak Peek:

(a very brief excerpt of things to come)

The Thirteen was everywhere.

Relatively unknown until the recent Battle of Marineford, news of their prowess and rumors of their abilities have now spread far and wide, through all corners of the world… even reaching the ears of those who have been lost in history for nearly a millennium.

No one knew just how many were actually working under this organization. Estimations of their numbers ranged from the leading thirteen to thousands of minions. What the World Government did know, however, was that their very established network had infiltrated almost every inch of society, from Marineford to Mariejois to the Revolutionary Army. Its members were spread all over the Grand Line, and their strange techniques made it nigh impossible to pinpoint the imposters in their midst.

Rumors of the organization's mounting influence had circulating for ages. The Elders had their suspicions, of course, but most rumors were not to be trusted. That was their first mistake.

As their correspondent finally made his presence known, the Gorosei took one look at the man and saw the barely concealed anger brimming beneath the surface, threatening to explode. Dangerous mismatched eyes, one red with pinwheel pupils, the other light purple with strange ripple-like patterns, narrowed in warning, and they knew they were in deep shit.

Their ancestors should have never agreed to that man's offer. There was no going back from a deal with the devil, and the now the entire world was about to pay the price for their failure.

-Remnants of a Shinobi's Fire-

Prologue

"There is a plot… a plot that aims to enslave every man, woman, and child… and there is nothing we can do to stop it."

−The First Council of Kings, 876 years before the Age of Pirates

The Konoha of today resembled nothing of its past.

Once known as the most peaceful of the Five Great Hidden Villages, today civil turmoil was rife under the leadership of the Rokudaime Hokage. Laws were absolute under Danzo's militaristic dictatorship, and the man had little tolerance for anything less than perfect obedience.

Ever watchful Root enforcers patrolled the streets, ushering subdued civilians back into their homes for the five pm curfew. What little non-Root shinobi that remained glared hatefully at their lack of freedom, but nevertheless kept their head down, not willing to incur the wraith of their new Hokage.

It was quite depressing, really. Konoha's famous Will of Fire was no more.

Familiar footsteps approached softly from behind, interrupting his thoughts, and the former Akatsuki leader slowly turned to face his sole surviving friend and partner.

"Has it started yet?" he asked, eying the eerie calm of the village below. It was a calm that could only exist before a storm.

Konan nodded, unfolding a map and gesturing to an area near the village outskirts.

"The rebel army has started moving. They should reach the village by sundown."

"Good," Pein responded. "We should be able to grab Uzumaki after Madara's army arrives."

"Are you sure about this?" Konan questioned hesitantly after a slight pause. "Madara's hiding something, but to openly oppose him like this?"

Pein's gaze was thoughtful as he eyed the deceptively peaceful village. From his perch up on the Hokage Mountain, he could see everything that went on in the streets below. More importantly though, he could finally see his destined path clearly. He had Uzumaki Naruto to thank for that.

"We proceed as planned." The Akatsuki leader's voice left no room for argument. "Madara doesn't suspect us yet, and we can use that against him. We'll pretend to bring him Uzumaki, and finish this once and for all."

Everything had gone to hell in the span of two minutes.

Cursing under her breath, Haruno Sakura, once esteemed medic and the Godaime Hokage's personal protégé, pivoted sharply on her left foot as the sword of a masked Root ANBU made a clean slice across where her head had been seconds ago. Quickly preparing herself as the nin charged at her again, Sakura's mind whirled as she calculated the movements of the enemy. Carefully bringing the exact amount of chakra needed to her fingers, Sakura brought her hand up at the last possible second and barely managed to brush the tip of her fingers across the Root nin's chest, taking the split second opening to inject her lethal chakra into the man's heart.

The nin was dead before he'd even hit the ground.

Not sparing the fallen Root member a second glance, Sakura pushed off the tree branch and continued on her path to the docks without breaking stride. Desperately pumping more chakra into her legs, Sakura willed herself to go faster as her mind furiously tried to process where exactly they had gone wrong. The plan had been flawless, with Sakura and Shikamaru, the two lead strategists, meticulously going through every detail. Preparations had taken two years, and the entire rebel force had trained intensely for this moment. Everything had been going according to plan—that is, until Madara had decided to join the fight alongside Danzo, bringing with him the force of the entire Akatsuki... by the hundreds.

Literally.

In addition to having found some twisted way to clone the bicolored plant-like Akatsuki Sakura vaguely recalled as Zetsu, it seemed Madara had also gotten a hold of Orochimaru's Impure World Resurrection technique. Four of Konoha's past five Hokages, including her own shishou, have been summoned, along with numerous elite nin from all five hidden villages. It was madness beyond Sakura's worst nightmares.

Body weighted down by remnants of poison and chakra running dangerously low after being forced to fight the revived Akasuna no Sasori for the second time, the pink-haired medic nin knew she was at her limit. I can't keep up this pace much longer, thought Sakura grimly, and I definitely don't have enough chakra left to fight off another S-class opponent. That was my last soldier pill. And Ino, Chouji... I can't believe I just left them to—

No. The medic nin angrily blinked her tears back. Don't go there. Don't talk as if they're already dead. What's done is done. Get your ass to the docks so their sacrifice wouldn't be in vain.

It had been two years since Akatsuki's initial attack on Konoha, and while Naruto had managed to defeat its leader Pein, Danzo had chosen to strike in Konoha's moment of weakness, proclaiming himself Hokage and beginning his reign of terror. Tsunade, Sakura's mentor and surrogate mother since her parents had been killed in an ambush several years back, had been brutally murdered while still unconscious. It was an incredibly cowardly thing to do, for Sakura had no doubt neither Danzo nor any of his lackeys could have even presented a challenge had her shishou been in prime condition.

Danzo's first orders as Hokage had been the execution of Uzumaki Naruto, jinchuuriki of the Kyuubi and Sakura's closest friend. Despite the fact that the very man he'd condemned to death had just saved the entire village from Pein's attack, Danzo and the council stubbornly claimed that Naruto, as host to the Kyuubi, was a danger to the village and therefore needed to die, for with his death the threat of the nine-tails will be removed forever. Immediately, an underground resistance had been established with Naruto at the forefront of the movement. Most of the Konoha Twelve and their senseis had gone AWOL as well, though several of Konoha's most prominent clans, including the Hyuugas, had decided to stay by Danzo in order to maintain their positions of power. However, given that the majority of Konoha's elite nin had fled underground and joined the rebel force, what they lacked in numbers they made up for in skill. The operation should have went off without a hitch. By all counts, Danzo should have died today.

Yet the one variable they didn't factor in, the single instigator of all this chaos and the original mastermind behind Konoha's downfall, had single-handedly turned their plans to ash and flipped Sakura's world upside down. Uchiha Madara, you bastard, thought Sakura in pure fury, fisting her hands hard enough to draw blood, isn't it enough that you've already ruined Sasuke-kun and destroyed the village? I'll die before I'll let you take Naruto from me too.

No one had anticipated Danzo's alliance with Madara. Sure, he was a power-hungry militarist old bastard, but as corrupt and primitive as his ways were, everyone believed he had Konoha's best interests (or at least what he believed were Konoha's best interests) at heart. Every order he gave, every mission he assigned, was aimed at propelling Konoha to the top of the shinobi food chain and establishing its status as the most powerful hidden village. For fuck's sake, he ordered Naruto killed just so the Kyuubi wouldn't fall to the Akatsuki's hands, seethed Sakura, so what the hell is he doing getting friendly with the person most eager to bring Konoha to its knees and—

There. Sakura snapped out of her inner tirade upon smelling the salt in the air and seeing the vivid blue of the open ocean at last. I made it. I can't believe I actually made it. Please please please let the others be okay.

The slight shift in the breeze was the only warning she got before a barrage of deadly senbon suddenly came flying at her at a near impossible speed. Gracefully twisting in the air, Sakura watched with narrowed eyes as the senbon embedded itself in the branch where her head had been less than a second ago. Poison, she realized as she watched the thick leafy branch slowly disintegrate into nothing, and a deadly one at that too. Carefully masking her chakra, Sakura quickly scanned her surroundings and got into a defensive stance, muscles tightly coiled and ready to spring into action at a moment's notice.

Root. There had to be at least 2 full squads. Damn.

Sakura knew she was trapped. She couldn't outrun them all, and she didn't have enough chakra to fend them off. But if she was going to die, she was going to take as many of these treacherous bastards with her as she can.

With a final burst of strength, she slammed her heel into the ground. The small quake that followed ruptured the earth beneath them, throwing the Root nins off balance for a moment. Sakura seized the split second opening and rushed the nearest one, landing a solid uppercut to his throat, breaking his neck instantly.

One down, eleven more to go. Sakura pressed her lips together in grim determination and watched warily as the nins circled around her like vultures.

There was a sudden, sharp, prickling pain in her leg, and she looked down to see the senbon that they had been throwing since the first attack had finally hit their mark. Head swimming and limbs weighted down with fatigue and poison, Sakura shakily jerked the needles free and pushed herself to her feet by sheer force of will. But it was no use—she'd reached her limit.

Sakura sank to her hands and knees, and eventually collapsed entirely. Her breaths came ragged, her heart hammered in her ears. Maybe it was the numbing, disorienting effects of the poison, but strangely enough she wasn't afraid. She thought fleetingly of her teammates and hoped they had escaped.

The remaining Root agents closed around their fallen target.

Sasuke-kun... I'm sorry I couldn't help you. And Naruto...

Naruto... Sakura's tired eyes snapped open as the realization hit her. Naruto would never forgive me if I gave up.

With a speed she hadn't know she possessed, she drove her fist into the sternum of her nearest attacker, collapsing his chest cavity and crushing his heart. Spinning rapidly, she whirled to confront the others, but found them all dead on the ground, a wickedly sharp kunai embedded deep between each of their eyes. Who—

Sakura froze, eyes widening in a mix of shock and fear as she locked eyes with her rescuer. Spinning crimson eyes was the last thing she saw before everything went black.

It was finally happening.

Decades of preparation, and his plans were finally coming to fruition. Uchiha Madara watched with a satisfied smirk as the transformation slowly took place, consuming anything and everything in its path.

Rays of ephemeral orange shimmered weakly across the darkening sky, before disappearing forever into the distant horizon.

The world had just seen its last sunset.

The darkness diffused gradually into a dark crimson color, occasionally pulsing with rays of intense, vibrant red. The ground took on a dull coppery tint, lakes and plant life following suit. Soon, everything was tinged red.

The only exception was a single silver sliver in the sky. An ominous breeze drifted through the landscape, red clouds slowly shifting to uncover the full circle of the omniscient moon.

Ten black tomoes spun lazily, gradually picking up speed as the illusion was cast.

And the fate of the world was sealed.

A week later, in various parts of the Grand Line…

The world's most unpredictable ninja twitched as he slowly came into consciousness, vaguely registering the presence of hundreds of powerful enemies before mind-numbing pain erupted from his stomach, and he knew no more.

Three thousand miles to the west, in the dark waters of the Florian Triangle, a heavily wounded shinobi sighed as he reluctantly got to his feet, and prepared himself to face the undead that came crawling once more from their graves.

Two thousand miles to the south, a tired trio struggled to maintain their cover, sprouting lie after lie to the Snake Empress despite their limited knowledge of the Outside.

Five hundred miles to the east, two kunochi tugged their hoods lower over their heads, and tried to remain as inconspicuous as possible, after their latest ride got commandeered by pirates specializing in human trafficking.

One thousand miles to the north, Cipher Pol's eighth division was in an uproar as their newest recruit single-handedly defeated all five of their strongest officers, without once looking up from her seated position.

Ten thousand miles inland, two teammates listened with identical bewildered expressions as their host told them about the crimes of the World Government, and insisted on inducting them into their forces after having witnessed their skills.

And halfway across the world, a certain pink-haired medic-nin blearily blinked her eyes open, and found herself staring at an entirely different ocean.

A/N: Rewritten to reflect more of the overall plot upfront. Let me know what you think! Your feedback and comments are a huge source of motivation!