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Naruto: The Best Naruto Neglect/Dark/Banishment Stories

These will be the best Naruto neglect/dark/hate/banishment stories by several different authors. All authors will get credited. Most of the stories will be abandoned stories. Enjoy

Hyuga_Tobirama Ā· Anime & Comics
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242 Chs

Chapter 26

A/N: I've always wondered why a bunch of crazy S-ranked ninja would join a criminal organization. Last chapter I presented my hypothesis; it's not canon to the best of my knowledge.

As to Kakashi's fate, it is possible he's deadā€¦or that Naruto lied to a dying, hated ninja for his own purposes. Remember that only one ninja died trying to kill Jiraiyaā€¦and many others were slaughtered by Pain's six bodies. No more will be said about him in this story.

As for the unexpectedly horrible corruption of Konoha in this story, especially Asuma's role, this has been foreshadowed in this story. (A Sandaime too weak to battle the council to allow the young Naruto to at least attend a civilian school would definitely be too weak to control his own son.)

Danzo's a true bastard in canonā€¦and in this story I just changed around some of his compatriots. Canon Konoha will survive because of people like canon Naruto. My Konoha has fallen to the corruption eating at its roots. Not that many things have to change in order for that to happen, by the way.

X-X-X-X-X-X-X-X-X-X

"You can come out now, Madara. I know you're lurking aboutā€¦."

The orange-masked muppet did appear then. "Your earth wall technique was impressiveā€¦and annoying. I could not see what you did to Sasori. It is good I deal with you today before you become too powerful. Your body will survive even after your brain is dead. For a few days, at least, until I can get that demon out of youā€¦."

Naruto gave no visible reaction to this fearsome sounding threat. No, he continued on with his semi-absent meandering thoughts.

"I wasn't sure if it would be you ā€“ or the other one, Pain. Both of you have interesting techniques for traveling long distances in a brief timespan. But I'm glad it was you. How are your lungs, by the way?"

Madara said nothing, but went on the offensive. His lungs, apparently, had been quite bothersome.

Naruto ducked the blast of black flame and danced out of the way, as if he were one of his graceful puppets.

"A nice greetingā€¦but I have to ask for parlay. My masterā€¦."

"What foolish prattle is this?" Madara grunted.

"My master would speak with you. Now."

Without a handseal, Naruto disappearedā€¦and then Uchiha Itachi came out of the cavern that Naruto had just vacated.

"Madara, you lookā€¦unchanged."

"Whaā€¦ Itachi! I was sure you were dead. I saw Kisame's headā€¦but I thought yours was kept for experimentationā€¦."

Itachi looked even more impassive than usual. "You think the Nine Tail could do the things he's reputed to have done. I have had the bijuu under my control ā€“ no thanks to your lack of instruction ā€“ for nearly six years. I found a bedraggled orphan dying of hunger in a slum of Grass Country's capital. You remember that mission? I was long delayed from returning, right. That was when I found the Nine Tailā€¦and made him mineā€¦."

"Youā€¦you never told me. Traitor!" Madara was shouting now, angry beyond measure.

"I killed Kisame in order to leave Akatsuki without seeming a traitor. The ring did nothing to me, of course, as I unraveled and defeated its secret protections."

Madara was so far beyond enraged that he couldn't form a word for a few moments. "I could have ended this farce of the Akatsuki long ago. I just needed the Nine Tail to make my final plans succeedā€¦. Konoha could have burned six years agoā€¦."

Itachi cracked a sliver of a smile. "I know."

"Itachi, my student, today I end your life and reclaim the Nine Tails."

"You may try."

X-X-X-X-X-X-X-X-X-X

Naruto prepared for phase two of the battle.

Madara was certainly unhinged. Fitting a voice synthesizer, like his Taro puppets had used, under Itachi's robes had taken a few minutesā€¦and was worth more than an army of ninja right. It had been worth the extra hours to return to Itachi's prison and collect him, exploding seals and all, just in case it was Madara stalking him. He had even fitted in glass eyeballs into Itachi's eye sockets.

It all looked real. Save that Itachi couldn't use his non-existent Sharinganā€¦and couldn't attack. Butā€¦Madara didn't even known which direction was up.

So few ninja used deception to the full. A pity.

Itachi's cloaked body wasn't a puppet, just an unwilling human with his spinal cord suppressed. Naruto moved Itachi's body, not Itachi. This is a technique that Sasori would have sniffed out in a second, but it was likely Madara didn't even know it was possible.

It was a fine deception.

Itachi weaved and bobbed, ducking Madara's increasingly angered and frenzied attacks. He knew better than to engage in a Tsukuyomi war with his ex-protƩgƩ, as Itachi was perhaps just a sliver more talented with that technique.

Phase two began, as small vials hidden in Itachi's cloak had their corks pulled by chakra strings. They began to leak. The liquid gases began to react to the air. The environment filled with small concentrations of an odorless gas.

It was a poison, but not the kind that killed. The kind that blinded.

Itachi led Madara on a chase, walking Madara right through plume after plume of the nasty creation.

From many hours of discussing Madara, Naruto understood that the man's depravations had likely made him immortal in some fashion because of his special form of Sharingan eyes.

Eyes which Naruto was now trying to actively destroy.

This poison wasn't the slow acting optic nerve poison that Kabuto had designed all those years agoā€¦this was a derivative, a much more caustic chemical.

Naruto slowed down Itachi movements, allowing Itachi's body to be 'wounded' by a massive fireball. Itachi screamed and fell to the ground.

As predicted Madara had to stretch out this act, make it symbolic. He knelt down next to Itachi's bodyā€¦and then he began to tighten his hands around Itachi's neck.

Not a ninja killing a ninja. A stab with a kunai through the throat, a slash of a katana, some quick and efficient.

This was a mentor taking the time and effort to personally, slowly kill the only thing he loved, at any level. It was a personal thing, a crime of passion and hatred.

To do such a thing, Madara could not use his time/space jutsu. His ghostly hands would do nothing to Itachi if he had his ultimate defense active.

In his sublime anger, he had forgotten the 'Nine Tails' was nearby. He had lowered his defenses and bared his neck for anyone to attack in his moments of distraction.

Perfect.

X-X-X-X-X-X-X-X-X-X

Madara looked into Itachi's eyes as he strangled his former student. "Thus always to traitors."

Itachi's struggles became more vigorous, but ineffective, while his eyesā€¦his eyes seemed grateful.

'What was going on?' He tried to remove a hand to interrogate Itachiā€¦then it happened.

Madara's body went slack. He tried to flee. He tried to leap a few kilometers away, as he normally could with ease.

Butā€¦nothing responded. Even his chakra seemed to ignore what his mind was screaming out. It was like his body was dead, while only his mind was still functioning.

He tried to use an eye technique, tried to use his spirit guardian Susanoo to protect him from whatever was happeningā€¦but, in the attempt, his eye exploded outward.

Madara's screams could be heard for a kilometer. For just a second. Somehow the brain's impulses had overwhelmed a chakra stringā€¦but just for a second.

Pained, anguished screams. Genuine screams of terror and frustration and helplessness.

Like the screams of a village in the face of a nearly immortal Kyuubi no Kitsune. A fitting, well deserved scream.

When Naruto sent out a puppet clone ā€“ as Madara wasn't stupid enough to damage his other eye, unless it was an attempt at vengeance for a betrayal ā€“ he was still of two minds about how to do this.

If Itachi had been right, then the type of Eternal Mangekyo Sharingan Madara had would keep him alive even if he experienced a normally fatal injury, so was it possible to permanently hobble him? Would that keep the regeneration from happening?

Or should Naruto attempt to destroy Madara's body?

No. A disabled Madara was almost as good as a dead Madara. After all, Madara had minutes earlier threatened to leave Naruto brain dead so that he could extract the Nine Tailed Demon at his leisure.

It was a fitting plan, even Madara unwittingly agreed. Wounded, trapped, unable to move ā€“ a safer option, for now, than killing Madara outright.

Naruto didn't want to have to keep tracking him down and using gimmicks to get the ridiculously strong ninja to make himself vulnerable.

The puppet clone bent down and selected a rock. A few blasts of elemental air chakra had the stone quite sharp. The weapon incapacitating Madara would not be a chakra weapon: that was more likely to be detected by his body as an attack.

No, this rock knife would have the honors.

The puppet clone used his free hand to pull the orange mask off the smallish ninja. He didn't even care to see what Madara looked like. He just wanted a clear shot at the man's neck.

The chakra strings squeezing off Madara's spinal cord were about to be physically aidedā€¦the effect made mostly permanent.

The puppet clone brought the stone knife down between Madara's first and second cervical vertebrae, slightly off of center. He loosed the hold his chakra strings had on Madara's spinal columnā€¦and the knife was performing much of the same task. Madara's heart continued to beat, his lungs to inflate. His body was alive; his mind was alive; but his body's ability to follow Madara's commandsā€¦that seemed gone for the time being.

Enough of the spinal column was destroyed to keep him trapped in his mind ā€“ but not too much to allow him to die.

The puppet clone gently pushed Madara forward, onto his stomach, so as not to interfere with the stone knifeā€¦which was still embedded in the spinal bone and severing a good portion of the ninja's nerve transmitters.

With a knife blocking things, regeneration of the nerves couldn't take place. Electricity didn't pass well through rockā€¦and nerves weren't strong enough to burrow through it.

The puppet clone stood watch over the still immobilized Itachi and the incapacitated Madara. An hour passed, then Naruto himself appeared, reasonably confident that Madara wasn't playing possum.

With the kind of pain he was in from a burst eyeball, his body would be shaking or he'd be screaming at the leastā€¦if he could.

Naruto had used the time to fetch some some superglue from the nearest village. He used the nasty stuff to seal the slight opening between the stone and skin. Then he ripped the leather thongs from Madara's strange orange mask and used them to help stabilize the stone knife in Madara's spine.

Naruto had feared this ninja for years. It was only a vicious deception that permitted Naruto to win this time. He wasn't about to let some stupid accident free him to start regenerating somehow.

That stone knife wasn't coming out.

A cordon of six Kage Bunshins lifted Madara off the ground and onto their shoulders. Six should ensure smooth movement, so as not to jostle the knife too much.

Naruto then returned Itachi to a sealing scroll. He'd deal with the once-talented ninja laterā€¦now that he had finally served a useful purpose.

The procession began. Naruto would be returning to near the Namikaze estate in River Country with his prize. He'd find anā€¦appropriate place to keep Madaraā€¦safe.

He wanted to crow and celebrateā€¦at this stroke of luck, at this victory. But he knew better.

There was still Pain.

X-X-X-X-X-X-X-X-X-X

Naruto was in Rain Country trying to figure out where Pain's main base was located. Ever since he'd secured Madara in one of his River Country bases, he'd been searching for Pain.

In the ever gloomy rain, Naruto had made no progress. He'd surveyed the villages and towns quickly, already guessing that was too obvious. Then he'd begun trying to find useful caverns, even those masked with genjutsu, in the surrounding hills.

There were many such caverns, some with interesting spoils, which Naruto gladly stuffed into storage scrollsā€¦but there was no Pain.

He stalked up the hill and used the technique he'd developed to deal with Orochimaru's hidden bases. The sound waves traveling through the ground ā€“ and up the hill ahead of him ā€“ would collapse any holes they found.

Holes, such as well-hidden caves.

Thus, a few hours later, a rather irate Pain, his principal body covered in wet dust and rock shards, and a woman with an odd sort of flower in her hair ā€“ Konan, if Itachi was to be believed ā€“ finally met Uzumaki Naruto, the host of the Nine Tails.

Pain did not immediately attack.

Naruto prepared his Flowing Red Death technique.

Konan looked over the young ninja with an undisguised amount of curiosity. "I expected you to be dead, little ninja," she said.

"Why?"

"Our true leader went mad and has been stalking you for weeks, almost a month. You must be some kind of genius to have avoided him for so long."

Naruto ā€“ the real one ā€“ laughed. He performed a sealless Kage Bunshin and prepared to replace himself with a Shadow Clone.

Pain spoke before Naruto left. "He did find you, didn't he?"

Naruto paused in his preparations. "He did."

"He claimed to be truly immortal. Not the false immortality offered by a religionā€¦or by body part salvaging or body snatching. Did he lie?"

"I have no idea," Naruto said. He was about to depart and let the battle happenā€¦when he felt something very odd.

He felt chakra sent off in burstsā€¦and returning just the same way.

Then he saw Pain perform a summoningā€¦and five more bodies, ninja bodies, appeared.

Now, to Naruto's sensitive chakra detection abilities ā€“ honed through his mastery of chakra strings and cables ā€“ the air was positively filled with tiny bursts of chakraā€¦an almost continual amount, filling the air.

Now that he was aware of it, it seemed very odd.

He had never been this close to Pain before, definitely not at the Waterfall Debacle. Madara had set to chasing Naruto before Pain got within a kilometer of the jinchuuriki.

What was this? This air filled with little chakra packetsā€¦. It felt like a young Suna puppeteer almost stuttering with his fingers as he or she tried to become proficient ā€“ and failing ā€“ in handling a puppet.

A puppet.

Pain and his bodies. The signals back and forth, from home base, controlling these bodies.

Yes, that was a discovery. Naruto had the Flowing Red Death ready; he was ready to replace himself with a Shadow Cloneā€¦but instead he stayed. This was too interesting now to leave.

Pain wasā€¦interesting.

Konan restarted the stalled conversation. "I personally looked for a long time for a method to deal with the mad, little man. How did you do it?"

Such a simple questionā€¦butā€¦

Naruto felt a lot calmer all of a sudden.

These godlike people had forgotten simple things: a powerful ninja body was still a body, still required air and signals from the brain. They spent too much time thinking big and overwhelming.

No one was better at 'big and overwhelming' than Madara was reputed to be. Hence this kunoichi's anxiety.

Noā€¦Naruto's early experiments and focus on the small, on micropuppets, on the details that matterā€¦all that still served him well.

Naruto realized that Pain and Konan were powerful, but they were different types of ninja.

They didn't think the same way he did. And he could win today because of it.

Pain the Puppeteer was dead without chakra, without his signal flooding the area. There was a way to cut his strings.

Unfortunately to use a wide-area chakra nullifying seal would mean Naruto couldn't use a puppet or even a Kage Bunshin nearby these Pain bodies and Konanā€¦. It would make defense easier, but offense nearly impossible.

The opportunity was still worth it. Naruto used a dozen chakra strings to begin etching the seals into the bark of a nearby three.

When he activated it, he would be without his best weapons, his Flowing Red Death would be impossible to performā€¦but his opponents would be at least as handicapped. Konan could be poisoned with as many poisons as Naruto carried around on himā€¦and his time in Grass Country left him an avid poisonerā€¦and Pain's bodies, without instruction from the home base, would flop to the ground, as useless as dead fish.

Naruto relaxed a bitā€¦and answered Konan's question, filling the pregnant silence. Even the local insects had gone quiet in the face of so much chakra used in the summoning.

"To be honest, I stabbed him with a knifeā€¦into his neck. I did not kill, but rather disabled. I have no idea if he's as immortal as you claim, as he's now defeated and held prisoner unable to move or speakā€¦."

Pain ā€“ or one of his bodies, the one who had summoned the others ā€“ frowned. "He is impervious to physical attack. Be honest."

"I am. I offered Madara something of great value. When he wrapped his hands around it ā€“ forgetting about me ā€“ I struck."

Konan nodded. "Yes, he can be wholly impervious or solid like a normal ninjaā€¦not a mixture to the two at the same time. To touch something with his handsā€¦he would have to leave himself vulnerable. A simple, elegant solution. What was this object of value?"

Naruto didn't understand why these seven ninjas weren't attacking. Why were they stalling? Reinforcementsā€¦there were a few Akatsuki still alive. But Kakuzu wasn't on Pain's levelā€¦and Zetsu was a disgusting creation.

"A deception. A deception he bought with his whole being."

The seeming leader of the Pain bodies frowned. "Madara was an ancient being with a powerful doujutsu. He would have seen through any deception."

Naruto's preparations of the chakra nullifier were ready. He had mentally counted up his poisons. He needed to time this just right, before whatever plot they were working on happenedā€¦.

"No, Pain. I believe him." That stopped Naruto for a moment. Why was Konan saying that? Naruto had told but half or a quarter of the truth.

"You and Madara both overvalued his experience and his Sharingan. He wasā€¦powerful in his prime, but he was increasingly mentally unstable. If this young ninja did something that resonated in tune with Madara's madnessā€¦it could very well have worked."

"Perhaps," the lead Pain body said. "Boy, I will offer this. Neutrality between us."

"What?"

"I offer neutrality. I will not hunt you. Nor will the Akatsuki, any longer. You have dealt with Madara so we need no longer bother with his ridiculous plan to capture the bijuu. The only problem I see is that Sasori remains highly interested in you for his own reasonsā€¦."

"Sasori is no longer a problem. I dealt with him. Now you tell me why you would declare neutralityā€¦."

Konan looked shocked. To her it was one thing to trick a deranged Madaraā€¦but to 'deal' with Sasori, a suspicious bastard on his best days, that was something else. Konan apparently undervalued Madara as a ninja.

Pain looked unsurprised at Naruto's statment. Instead he answered in a calm, level tone, "You have cost us too much of our capacity to keep this war going. I don't know how many Akatsuki you've truly dealt withā€¦but I know we're well below half of our needed senior membership. Our drive to enforce peace around the worldā€¦had gotten distracted by this quest for the bijuu. Because of Madara. I have no problem ending the side quest in order to fulfill our main goalā€¦."

"You would kill for peace?" Naruto asked.

"The only path to peace is through searing pain," the lead Pain body asserted.

"If you believe that, then watch. In the coming years, I will prove a different method."

Konan looked like she wanted to argue about such a bold statementā€¦but Pain's main body cocked his head and said, "It is possible you might do just that."

"Let me make a promise, then," Naruto said, improvising. "If I ever see you or Konan again, I will assume you've betrayed our neutrality. I know your secrets Pain. I figured them out after you summoned your other bodies." With that statement, Naruto powered on the chakra neutralizing seal.

(Naruto would only realize later that the storage scrolls holding his food and tent had been destroyed by the neutralizing seal. After that, they were little better than fancy paper someone had already scrawled on.)

Pain's bodies dropped to the ground like puppets with cut stringsā€¦which was exactly what they were. Unfortunately, Naruto false legs was also attached to him with chakra strings...and his leg fell out underneath him. His physical training gave him good enough balance that he didn't fall down, but it was awkward for a brief moment.

Naruto turned to a doubly shocked looking Konan. "Didn't know a cripple could be a ninja, huh? Well, some of us can. Even missing a leg, I can take you, all of you. Now, tell your leader when you manage to resuscitate him, 'Keep Kakuzu and Zetsu on short leashes.' I know how to destroy both of themā€¦," he said, bluffing, "and I have more than one good idea of how to deal with you, too."

"I will try," Konan said, her eyes swiveling between Naruto's false leg and the six motionless bodies of Pain. "Zetsu isā€¦difficult, though, when he becomes fixated."

"If Pain gets any ideas regarding my show of power todayā€¦remind him. I had once thought to use an optic nerve poison on him. It worked on Uchiha Sasuke, from what I understand, and another variant did some interesting things to Uchiha Madara. But, on himā€¦it wouldn't have worked, would it? Destroying the eyes of theseā€¦bodies would have been, at best, a temporary victory. Noā€¦I understand how to deal with him. And I can and will do it again, if I see him again."

Naruto turned his, spotted a likely tree branch, hopped three times, and ripped himself a temporary crutch.

He turned and began hobbling his way down the hill. He wasn't sure how far the nullifcation stretched, but he'd rig up a new temporary leg as soon as he could. (He'd left the old one behind for it was too difficult to balance on one leg and bend down to pick it up. He also didn't plan to show Konan any more of his shame, of his weakness.)

"How?" Konan called out. She needed to know how to fix this, how to repair her best friend's bodies. She obviously hadn't yet figured out she needed to drag the bodies away from a sealing array she couldn't seeā€¦or to wait for the seal to exhaust its power.

"Never screw with a sealing master on ground he's had time to prepare." He didn't know if the wind would carry his words. He didn't care. She wouldn't understand.

As it was, Naruto wasn't sure he understood why he did all that.

As he left, he asked himself a question. Why?

Why leave them alone? Why accept this 'neutrality?' He knew they were likely to betray him in the future, but he was honestly interested to see if Pain's methods would work in the slightest.

Peace through warā€¦a failure every time it had been tried. The burning of a forest could provide vibrant new growth a few years after the devastationā€¦but people were different from trees and plants. People remembered; they held grudges.

Of all people, Naruto understood this. A grudge against the fox had led to a horrible childhood for him.

His background had left Naruto thinking about peace for a long timeā€¦and he had developed a plan. Something to do now that the legend of Taro had faded; now that Naruto no longer needed to prove his strength as a ninja.

Naruto, a cripple with a missing leg, was as strong as they got. Ninjutsu for ninjutsu, he would lose; in taijutsu, he would lose to a masterā€¦but in an unrestricted fight, Naruto could figure out a way to triumph.

He wanted to see if his idea would workā€¦if it would work better than Pain's.

It was all curiosity. Powerful ninja had very little to entertain them once they reached the summit. Something interesting, something curious shouldn't be sacrificed until it bored the mind. That was why Naruto hadn't immediately killed Sasori three weeks ago ā€“ he'd wanted to exhaust all the knowledge, all the promise Sasori had.

All the amusement.

As the rain stopped (and would remain stopped for nearly a month), Naruto realized ā€“ to his mounting horror ā€“ that he was just as crazy as these other S-ranked bastards. He found his chakra working again, henged a Kage Bunshin into the shape of his prosthetic, and resumed a more graceful walk off the hill.

His mind returned to the idea of insanity.

Toying with people; killing them in ways that amused him. He'd left Pain aliveā€¦so that there was the promise of something interesting, something challenging in the future.

The Grass jounin council had been right to expel him, as Taro of the River, all those years ago. Naruto shivered, not from the chill air, and set out back to River Country.

He'd try not to think of this again.