With Yahiko surviving the fight with Hanzo, things happen very differently once the wonder trio take over Ame. As Yahiko becomes the new leader of Ame, he begins to wonder about his childhood declaration of wanting to be on the top of the world. No Madara, Dark!Naruto
Chapter One - 'Measure for Measure'
Due to the fanfiction site screwing up, there may be some chapters that are missing dividers. My apologies for the inconvenience, and I will try to fix it as soon as possible.
An orange-haired tall man with bright blue eyes walked through the hallway in a trance, setting aside his thoughts over recently acquired intel on the location of an otter summoning contract in Kiri for the time being. Opening the door showed the light streaming in from outside, as he walked out the mouth of the head of a statue, built up high on Ame's neo-techno landscape. Walking down to the end of the outstretched tongue of the monstrous sculpture, he sat down, and thought, head lying on his hands, even as the rain Ame was named for began to fall.
Things will definitely come to a head soon, he thought, as he surveyed his beloved Ame. For years, decades now he had worked tirelessly from behind the shadows to organize an international network of saboteurs and spies, and it was beginning to finally pay off. The instant that the brotherhood of Akatsuki was outed, he had no doubts that war would be coming to Ame, his Ame, once more, as the rest of the shinobi world wouldn't hesitate to band together and eliminate a threat to their very existence. This time, however, this would be the last war. Even now, one of his most loyal agents, and one of his most competent, if a bit too addicted to the taste of revenge, was setting up a meeting in the hidden village where things would come to a head in eight months. All Yahiko had to do was wait it out another eight months, and the process of things would finally begin to accelerate.
Yes, Yahiko chuckled, once the Chunin Exams finished, the great weakening of the hidden villages would come about, as the Akatsuki would transit into the second phase of his three-phase plan. Every day that they could stave off discovery of their schemes was another day that the chances of ending the bloodshed and cycle of hate for once and for all would increase, if ever so slightly. If not for the fact that he now hated Jiraiya, and that the old Gama Sennin was too loyal to Konoha, whose existence ran counterpoint to what Yahiko had planned, he would have made his old sensei proud.
Shuffling his body back a bit, Yahiko lied down, letting the raindrops splash over him, wetting his hair down. He thought about his life over the last few decades.
How does one go about actually achieving peace? Yahiko of Ame, formerly an orphan on one of Ame's satellite villages, and now it's leader, had once declared that he was going to rule the world, with his motivation for doing so being that he could enforce a peace as a result. That had been a midsummer night when he made it his goal, yet now it had faded into the background for something else. Yahiko had never told his childhood friends and fellow stragglers Nagato and Konan, but he had witnessed his parents being killed by Hanzo's dogs at the age of seven. They were shinobi both, but they had been caught up in a rebellion against the feared salamander summoner. Yahiko had barely managed to escape, and had slipped through the cracks of the dystopian society as an orphan. Although he had matured as he grew up in temperance, he still possessed that same burning desire to be on top. But to first rule the world, one would have to take over the world.
However, years of fighting as the leader of a rebellion against Hanzo had tempered him, and he was no longer ignorant to the true sacrifices and horrors of war. If he wanted to take over the world, he would have to go through years of war, taking over hidden village one by one, breaking the will of tens of thousands to ensure they would not resist, and once he finally unified every vestige of shinobihood on the Elemental Nations, would have to keep them repressed to ensure they would not fight each other. That was just for the ninja villages alone, not counting the interference he would have from the daimyos and their samurai. More and more Yahiko began to realize this was an impractical solution, and so he began to look at other ways to bring about peace.
Yahiko's small council of governance, formed up of the last original members of his former band that had deposed Hanzo, came up with a solution. Instead of fighting directly against each Hidden Village, many of which dwarfed Ame's military capacity and would seek the slightest excuse to expand their circle of influence, they would have to fight and manipulate from the shadows. Instead of fighting and forcibly breaking the will of a Hidden Village, they would force the villages into a dearmament. How? The biggest thing was to cut off the financial lifeblood of every village. For this, Yahiko recruited the ancient bounty hunter/mercenary known as Kakuzu, formerly a jonin of Taki, whom was banished after failing to assassinate the Shodai Hokage.
Under Kakuzu, Yahiko organized a small handful of his best shinobi to strike out into the wild. The original story that was delivered to all the other nations (who were under the impression that Hanzo still ruled in Ame) that a small group of jonin had gone nuke-nin all at once. In reality, however, the jonin ninjas were to take on as many missions from savoury and unsavour characters alike in smaller nations that lacked a ninja village. People who might have once hired ninjas long distance from Konoha or Kumo now hired Ame's 'nuke-nins'. On completion of the mission, each mercenary would funnel some of the mission money back to Ame. To ensure that the money-grubby Kakuzu stayed on Yahiko's side, the orange-haired leader gave him a cut of each mission.
Kakuzu took a few apprentices on as well in Ame. Between his arrangement with Yahiko and having some new partners to assist on his bounty hunting, Kakuzu enjoyed a greater amount of bounty captures, but slowly began to focus on the heads of those targeted by the hidden villages, such as nuke-nins and civilians a village might hold a grudge against. While Konoha and Iwa managed to operate their military budgets in the billions of ryo each year, their coffers had declined with the succession of the Second and Third Great Shinobi Wars. Konoha's most infamous nuke-nin, Orochimaru of the Sannin, had a price of 500 million ryo for his head alone, and anywhere from another 30 to 75 million ryo for each abandoned base that a person could provide the Hokage with the location of.
But it wasn't enough. Yahiko could slowly drain the hidden villages of money as much as he wanted and as long as he wanted, but the money still wasn't enough. You could take away some of Konoha's missions, but as long as they still had legends like Jiraiya of the Sannin, Kakashi of the Sharingan, the Green Beast, ANBU Squads 7 and 12, and the up-and-coming Itachi Uchiha, many would still come from afar to Konoha. As long as each of the main villages had over three thousand shinobi each between their active and reserve forces, they could still take enough missions that Yahiko's plotting would only put a dent in their savings.
So not only would he take away their money, he would take away their manpower.
Yahiko's friend Nagato was the most instrumental for a tenent of his 'denial-of-resources' war against the rest of the shinobi world. Nagato possessed the legendary Rinnegan, a doujutsu that had not been manifested in any one person since the time of the Rikudo Sennin. While most people knew about the ability of a Rinnegan wielder in being able to wield all six natures of chakra, little was known about its other powers. One particularly useful ability was its power over summons - any animal whose contract Nagato had signed would be forced to obey Nagato. The other facet of its abilities with summons was that Nagato had a sixth sense of the location of summoning contracts, and could locate any contract within a radius of three hundred kilometers.
Unlike what Yahiko, Nagato and Konan's sensei, Jiraiya of the Sannin believed, their meeting with the three Sannin was not the first time they saw Jiraiya. When Jiraiya and his teammates were fighting Salamander Hanzo, whose summon had created craters in the ground, and caused a nearby cliff to collapse, causing dust to scatter and choke the air and sunlight for days, even with the constant rain. The Sannins had summoned their boss summons earlier in the fight, wrecking the vegetation, knocking down the few trees that grew in the rainy conditions, and flooding the plains. After the battle was over, Yahiko surveyed the damage for a week. It was muddy and dirty, and nothing would grow in it. Ten years later, he came back. It was still as barren as the day he had last seen it.
Following that, Yahiko had gained an unnatural loathing for the use of summons in battles and war. A normal shinobi could cause quite a bit of destruction with their jutsus, but they were still human, beings who rarely exceeded six feet and seventy kilograms, and even most ninjutsus had little in the way of an attack range. The larger summons were perverse contrasts - they would destroy and destroy and destroy in their fighting, whether against another summon or against groups of shinobi (or in some cases, such as Manda, to even go so far as to devour innocents). As a result, Yahiko made the stealing (and destruction in a few rare cases, again such as the snake contract if he ever got his hands on it) of summoning contracts, or killing the lone holders of these contracts, a top priority - if his sensei Jiraiya lost the ability to hop around with a giant toad, covering hundreds of miles in only a few hours, while leaving giant imprints of toad pads in the ground, who was Yahiko to care?
Additionally, Nagato was a machine at infiltration and spying. The Rinnegan also gave Nagato an inhuman amount of chakra, and with this he was capable of great feats, such as maintaining six clones full-time. While the clones, being a bastardized form of Nagato's Shōten no Jutsu that he had made from yin/yang chakra, were mediocre in strength and prowess, Nagato could maintain all six clones at once, while himself concentrating on a different task. He had a clone keeping track of day-to-day happenstance in Kiri, Kumo, Iwa, Konoha, Taki and Kusa, with the identity that each clone possessed slowly but surely wriggling its way into the inner core of the power structure of each village. It was a boon, to be sure. With his instant perception of events happening in six different nations, Nagato was able to plant information he could find from one village in another village; in one instance, he had once leaked a mission with four Konoha jonins to an office in Iwa. A retired shinobi of high standing in Iwa couldn't pass up the temptation, and had sent out an ambush against the Konoha jonins, successfully killing them all. To be sure, this was still slow going for Yahiko's plans, but every shinobi dead or crippled was a shinobi who couldn't perform missions. Once a village's number of shinobi dropped, they would have an excess of missions, and therefore be less tempted to go to war - a shinobi war was fought not for territory (that was the field of the daimyos) but for area of influence. In the Third Great Shinobi War, Taki (who was on Konoha's side, and therefore part of the victor against Iwa) managed to make headway with client contracts into the borders of the Land of Stone, while both Suna and Konoha began to take missions in Bird Country away from Iwa.
Still, Nagato used this ability of his to his maximum success. In each of the six villages he had set up a brotherhood of like-minded people, men and women who sought the end of war, going so far as to accept that it wasn't their own village that had the divine mandate to come out of the arrangements on top. It was they who would do the grunt work for weakening their respective villages. The Akatsuki, that was what the brotherhoods became known as. Red Dawn. It was fitting, Yahiko had often mused. They would bring about a new dawn, fueled by the sacrifice of blood red.
Eventually, Yahiko realized there was one weapon he had overlooked - jinchuuriki. Eight tailed beasts were possessed by five Hidden Villages.
There would be problems. How could he get rid of the jinchuuriki, when the bijuu were an even bigger threat to all of man? He couldn't very well kill a jinchuuriki if he or she let their bijuu free in the process. Digging through old scrolls left behind in Hanzo's personal library, he began to research the background of the bijuu. They were nine oni spirits from the realm of Makai who had broken the dimensional barrier and crossed over into ningenkai. From there, they managed to accumulate a chakra shell around their spirits as a form of a body. Eventually, they gathered together so much power that they could manifest physical bodies for short periods of time (as theorised by many scholars based on an old law where a large amount of energy could be converted into a small amount of mass), and it was reported that a few of the middle beasts of the hierachy often walked amongst humans.
Studying, he found that the chakra that each bijuu gathered around them wasn't elemental, but rather yin/yang chakra, a chakra that few scholars knew much about. What little Yahiko found was that yin/yang chakra was related to both nature chakra and the elementally neutral normal chakra people used for most jutsus, but was in a class of its own. Yin/yang was perhaps the most dangerous chakra of all, as the Yin side began to corrupt whatever consciousness the bijuu had, and any inbalance in the chakra was especially dangerous, becoming what many scholars had termed as yokai.
It was, however, possible to purify the chakra of the bijuu. In fact, Yahiko began to wonder if the deities above had intended for what he had planned to happen - how else would his closest friend have been Nagato, who again was useful in his exploits, the Rinnegan being the only known tool that could control yin/yang chakra? With experimentation, Nagato would probably be able to neutralize most of the lower bijuu, and greatly weaken most of the upper end. Few people knew it, but there wasn't that much of a power gap between the Ichibi and the Kyuubi - people think that the tails are the only indicators of a bijuu's power. In reality, that isn't quite true. To be considered a bijuu, an oni spirit must first have enough chakra to be able to form a chakra body of a certain size, and then enough chakra remaining over that they could form a chakra tail. In that sense, the Kyuubi merely held nine times the reserve chakra of the Ichibi, while their base forms had about the same amount of chakra (although not exact - the Nibi no Nekomata, being the smallest of the bijuu and barely crossing the size threshold to be considered a bijuu, was actually weaker than the Ichibi no Tanuki, whose base form dwarfed the Nibi's). As such, Yahiko was confident that if they could grab a lower-class bijuu to work on, their results should carry over to the sealed Rokubi, Nanabi, and Hachibi.
But that still begged the problem of how they would secure each bijuu and jinchuuriki. Three jinchuuriki were in high-profile positions - Yagura, the Sanbi vessel, was being trained for the position of Mizukage in Kirigakure, Han, the Gobi vessel, was the son of the current Tsuchikage, and Kirabi was the brother to the Raikage-select. They would have to be the last on the list to do anything with. In fact, the only vessel who wasn't actively affiliated with a village was the Yonbi host, who was a traveller who only assisted Iwa when they called on him.
And even when he crossed that road, how exactly could he prevent the bijuus from becoming corrupted again? He could kidnap all the jinchuuriki and seal the oni spirits into new vessels every time their old ones died, but that would become a headache, trying to keep that much power restrained. Even sealing the lower demons into inanimate objects would only work as a temporary solution.
In his search high and low throughout the Elemental Nations, Yahiko found one man who took completely after his own heart - Akasuna no Sasori. When he first met the red-head in Suna, the puppeteer was a rising star in the desert village, at the strapping age of fifteen. Sasori had lost both his parents in the Second Great Shinobi War to Hatake Sakumo; what enraged him was how only a few years later the political landscape had changed, and Suna had made an alliance with Konoha. How could the Sandaime Kazekage so easily ally with their once-enemy?
The last straw came for Sasori when he learned of the Kazekage's plans to kill Awai Tsubu, the second Ichibi jinchuuriki. The Kazekage would then seal the Ichibi while it was still weak from being released into a newborn child. It was one thing for the Kazekage to kill Tsubu, who was Sasori's friend - while Sasori wouldn't allow it if possible, he understood on an intrinsic level that it was a necessary cycle of things. However, what truly galled Sasori was that the Sandaime planned to use a weak seal on the newborn - the seal would allow the Ichibi to drive the child mad, and when the child fell asleep, the Ichibi no Tanuki could take over and cause havoc. The Kazekage would do this to a child just so he could have a weapon of war.
Sasori originally planned to defect. However, Yahiko convinced him otherwise, noting that he was allowing things to go as they were. Heartened by Yahiko's words, Sasori challenged the Sandaime to a duel of honor, eventually killing the Sandaime in battle, and becoming the Yondaime Kazekage in his stead. Alas, the damage had been partially done, as by then the Sandaime had had Tsubu killed, and the Ichibi temporarily stored in a tea pot.
So enraged he was when he learned this fact, Sasori had called in Yahiko. Under Jiraiya, the three Ame comrades had each learned from one of his fields. Nagato had learned ninjutsu. Konan had managed to combine taijutsu with a bastardized version of natural chakra to become an adept at wielding paper, even being able to turn her own body into the stuff. Yahiko, however, had learned fuinjutsu under the Gama Sennin. It was with his knowledge of seals, and Sasori's own indepth talent coming from years of puppetry, the two released the Ichibi into a specialized field built to slowly drain the Tanuki oni's yokai - it wouldn't take away the oni spirit's yokai permanently, but it was an effective method of torture. It was there that they discovered the spirit of the priest Shukaku, who had connected his soul to the tanuki's own years before, driving the spirit of the wind insane.
In the course of over fourty-eight sleepless hours, the two, along with Nagato, managed to extract the spirit of the priest from the Ichibi. While the Tanuki Oni was at the weakest he had ever been since he had crossed over into ningenkai, with his yokai being drained from him and having a part of his soul ripped away, Yahiko bombarded the oni with questions. He learned that while in a vessel, all demons had their yokai siphoned off by their hosts, but the process was far too slow to put even a dent in the bijuu's reserves. However, if a bijuu ever had all its yokai totally drained, then it could be exorcised and properly sent back to Makai, though they would still have the power to cross dimensions again.
Hanzo's private library came into use again, as Yahiko managed to find some ancient sealing research. Specifically, he found a series of seals that dealt with absorbing nature chakra to convert into electricity or heat, as opposed to the towns and cities of today having small groups of people whose job was to refuel power sources with their own chakra. Yahiko could only find parts of the seals that could convert nature chakra; nevertheless, between him and Sasori, they were able to complete the seal, then modify it for the use of yin/yang chakra and yokai, so as to drain a sealed bijuu's vessel and add it onto the vessel's own chakra pool, and modify it again so it could be put on top of a demon seal instead of being required to be put in with the original seal, as well as being invisible after it was applied, even when the vessel was moulding chakra. It was around this time that Yahiko finally managed to bring Roshi of Iwa into the fold of his organization. Roshi and the Yonbi agreed to be test subjects for the seal.
There were some surprising side effects even when Roshi had only absorbed 10% of the Yonbi's yokai. For one, Roshi, who was in his late thirties, had begun to seemingly regress in age, and his healing factor had also gone up. The Yonbi suggested that Roshi would be long-lived, perhaps living in excess of a thousand years, as his chakra would regenerate his cells instead of dividing and shortening the telomeres. It was then that Yahiko decided that each jinchuuriki would have to be convinced of his plans. Once all eight vessels (or vessels to be) had undergone the same process, then they would have the power and the lifespan to safeguard the peace for centuries to come.
After that, Yahiko retreated back to Ame, while Sasori built up Sunagakure's own power, slowly so as not to attract attention. The two watched as clashes between Iwa and Konoha brought about the Third Great Shinobi War. While Yahiko was able to keep Ame out of it, Suna was expected to engage in the war. Sasori went straight into the thick of battle, slaughtering hundreds of Iwa shinobi. Both were impressed at the debut of the legend of Namikaze Minato, the Konoha no Kiiroi Senkō, in the war, with his use of his legendary Hiraishin no Jutsu. While they had devised a seal that could suck the energy out of demons, he had created what appeared to be a bastardized version of a summoning seal that effectively allowed him to teleport throughout the battlefield. This worried Yahiko - Minato, in only a few years of jutsu development, had probably become stronger than him, Nagato, and Sasori, all three powerful in their own rights. In only a few more years, Minato could probably defeat the three of them all at once.
Shortly after the war, the Ichibi was finally sealed into a vessel, a redhead named Gaara, who was the newborn son of a capable high-level Jonin, one who might have become the Yondaime Kazekage if not for Sasori's own legend. It was after the ceremony that Yahiko had begun to worry - while he had tied together many loose ends, two things could disrupt his plan still - the first was that of Namikaze Minato. The man was becoming so powerful and legendary that he could destroy all of Yahiko's scheming. The second was that of the Kyuubi no Kitsune - although it had not been seen on the mortal realm for eighty years, it might come back at any time, and Yahiko was unsure if it could even be sealed. While peace was all very well for the world, it would not do if the king of all bijuu destroyed it beforehand.
It was amazing how things seemed to click together, as if indeed the kamis were indeed looking down on Yahiko. Only nine months after Sasori had sealed the Ichibi no Tanuki into Gaara, the Kyuubi no Kitsune appeared on Konoha's doorstop, and Namikaze Minato sacrificed himself to seal the Kyuubi into a newborn child. Even better, the power behind the seal was assured, as intel from Konoha had suggested that Minato had summoned the Shinigami to seal away the fox, a deed for which Yahiko had to admit he admired the blond man who had a similar appearance to his own.
Over a thousand shinobi died in the battle, however, and Sasori took the chance to finally flaunt Suna's muscle, as he immediately went into mediation between Leaf, Stone and Cloud. The recognized ninja of the Red Sands convinced the Raikage and Tsuchikage that they would be able to reap enough of an upfall simply from the extra missions they would get that Konoha could no longer perform, and that to press war could cause fractures to occur in the semi-stable system of the Five Great Hidden Villages that had worked for sixty years so far. Yahiko often was amazed at how the Kyuubi attack managed to solve things for him - he had originally estimated that it would take twenty years for his plotting to come to fruition. After the end of two decades, the manpower of the hidden villages would finally fall at an accelerated pace, in comparison to the snail's pace for the years preceding that. With Konoha losing a thousand men at this point in time, as well as their Yondaime Hokage, the tensions between nations saw a downward pressure, giving Yahiko a bit more wiggle room to operate.
But what shocked him was the news that came back from Konoha, as he learned of the utter malice that was directed at the Kyuubi vessel. In retrospect, it didn't surprise him - in every other nation, the eight tailed beasts numbering from one to eight had been presented to them by the Shodai Hokage, practically gift-wrapped (Yahiko shook his fist at the clouds every time he thought of the man, damning him for giving the hidden villages what accounted to forces of nature). While normal civilians and ninjas might fear their jinchuuriki, they had no real cause to hate them - no bijuu had ever killed their parents, crippled their siblings, caused their wives or daughters to miscarry because of the sheer killing intent. But the Kyuubi had attacked Konoha and slaughtered over a fifth of their shinobi forces, wiping out part of an entire generation.
The only good thing that came out of it was that three of Yahiko's agents were able to infiltrate Konoha so easily and kidnap Naruto at the age of five, taking him to Ame, while leaving behind a seventh Nagato clone. In Ame, Yahiko was in for the shock of a lifetime.
When it comes to high-level seals, every master of seals has their own little quirk, their own little trademark, so that one seal master could recognize another seal master's work just by identifying little intricacies of a seal. For example, Namikaze Minato had a thing for spirals. The blue-eyed carrot-head wasn't quite at that level yet, but he could easily identify his own sensei's work. What enraged him was that he discovered two seals on the back of Naruto's head, covered up by the young boy's blonde hair, that were both done by his sensei Jiraiya. The first seal was a suppression seal - it would cut down the intensity of a person's emotions, doubtlessly done so that young Naruto wouldn't feel rage and hatred at the village that had been mistreating him, and possibly let loose part of the Kyuubi yokai in the process. The problem with the seal was that it slowed down the target's neuron impulses, which would make it harder for Naruto to think and understand concepts, slow down his reaction time, and screw up his body coordination. Yahiko wasted no time in taking that one out.
Where the suppression seal angered the leader of Ame, the second seal absolutely infuriated him. It was a seal that, when activated, would cause hypersensitive perception for a few minutes. Most ninjas couldn't use it because it caused too much strain on the body, but even with the suppression seal on his body, Yahiko guessed that Naruto was able to stand it because of the Kyuubi. Yahiko had a fairly good idea of what the seal was used for - while in the hypersensitive state, a person was more receptive to anything that was said. Yahiko's blood boiled as he could imagine what had happened - Naruto at the age of two, three, four, having his seal activated, while the Sandaime stood over him, uttering words such as, "Be loyal to Konoha and your Hokage no matter what", "Put your teammates before yourself", "Never raise a hand against the civilians", "Believe in the Will of Fire".
The second seal was easily destroyed as well, but Yahiko had to keep Naruto in Ame as a result to get rid of the brainwashing. The young Naruto was torn - he realized what had been done to him and felt betrayed by Konoha and the Sandaime, who he had viewed as a grandfather figure, as well as being enraged at the citizens and shinobi who took out their losses on him ("They live in a military village, and they suddenly can't accept that that means friends and relatives might die?") yet still had a difficult time resisting the mental programming that the second seal was left behind. So several of Ame's psychologists had to work with Naruto for a bit under a year.
What was disturbing was when Nagato had brought himself Naruto into the sun-haired boy's mindscape. Bypassing the Kyuubi, deciding to talk with the kitsune later on, Nagato instead wanted to look at Naruto's earliest memories, those during and right after the sealing. Naruto wouldn't be able to remember these memories until he went through intense meditation, but Nagato had a pair of eyes that were said to be a fault in a god's plan, and had become mentally strong enough years ago on the level of Konoha's Yamanaka clan to search through another's mindscape. From there, he looked through the council proceedings that had occurred right after the Kyuubi attack was stopped, which Naruto had been present at even as a newborn, hoping to find information that could be used for their own goals.
But right after that was a meeting between Sarutobi Hiruzen and Jiraiya in the Sandaime's private office. It was there that Nagato learned Naruto was the Yondaime's son, and Jiraiya's godson, and it was there that Jiraiya applied the two seals to the back of Naruto's cranium, quite willingly. Nagato and Yahiko debated over giving Naruto this information, and decided to wait until after they were sure the psychologists had managed to help Naruto out of his brainwashing.
Needless to say, Naruto was greatly distressed. His grandfather had betrayed him, and his godfather basically sabotaged his body before ditching his duties, despite that he was the Yondaime's son. He wasn't even willing to think about what might have happened if he had just been a random orphan off the streets who the Yondaime chose to contain the Kyuubi. Yahiko for his own part was upset - when Jiraiya had been teaching him, he had often preached about peace, trying to end the cycle of hatred, and so forth, and yet, he would do something like this to his godson? Yahiko wasn't arrogant enough to think that he could cleanse the world of evil, or that he was a god, but after seeing the amount of abuse Naruto had gone through from the day that he was born, he swore to do his best to expunge corruption so that another like Naruto wouldn't happen, ever again.
Eventually, Naruto left Ame to go back to Konoha, as Nagato had overstressed himself in trying to maintain a seventh clone for over a year. Before Naruto left, however, Yahiko had personally trained Naruto thoroughly. While he couldn't offer any jutsus at the time, he taught Naruto how to think and act as a shinobi, and some methods on chakra control. Naruto and Nagato finally spoke with the Kyuubi, coming on their own terms to the conditions that the Kyuubi wanted in return for Naruto's draining of his yokai. As Naruto had replaced his doppelganger back in Konoha, Nagato's spy-clone inducted him into Konoha's brotherhood, and Naruto slowly rose through the ranks.
Eight hundred kilometers away, at the same time that Yahiko was deep in his introspective, a humming sound filled a dark chamber deep underground. Only one person was there in the flesh, his eyes closed, but that was OK - he had the sheer amount of power that was required to hold the Gentōshin no Jutsu for hours on end. Seventeen holograms appeared in the room; although there was a slight colour to be had from the holograms, most of it outside of the hair and eyes were lost by a shadowy filter. None of the technical details mattered much to the wielder of the technique - at the moment, he was more concerned with his duties, acting as moderator and mastermind all at once.
Doing a double-check to make sure that all members were accounted for by sensing the number of chakra transitions, the young boy opened his eyes, revealing sparkling blue. When he spoke, his tone of voice was crisp and clear, yet tolerating no nonsense. "Let the meeting of the Konoha brotherhood begin..."
OK, a lot of the background for this story will be answered in the next chapter, but I'll list a bit of it here.
Yahiko fought through the Ame Civil War, and he's seen a lot of friends die in his quest to despose Hanzo, nearly dying himself. As such, he truly knows war, both from the outside and the inside, and the cost of it. His boyhood dream of becoming a god of the world has dwindled as a result of realizing the sacrifices he might have to make on the way.
As a result, he's playing it safe and going through it a different way. As opposed to outright war, Yahiko is trying to weaken the military power of all the hidden villages (besides Ame and Suna) through sabotage efforts and other such tactics. Denial of resources is his big thing - take away summoning contracts, and several shinobi lose a highly flexible weapon, and villages weapons of mass destruction during wars. Take away jinchuuriki, and you can't achieve sheer slaughter. Kill off thousands of ninjas, and nobody will go to war because a) they don't have enough manpower, b) what manpower they do have isn't enough to fulfill the missions they're contracting, and as long as they have plenty of missions, everyone's happy for the time being. During that 'time being', Yahiko will continue to exert force and pressure and continue weakening the hidden villages.
The bit on shinobi wars is just my thought - ninja villages aren't really built for administering territories. They're ninjas. So Shinobi Wars are fought for prestige and influence than for land.
Naruto's pairing is already decided so don't bother trying to flood the review box with "OMG NARU/HINA4LYFE!" :P You'll see what it is next chapter, but a small hint - it's an extremely rare pairing (I don't think it's even been done before) and the girl isn't actually even in the character selection form yet. There's a really small hint in this chapter as well, but I won't be surprised if nobody can see it. It's not really even a hint - more of an absence of something.
The only thing I'd like to hear thoughts on is how to deal with Kirigakure in this alternate universe. For those who've been keeping up with the manga, it's been revealed that Yagura, the Sanbi container, was the Yondaime Mizukage, the guy who had in place the 'Bloody Mist' policies, but the Godaime Mizukage thinks Yagura was being manipulated by somebody (Madara). I have a policy of subtly altering things in my work as new details come out in the manga, but if there isn't any Madara here, then should Yagura be by default a more benevolent Mizukage, or a guy who still has the same policies as in canon?