A/N: Small author's note at the bottom.
Interested in seeing responses.
Don't own the Naruto series or any characters, if I did, there would be no way Nagato would have been allowed to wander around on his own.
The first year of the life of Naruto was one of isolation. Later in life, he would have a vague memory of white rooms and faint, gentle humming, and above all else, a pure and deep calming silence. While his memories would only become firm upon his future residence in the Hyuuga Estate, those early days would stick with him.
Kept in a heavily guarded ROOT defensive bunker buried deep below the Hokage Monument, ringed with hundreds of feet of fuinjutsu defenses and traps, the host of the Kyuubi was raised in complete and total observation. Nono took care of him, fed and changed him, and sang softly to him, giving him a warm human focus for his attention, but the baby was under constant study.
After all, when one had a weapon available for research, ignoring it was foolish.
Kohona, in the past, had mostly eschewed more morally questionable methods of acquiring military power. While Hashirama was so powerful that he didn't need to resort to such things, his brother Tobirama was more open to the concept, creating jutsu like Edo Tensai and chakra consumption seals.
Heavily influenced by the Nidaime's beliefs, Danzo was quick to use his authority as Hokage to ensure no avenue towards greater military power was left unexplored. At the same time, he realized that many shinobi distrusted him, and his methods, seeing him as little more than a power-mad warmonger.
He could move forward with some of his plans, but the majority would have to be done either secretly or very slowly over time. And he was not getting any younger, he could not wait for new generations to grow up under his influence before making his moves. Instead, he would have to act incrementally.
The most frustrating part of the entire situation was that, at least in his own mind, Danzo did not consider himself a warhawk. While certain not one to shy away from violence or political maneuvers designed to weaken a foe to direct assault, the truth was that he fully realized Kohona could not conquer the world.
In his own way, Danzo wanted peace as fervently as Hiruzen had. The difference was that Danzo was not going to blind himself with rose-tinted views of how the world worked. If peace was going to be anything but exhausted time-outs when wars got too bloody, the word might as well not have any meaning.
People tossed around the word peace, the concept, the image, without any real plan of how to get there or – far more importantly – how to maintain such a state once achieved. Danzo had taken in the words of the Nidaime fully – only through control could mastery be achieved. Only through control of the body did one become a threat. Only through control of the mind could one master their own fears and biases. And only through control of the spirit could one find the resolve to do what others were too weak to perform.
The only true path to peace was overwhelming power, power so supreme that no one but a fool would challenge it, and ruthlessness to use such power. Power so overwhelming that war itself became suicide, that violence brought about a reaction so severe that no reward was worth the risk.
Danzo did not yet know of such a source of power, but he was constantly looking. And the Kyuubi was nothing if not power incarnate and made flesh. Unleashed in all its glory, it could burn the entire world to ashes, wreck entire nations and leave behind untold devastation. And it was trapped and vulnerable in the body of a tiny child.
In that vein, Naruto was studied intently, in every possible aspect.
Chakra researchers studied every bit of his chakra network, while tissue samples and blood draws were examined, recorded and pondered. Clones of the boy were grown using horrific chakra methods, introduced to bijuu energies, dissected to see changes, and compared to the real child. The results were startling – the bijuu was slowly morphing the child's basic biology. Muscles required more energy but were, even at barely three months old, far stronger than comparable human tissue. The immune system was like a fortress. Bones were harder than iron while retaining far more flexion than human bone, while early sensory tests showed the boy's senses would be predator level one day.
Other experiments attempted to weaponize extracted chakra with little success - when not imbued into a living thing, it degenerated rapidly. But sealing was always an option, and Danzo's scientists were even able to siphon and store small amounts of the chakra of the Kyuubi in blood-bound seals. Triggering such a seal would flood the human in question with corrosive, burning youkai. Before it burned through their chakra network, they would be pushed into a berserker state, killing anything around them. Danzo was so pleased by the result he began training an entire new cadre of throwaway assets to use such a thing.
He had many more assets to use than he had in the past. The chaos in the fallout of the Kyuubi left literally hundreds of orphans, some with minor shinobi backgrounds. Additionally, he was able to co-opt more than a few nearly dead ninja from ruins around the village and extract valuable bloodline data – including two additional lines of kikachu from the Aburame and a set of the Akamichi food pills.
As for the orphans, almost all of these vanished into ROOT in short order, although Danzo was careful to make sure a few dozen were handed over to the orphanage as a public show – mostly those with no real potentials. Danzo firmly believed in long-term planning, and with a wide selection of recruits had enough manpower to begin building a private army. While ROOT was powerful as it was, it was limited in manpower and more than a few of its members were already well known. Having a collection of completely anonymous shinobi with no known links to the Leaf would be of immense value in black operations.
His training methods did not change in form, but did so in function. Previously, with he'd forced paired orphans to fight their closest friends to the death as the last step to ensure their emotions were crushed. While it was certainly effective, it had the unfortunate but obvious side effect of halving his potential manpower.
The near-total demise of the Kurama clan during the Kyuubi incident, however, had opened up new opportunities, as the last heir was taken by ROOT in the chaos. Able to not only create genjutsu so vivid they could almost not be detected or broken, the clan also had detailed records on the psyche of humans and memory – needed as their powers often drew on the victim's own mind and memories.
Combined with some assistance from the Yamanaka members of ROOT, therefore, Danzo had altered his training finale. Every recruit was put into a full-sensory genjutsu and made to believe they were forced to kill the partner they had trained with since induction. Afterwards, a memory seal warped their memories, making them not recognize their brother or sister in arms, allowing Danzo to keep both recruits from a pair and still deaden and destroy their emotions.
The ANBU itself was now riddled with ROOT, although he was careful not to replace any of the captains with ROOT members. Captains needed charisma and leadership ability, and his ROOT agents did not perform well in such tasks. He rather used ROOT to boost the overall power of the ANBU forces, allowing some more powerful ANBU to move upwards to lead entirely new units, while he began restructuring the Academy and ninja program itself.
Much of that was still ongoing. After months of work and no sign that Danzo was suddenly going to invade Iwa or Kumo, many of the jonin and the more wary clans stopped worrying so much. He was careful never to put forth concepts that seemed too risky, instead simply having his ROOT handle all such things – they had a much freer hand now without the oversight of Minato.
Thus far his success in the council had been small – revisions to textbooks, moving D-ranks to being something performed by Academy Students as E-rank while changing the new d-ranks to mostly being training-related simulated missions or guard/protection details inside secured areas as practice. While Kohona would normally be in a slump, Danzo had struck deals with more than a few ruthless business types, and his ROOT were performing a wide array of unethical missions that raked in heavy S-Class fees.
While he was pleased with his efforts in strengthening the village so far, his greatest achievement had been managing to retain the services of both Jiraya and Tsunade, albeit on limited levels.
Jiraya, despite his opposition to Danzo's plans and ideals, was a fairly easy sell. Danzo promised the man he could have complete insight as to Naruto's training and how he was raised, and that he would be the one who explained to the boy about the Kyuubi, his heritage, and his future. Additionally, he promised Jiraya that if he felt the training was detrimental to Naruto's stability, he would allow the Sage to train the boy himself – in secret, of course.
Given that the man could not even look at the boy without being wracked with guilt, it was all to easy to convince the Sage to go along with his plans. Danzo even managed to summon that stupid smile Hiru liked to pull out at the sight of the Sage holding his godchild.
Jiraya, ever hopeful of the lighter, brighter side of humanity, wanted to believe Danzo had good intentions. He knew better…but he also knew, deep down, that given all his own failures, he was not suited to raise the boy. If his sensei had survived and not been slain killing Orochimaru, perhaps he would have left him in his care.
Instead, he went about his duties, running and expanding his spy network. Concerned about his godson, he expanded it into the one place he never really bothered to before, Fire Country and Kohona itself. In another life, one where Sarutobi survived, he would have never thought to do such a thing, and Kohona would have paid dearly for his oversight. Danzo did not mind, and after dropping a few hints that it was always possible that enemies might discover Naruto to kill or kidnap him, was delighted when the man focused more on said spy network than his usual whoring and writing activities.
As Naruto turned five months old, he'd even convinced Jiraya to write up a sort of primer to fuinjutsu for Naruto, which he then distributed to his own ROOT forces. The seals inside were simple but more than a few showed innovations Danzo wasn't aware of. More importantly, some of the basic theory was reworded and included into academy textbooks. When Jiraya returned and saw such an upswing in interest in fuinjutsu, he began trying to convince Danzo to allow teaching of it in school.
It had been difficult to hide his amusement as he 'grudgingly' agreed to allow Jiraya to write up a complete fuinjutsu textbook and design a course in sealing. The additional power this gave even young genin teams sent survivability ratios and mission success rates skyrocketing.
Retaining Tsunade's services had been hardly more difficult.
The last of the Senju did not want to return to Kohona, and feared that the cold Danzo would have forced such an issue. Indeed, he had sent out a summons recall for either her or Shinzune, to help deal with the massive amounts of injuries from exposure to the bijuu's chakra.
At the time, Tsunade had agreed with ill grace, but was surprised when ROOT agents informed her that the majority of the wounded had been moved to specially constructed facilities outside of Kohona. She and Shinzune had treated some of the worst cases there, and that was where Danzo had shown up.
Tsunade expected a cool demand she remain in Kohona, but the elderly nin just shook his head. Instead, he revealed his ROOT had already discovered her homophobia and her drinking problems. He felt these made her too much of a liability to the shinobi to bother re-activating her, at least in a formal manner, but that he did need her help.
Rather than force her to return to the village, Danzo cunningly offered a different plan. Kohona would pay Tsunade to spend a few days every other month examining Naruto, and determining how the Kyuubi affected the child, and then she would be free to go about her business. Kohona would pay her enough to drink and gamble and forget, and while she was required to get close to Kohona, she never had to gaze upon the village or enter it.
Tsunade, despite her broken spirit, was no fool. She felt, based on the words of her old sensei, that she had a good grasp on the warhawk and his ideals. The rather hesitant mention of 'research' and study had not been extensively detailed, and most of all, Danzo had not even tried to force the issue of her staying.
She had accosted him in the labs near where Naruto was kept, arms folded, honey brown eyes narrowed. "I have a question, Danzo. Why are you not trying to force me back?"
Danzo merely arched his good eyebrow. "Tsunade, unlike Hiru, I am not one for sentimentality. And to be honest, you simply are not the force you once were. You were once mighty, a powerful kunochi feared the world over. You lost your brother and your fiancé and let that destroy you, unlike many others who suffered worse losses yet kept themselves fighting."
He let his expression slip slightly into a sneer. "I will not argue that you owe Kohona anything, as you have made it clear you do not feel the same. But you are, in terms of military power, useless to me. You cannot fight, you have no spirit, and you have no doubt not bothered to train in years. Frankly, the only use you have to me is as a medical researcher. Your apprentice, on the other hand, is highly skilled and very useful in the Kohona General Hospital."
Tsunade gritted her teeth at the old man, but said nothing as he continued. "Ultimately, like your teammate Jiraya, you are filled with regrets. A fool once said that regret can change the nature of a person. That may be true, but only in the shallowest of senses. "
She shook her head. "And what is it you want me to research?"
To be honest, Danzo had expected her to be more resistant to the sort of studies he had in mind, but despite herself, Tsunade was at heart a medical researcher. She had long wondered about the effects of youkai on humans, and despite being one of the few that could treat exposure to it there was still plenty she didn't know.
Of course, Tsunade told herself she went along with Danzo's schemes to keep an eye out for Minato's child. Whenever she could she took the opportunity to play with the boy, swallowing back painful memories of helping to raise Nawaki. Danzo merely tightened the noose when he suggested that Tsunade teach the child as he grew. When Tsunade was surprised by this, Danzo told her that he would not be going into ROOT and was expected to live a strict and military but otherwise normal childhood.
Given that Shinzune was delighted with her position as Head Medical Doctor at the hospital and already making friends, something she couldn't do roaming the Fire Country and trying to keep Tsunade from sinking into depression, Tsunade found herself trapped. But as she gambled and drank and sank into a sort of malaise, she comforted herself by believing she was looking out for Naruto, even as Danzo's research requests turned darker and darker.
If Jiraya and Tsunade had sat down and talked, perhaps they'd realize they were being played. But Danzo was careful to ensure he never scheduled them to be in the village at the same time, and the antipathy Tsunade had in her own past was enough to make that potential contact almost an impossibility.
With the Hyuuga, Yamanaka, and Aburame clans backing him, the support of the Sannin, and of course having Hiru's two advisors in his corner, Danzo felt plans were moving along nicely. It was time to reveal the identity of the false jjnchuriki, even while he prepared the modifications to allow a young Naruto to grow up in the Hyuuga family.
He eyed the pair of main-branch Hyuuga eyes taken from a young boy during the Kyuubi attack, and smiled thinly to himself. After all, the best disguises never used chakra and hid the truth in plain sight. He motioned to one of his ever-present ROOT ANBU attendants.
"Send for Nono, and have the container prepped for surgical alteration."
Still building up the background so far. Progress is slowly coming along.