A high-risk gambit by Danzo leaves an infant Naruto with the legendary Wood bloodline. Watch a multi-element-wielding Naruto on the way to fulfilling his dreams. Mokuton!Naruto

Extended Summary: A Danzo more savvy leaves an infant Naruto with the legendary Wood bloodline, and causes some other changes as well. Watch how a Naruto with multiple elements fulfills his dreams.

...SPOILERS even up to some of the latest chapters are abound from the very beginning of the story. You have been warned.

Notes

Hokage names (Family name first)

Shodai (First): Senju Hashirama, Nidaime (Second): Senju Tobirama, Sandaime (Third): Sarutobi Hiruzen, Yondaime (Fourth): Namikaze Minato

Prologue:

"...age-sama."
"Hokage-sama."

Hiruzen shot up, kunai in hand.
He must have nodded off.

The ANBU didn't visibly react to the Hokage's jumpy, dangerous move.

"Hokage-sama. There's an emergency." Stated the ANBU evenly.

"What is it?" Hiruzen said rubbing his eyes.

"Uzumaki Naruto is in possibly critical condition. Foul play is suspected."

"What?" Hiruzen shot up from his seat again, and moved to the ANBU's side.

"Take me to him." He demanded. The squirrel-masked ANBU led the way.

A frantic Sarutobi arrived at the hospital, outside the room Naruto was kept in, and asked -or rather demanded- of the medic-nin who seemed in charge to describe the problem and determine its cause.

"Well, Hokage-sama, it seems that this young one was injected with something potentially lethal, and his tenant intervened." The medic-nin, Yakushi Hoshi, explained and continued before the Hokage even asked:

"I do not believe that there will be any permanent negative side effects, but young Uzumaki's chakra coils have expanded to many times what they were before."

"Who could be responsible, and what was Naruto injected with?"

"You might wish to take this conversation elsewhere, Hokage-sama."

Hiruzen took the hint and played along, taking the medic to a storage room and signaling his ANBU guards to erect a soundproof barrier.

"You may speak." Hiruzen made it clear to the man that he was not being given a choice.

"It appears, sir, that the child was injected with a product of the First Hokage's genetic material-" a rare look of incredulity showed on Hiruzen's face, but he quickly squashed it. "...and now has the chance to develop the Mokuton bloodline limit."

"What are his chances of dying, Hoshi?" Asked the Hokage next.

"Slim to none Hokage-sama; the danger has passed now." Hoshi stated.

Hiruzen set his wrath aside and allowed his nature as a scholar to shine through. "How likely is it that he will fully manifest the Wood Release?"

"When the beast's chakra started leaking into his system in ample amounts, it was turned into a number of tree branches; the process is also at fault for the enlarged chakra coils.
I had the rest burnt, but I kept this piece of the sample." Hoshi presented his leader with a piece of tree branch, adorned with some greenery.

"So, the child's chances of being able to use Mokuton are quite high."

One and a half day ago, Root base:

Shimura Danzo, the commander of the covert "Root" military unit, was weighing his options in a dark-covered, hidden underground area, for he was certain that something drastic had to be done in order to allow for the survival of the village; dominance was not even an option yet - Danzo was a realist, and far from a fool.

Even though he never liked the "Yellow Flash", that Namikaze boy who became the Fourth, he had to admit that his death was an enormous blow to Konoha, both in power and morale.

Add to that the fact that Sarutobi was certain to be heavily affected as well, sentimental fool that he was, by his wife's death...

What was worse, his old rival had been relaxed in his certainty that he was not going to carry the full responsibilities of the Hokage seat ever again. Danzo allowed himself a scoff - a Hokage never retires.

Thus, Konoha had a weakened military, and as Hokage, a Sarutobi who was bound to be an even weaker leader than he had been in the past, by far.

So what could Danzo do?

Any plan he made would have to be based on the new generation, at least in part, but how?

Of course... the Jinchuuriki. The Namikaze (Uzumaki, he mentally corrected himself) infant, literally born yesterday.

But could he make it his tool? And would that be enough?

No to at least one question, probably both.

If he were unable to make it his tool, then he would have to assume the Hokage position himself in the future. But as he was, he would be unable to.

Could the technique he had found in the stolen Uchiha forbidden scrolls on the Mangekyou, Izanagi, help him become strong enough to seize the next chance and take over Konoha?

He did possess a Mangekyou and -to an extent- Mokuton, but he would need many spare Sharingan to put into his special arm, and possibly a better Sharingan than his current one for his eye socket. Especially if he could find one with a knack for mind control...

So, he had two challenges directly in front of him: find a way to strengthen the Jinchuuriki, and find a way to get several Sharingan without being put in danger.

He would have to think on this further.

The day of the injection, at a different Root base

It took him a lot of brainstorming, but Danzo was confident that he had the best solutions that could be crafted.

His plan to get a number of Sharingan was a piece of brilliance that was as good as any plan he had made in his life, and that was saying something.

In one fell swoop, he could get all the Sharingan he wanted, and at the same time dispose of a thorn in the side of Konoha, the Uchiha clan.

Even in the absence of Uchiha Madara, the clan had remained arrogant, if not worsened, and taught its children to value the village far less than the clan.

The Uchiha were not the only clan full of arrogance (the Hyuuga and to a lesser extent, almost all of the other shinobi clans were good examples), nor the only to put themselves above the village; but the degree to which they put the interests of their clan above Konoha's was worlds beyond any other.

It was only a matter of time before they tried a coup d'etat, really; with catastrophic results to all parties involved. Better make them do so on his own terms.

So he would have them all killed, with the (unwilling) assistance of Sarutobi! It would be easy to mislead his two fellow elders, after all. And then, they would overrule Sarutobi in the matter.

If the Uchiha felt that they were being cast out, it would take months for them to consider revolting, not years and decades.

In the confusion of Sarutobi's ANBU exterminating the Uchiha clan, he would have some of his best operatives steal any Uchiha eyes they could, as well as a few full corpses if possible.

Thanks to a forbidden technique that Tsunade had invented and Danzo had managed to get his hands on, he would be able to use the genetic material from several highly skilled Uchiha to impregnate chosen women at any moment he wished; truly loyal Sharingan-using living weapons - and the process didn't even require living tissue, let alone semen.

He already had some samples, but they were of inferior Uchiha and somewhat badly preserved; besides, the more, the better. And coming Uchiha generations would be able to interbreed to a degree without full-blown incest.

That was the gist of his plan for the Uchiha and their eyes.

His plan for the Jinchuuriki, however, was one he had far less confidence in, but was the best one to use with his and Konoha's current resources.

It would be necessary, since whoever had released the Kyuubi was probably still around; and if it were a still living Uchiha Madara, who, strangely enough, was the most likely culprit, especially considering the fact that Senju Hashirama, apart from his wonderful bloodline limit, was overrated as a shinobi...

Nobody but Madara could have delayed the Fourth enough, after all. If it had really been him, then the J... Uzumaki Naruto would have to be able to partner with the Kyuubi to keep both of them nearly immune to controlling genjutsu. (Madara had been only barely capable of controlling the Kyuubi alone. If it worked with a strong host, genjutsu was out.)

The only option to make the most hostile of the Bijuu (except for Shukaku?) willing to fully support its host would be the Mokuton, since unlike the Sharingan, it soothed the forces of Nature and made them more docile, liable to obey of their own volition.

The special Uzumaki chakra, the other Bijuu-controlling ability Danzo knew of, could only restrain and/or suppress them - even if Uzumaki Naruto were female, it would be out of the question.

Thankfully, not only had he kept samples of his own of the First's genetic material from decades ago; he had managed to improve upon Orochimaru's own work with Mokuton, thanks to a prodigious medic-nin with a secret allegiance to Root, Yakushi Hoshi.

With his top-quality samples and improved methods applied to an infant scion of the Uzumaki clan, with their superior life force (comparable to the best of Senju, and the life force of his mother Kushina was probably greater than Hashirama's), let alone one carrying a creature which mixed excellently with Mokuton, should result in a procedure so successful that they would theoretically have a Wood User at least as good as the First himself.

Unless he died as a result, which was a possibility, even on an Uzumaki infant with the Kyuubi and both parents being easily Kage-level. Underperfoming was also a possibility.

This plan was quite hazardous but in the end, potentially even more rewarding than the one for the Uchiha.

He didn't really trust Sarutobi, but he at least could count on him to instill a sense of loyalty towards Konoha and the seat of Hokage in the child; his "grandfatherly" act was quite popular, however much it disgusted Danzo.

In order to not be suspected of being the one behind the Mokuton incident, he would request Sarutobi to give him the child once again until after he "found out" through "trustworthy sources" that Uzumaki Naruto had that bloodline, at which point he would ask repeatedly.

Of course, the "finding out" would not happen until his rival discovered Orochimaru's recent experiments and his being responsible for the past Mokuton fiasco, to cast most suspicions on the latter first.

It would not take long, since Orochimaru had started becoming more and more reckless in his kidnappings after being denied the Hokage position.

The only reason Danzo would ask to train the boy would be because not doing so might seem out of character to his old rival. Danzo knew full well that there was no chance he would be allowed to, and if he kidnapped the Jinchuuriki, he would put himself and Root in too great a danger...

Danzo's time alone was at its end, he had to return to the surface. If he were not a Konoha Elder, it would be easier to be absent without anyone noticing, but he could not resign until after he had concluded his machinations against the Uchiha clan.

He summoned two skilled operatives and a messenger, each one separately; Danzo put one operative in charge of the distraction team, ordered the other to administer the samples, and had the messenger insure the cooperation of Yakushi Hoshi, without any of them being aware of the others' assignments.

The child would have Mokuton before the dawn of the third day of his life.

...Back to the Uchiha clan matter. If Danzo played his cards right, he wouldn't even have to lie; that he believed an Uchiha was behind the Kyuubi attack was technically true.

With thoughts of what he would say to his fellow "esteemed elders" to make them isolate the Uchiha, he departed.

Nearly eight years later

The Uchiha situation was going even better than what Danzo had had as his "best case" scenario.

Never had he anticipated that they would have a Kage-level (or very nearly so) Uchiha on their side; the boy was capable of leaving his clan in such a weakened state, that his Root were certain to manage to finish the job and procure a number of bodies and eyes.

First though, Itachi would need the Mangekyou. Danzo had already copied samples of Itachi's and Uchiha Shisui's handwriting with his Sharingan, something he needed for the next stage of his updated Uchiha plan.

He would tell Itachi about the requirements of the next form of the Sharingan -though it was likely he knew already- and then force his hand by forgery, making him think that Shisui wanted to meet him alone and giving Shisui the same impression about Itachi.

His Root operative would retrieve the entire body and leave a "suicide note" that Danzo himself had written.

Danzo couldn't believe it.

Itachi had not only managed to nearly finish the job, but survived the process.

What's more, his Root agents were missing. It was fortunate that he had had more ready to deploy and got the bodies and eyes he wanted regardless.

This smelled of foreign intervention; had Itachi gotten assistance from another village?

Danzo did not like the idea, not at all; the alternative would be that Sarutobi himself had joined in, but Danzo immediately dismissed the notion; the man had become too spineless to get his hands dirty.

Then again, there was the possibility of Madara; after all, he held a grudge against his own clan.

The latter possibility made Danzou's blood run cold.

Madara might have been in the village, cutting skilled shinobi down, and nobody had even noticed; not that the presence of foreign agents capable of sensing and capturing/exterminating some of his most stealthy and cautious Root members was a much better prospective.

The only other members or former members of Konoha capable of those things were Orochimaru and Jiraiya but had it been Orochimaru, he would have stolen a number of Sharingan and bodies himself and had it been Jiraiya, he would have taken the Root agents to Sarutobi to interrogate.

Danzo was not deluded enough to think that his operatives would be able to even commit suicide against a Sage-mode Jiraiya, nor hold out as much as the month that had passed in the hands of the skilled interrogators of Konoha, no matter the emotionlessness or seals; so since Danzo had not been hunted down, Jiraiya was not responsible.

If hostile agents of legendary skill had infiltrated the village, Danzo would have to speed up his plans for strengthening Konoha.

Perhaps he could include the remaining Uchiha heir in his plans, and turn the only truly foolish act in Itachi's career into something positive for Konoha; or at least stave off the famed Uchiha arrogance.

But first, he had to deal with the fact that the fool Sarutobi had not trained the already turned eight Uzumaki Naruto at all, one of the few things to ever frustrate Danzo considerably.

Do you guys like this piece? I'm not sure whether I'll continue this, I may put it up for adoption and just beta for whomever takes it. (Note that the enlarged chakra coils are so that they aren't as pressured by the Kyuubi's chakra, so that Naruto has enough chakra control to use ninjutsu.)