The True Maelstrom
With the Hokage
As the third Hokage headed back to his office after another council meeting, he finds Danzo waiting n his office. "What are you doing here, Danzo?" he asked with a guarded expression. It has only been five years after the Kyubi attack and the Hidden leaf is still desperately trying to increase their strength. The losses by the Kyubi were very high, and only the fact they now have a new container for it is keeping the other villages at bay. No one wants to fight the Kyubi.
"We both know why I am here, old friend." Danzo started. "I wish to train the Kyubi kid." Sarutobi just sighed, this argument has been going on for years now.
"Your training methods are far too harsh for a child of his age, even with the beast's chakra enhancing him." the Hokage stated, again. "Not to mention the fact I won't allow him to become another emotionless drone that you have in your 'Root'." Danzo's visible eye widened slightly, but it was enough for the Hokage to notice. "Yes I still know about Root. Don't act so surprised."
Before Danzo could say anything further, Jiraiya came in the office. "Do you always have to use the window, Jiraiya? Can't you use a door like the rest of us?" Jiraiya smirked at him, but shrugged his shoulders stating it was more convenient this way.
Danzo, ignoring Jiraiya said, "Are you still going to deny me the right to train the brat?" this got Jiraiya's attention. He turned to face Danzo, telling him that as his god father, it was also his choice weather or not to allow him to train Naruto.
"Your methods are far too harsh to train Naruto, Danzo. Not to mention if you were to succeed in making him an emotionless slave like your other root agents, you would effective destroy this village you are so determined to protect. His emotions are also what is strengthening the seal that keeps the Kyubi at bay. If you take out his emotions, you are effectively releasing the beast on us all. Not to mention the training itself is harsh enough to weaken his body for a time, which would also weaken the seal enough to let him escape."
Danzo, at hearing Jiraiya's explanation, took a step back in shock. Knowing how bad that would end, he had no choice but to concede to Jiraiya. He was the only seal master in Konoha. He knows better than to doubt the sage in matters with seals. But he is not crafty for nothing. "How about a compromise then?" Danzo asks.
Both Sarutobi and Jiraiya are curious as to the idea, and let him continue. "I will forgo the emotion training, with the exception of meditation to calm him down, as well as keep the training tough, but age appropriate." Both the Hokage, and the Sage look at each other, silently communicating. After a while, both smirk before Jiraiya turns to him.
"We will agree with this, on a couple conditions. Nothing much. The first one is either myself or one of sensei's ANBU will supervise the training every step of the way. This way we will receive daily reports on his progress or even what he is learning." This angered Danzo, but he reluctantly agreed. "The second is one I find to be more important in some matters. I want you to make sure he eats right. A lot of shops have been either refusing him or overcharging him ridiculous amounts. The fools think that by starving Naruto they are hurting the Kyubi, when they are really making it easier for him to be able to escape. This one is my personal request, while the first one is sensei's." Danzo actually had no problems with the second one so he agrees readily to it.
"I think sending someone to these store owners and giving them an appointment with Ibiki or Anko will help with their disposition. I will use my root agents, as I know using the ANBU would make them scream favoritism." both Jiraiya and Sarutobi agreed, all three showing evil smirks.
With Naruto
'Faster, Faster, Faster!' thought the little blonde five year old was mentally shouting at himself. A small mob of people were chasing after him, some of them armed with rocks or garden tools. Young Naruto Uzumaki was for the second time this week running for is life from another group of people after him. He didn't know why they were so angry at him, but he knew he wasn't safe at home. He wasn't really safe anywhere as no one was willing to assist him. Most of them would actively try to get in his way to slow him down if they could. Always calling him demon, telling him he should die. His only chance was to try to make it to the Hokage's office. No one has ever dared chase him after he got in the tower.
Unfortunately, before he made it, he was tripped. A lone rock flew in from the side causing him to lose balance dodging, only to trip over the handle of a broom someone on the side held out in front of him. Before he could get up, his chasers finally surrounded him. He did the only thing he could at that time, curl up into a tight ball and scream for help. His pursuers only laughed at him, saying there would be only death to the demon before they started beating on him.
Only about ten seconds had passed when the beating stopped. When he looked up all he seen was an ANBU with a dog mask hovering over him, while the bodies of the ones that attacked him were all on the ground, dead. Naruto was shaking, absolutely terrified of what almost happened to him. Once the ANBU confirmed he was now safe, did he then pass out.
With the Hokage
With his meeting with Jiraiya and Danzo finally over with, he proceeded to fight the most dreaded of S class opponents, paperwork. After about an hour he managed to finish and put up the work when the door to his office slammed open, and a very pissed Kakashi came in with little Naruto who was bruised and cut up. He then proceeded to place the boy on my couch and informed me of what almost happened, and what he did to the ones attacking the child. He rubbed the bridge between his nose wishing he has some more sake as he can feel a major headache coming on. I told him about the deal with Danzo and the stipulations he had with the training, and ordered Kakashi to be the one to supervise the training himself.
At this time Naruto woke up, and slowly looked around, until he seen us. He immediately got up and ran to me crying. His injuries were already almost completely healed. He was asking why does everyone hate him. Knowing Danzo, he would actually tell him about the Kyubi before training, I decided to tell him everything about it myself. I explained how the fourth Hokage sealed up the Kyubi inside him, and how he is a hero for keeping us all safe from it. I kept his parentage a secret from him still. While he could be trusted with it, I wanted to wait to tell him until he was strong enough to protect himself. 'After Danzo's training, I will tell him then.' he thought to himself. He told Naruto about Danzo starting his training in the morning, even telling him Inu will be there to watch his training in secret, so he is not pushed too hard. I took him to the apartment in the tower that is usually reserved for the Hokage and told Kakashi to inform Danzo about Naruto's condition. I have a feeling this training will be the toughest thing he will ever have to go through for a very long time.
AN: It has been a long time since I had a good enough idea to put down. This story was intended to be a very powerful (but not godlike) Naruto type of story.
The training with Danzo would put him at jounin levels at the time the rest of his generation would have graduated the academy. For the teams, meh I don't care, they can be the same or changed. But the pairing for this is either Naruto / Ino, or Naruto / Sakura. Now if you decide to change Naruto into Naruko (female) for this story, then the pairing has to be Naruko / Sasuke, or Naruko / Kiba. No harem or multiple lovers.
As for skill set, Naruto / Naruko will of course be straight wind user like in cannon. This means he will pretty much never use anything other that wind jutsus, or reinforcing weapons with wind. Since he / she is being taught by Danzo, (who in canon is also a powerful wind user ) it means wind jutsus aplenty. They will also have the shadow clones, rasengan, seals training, and weapon training, (either claws, or nun-chucks which is something I have never seen Naru use in any story).