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Disclaimer: I do not own naruto but I do own this idea
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Three weeks since initial confrontation / 14 meetings since initial confrontation
"Knock, Knock, Knock"
Naruto groaned loudly as he looked up from his bed at his alarm clock. Ten PM.
"Go away" he grumbled as he pulled his pillow over his head only to be answered by further knocking.
With a groan and a loud thud he slid off his bed and left his bedroom, heading towards the door. With a yawn and sleep filled eyes he fumbled with the door for a minute before remembering to unlock the deadbolt and finally pulled the door open a fraction.
"What is…it?" He stared blearily at the man in shinobi armor and the white bear mask
"The Hokage has requested your presence"
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Naruto stood in front of the doors to the Hokage's private study and felt himself swallow nervously before a nudge from on of the ANBU that had escorted him reminded him that if he didn't go in willingly he would probably get dragged in. So with a sigh and a shrug of his shoulders he pushed the door open and stepped inside.
The first thing he noticed was how dark and smoky it was. The next thing was that the moment he stepped away from the door it had closed on its own. The next was that the room was utterly silent apart from the quiet scratch of pen on parchment. He was left blinking for several seconds trying to adjust to the twilight darkness that filled the room. Belatedly he realised that the only light in the room was coming from a small lamp on the large desk in front of him. He then realised that the source of the smoke was the pipe that was resting idly in the hand of the Man sitting behind said desk.
The Hokage.
Naruto again felt himself swallow reflexively. The old man seemed not to notice him as he sat in a well cushioned chair, hunched a small scroll writing something. After a minute or so he put down the pen he was using and pulled a small stamp from his robes, firmly pressing it into the top right corner of area he had been writing on and after gently blowing on it for a few seconds he carefully wrapped the scroll up and tied a small piece of string around it before placing it to one side. Only then did he look up at Naruto and Naruto had never seen such a serious look on his face.
"Sit" he said with a small gesture to one of the chairs in front of the desk.
Naruto hurried over to the chair and sat with the air of a dead man.
"You likely do not need to be told why you are here, Naruto." The man once known as 'The Professor' said.
"My…training of Sakura" Naruto said with a slight wince
"Indeed…though Training is hardly the word for it. Brutal unabashed beatings seem more like it." Naruto winced at the vehemence in the Hokage's voice "but…I cannot deny the results…it has been three weeks since you began your nighttimes sessions with Sakura and while both of you may put up a very convincing act that nothing was going on, for a person who has the ability to watch your meetings it is obvious that both of you are improving rapidly." He paused as he seemed to think something over "very rapidly. If it didn't conflict with what I am going to do tonight then I would have awarded both you and Sakura with the rank of Chunin. Unfortunately that would reveal what you have been doing and that is something neither of us want"
Naruto winced heavily as he thought about what Sakura would do to him if she knew that he was Zan. Then he repressed a shudder as his imagination helpfully supplied him with several gruesome images of his own demise before his mind suddenly jumped as it processed the entirety of his commander's words.
"Um sir?" Naruto flinched as the Hokage's gaze swept to him "what did you mean when you said that neither of us wants it to be revealed"
"Simple Naruto. You made your bed now you have to sleep in it" Seeing the confusion on Naruto's face a shark-like smirk flashed across his face "I suppose this is going to require a bit of history."
The Hokage leaned back into his chair and puffed on his pipe for a few moments. Finally he rested his head on a hand and began to speak with such a commanding air that Naruto couldn't help but pay his utmost attention to.
"Several years before you were born an ex-shinobi named Danzo created a new division of ANBU known as 'ROOT'. It consisted of various people who were deemed too weak, too reckless, too young, or of dubious mental health, that they could not be sent reliably on missions of any kind. It looked like a good idea in the beginning. A place for people to be rehabilitated for regular shinobi work or be brought into the fold early on in life. Unfortunately a few years down the line we found the truth…the young ones were being indoctrinated into soulless emotionless machines, the crazed were pushed past the brink of sanity and turned into berserkers, the reckless were put through a training regime that ripped them apart and turned them into monsters, and the weak…they were really the only thing I couldn't really say much on...the weak he turned into true shinobi…killers of the night. True assassins. But because of his various other regimes…we shut ROOT down and tried, almost always failed, to rehabilitate those he had had a grip on."
The old man slowly rolled his shoulder as he paused for a few moments and various crackling sounds could be heard from his protesting joints.
"But rumors have surfaced that point to Danzo, rumors that seem to indicate that while ROOT may have been officially disbanded that Danzo has still been recruiting and that ROOT continues to operate." His eyes suddenly snapped to Naruto and held him firmly in place "This is something that has caused me no small amount of grief. If Danzo does something stupid it will be Konoha who will be to blame…so I need a counter to his ROOT. A counter that you have given me Naruto-" He carefully hid a smirk in anticipation of Naruto's reaction
"-or should I call you 'Zan the Supreme-commander of Jiyuueigyou' "