Naruto Uzumaki, the story of the chosen one

Now it really begins!

Ok. You've all been great support! This story's getting lots of love too :P so, people have chosen bits and pieces. This will happen through time skips, Narutos training will last 6 years (he'll be twelve at the end) and... well no spoilers~ enjoy.

"Talking human"
"Bijuu/Kami/Yami/Shi talking"
"Jutsu"
'Thinking'

~~begin~~

A cool breeze, the smell of eggs and cinnamon, and a child suddenly awake, panting. Naruto searched the room, hoping and praying that the previous day was not a dream, praying that he wasn't back in that cramped and dank apartment. The aroma of sweets and eggs should have told him this, but he would not believe his nose, that was.. until he saw his father, asleep in a nearby chair.
Minato was leaned back, worried shone on his face, even in his sleep. He would move ever so often, as though he was attempting to wake up, or grab for something 'or someone kit' Naruto shook the voice off, as he felt his father was more important at the moment.
An idea popped into Narutos head as he climbed into his fathers lap, who, at first, tensed. Soon Minatos muscles were relaxed as he held his son, the worry he bore soon fading into happiness. Naruto tried to snuggle in closer to his father, tried to hold his father, smiling at the warmth he was feeling for the first time in his life, and soon he was asleep.
Only a few minutes later, Shi knocked lightly on Narutos bedroom door, thinking that Minato would answer the door. She waited for three minutes until she ultimately decided to creak the door open.
She looked around the room, only to smile and sigh as she saw the father son duo asleep on a chair. How she wished to leave them there in their small slice of heaven, but Kami had prepared food, meaning if they were late.... well we'll leave it at shi's ass still hurts thinking about it.
"Naruto-Kun, Minato-san, it is time to wake up." The two released a snort simultaneously, causing the death queen to begin giggling before she lightly shook the father.
Minato opened his eyes slowly, as he would rather have stayed asleep. He was about to get up when he began to feel an added weight on his lap, causing him to look down. As he saw his son lying on his lap he smiled softly before he kissed the boys head, waking him up.
Naruto followed his fathers previous actions, almost to a point, save for rubbing his right eye and yawning.
"Good morning papa..." his voice had changed from the high pitched scratchy tone it had once been, now it was a tad bit deeper, and flowed easier.
His voice was not the only thing that had changed, over the night his hair had become an amalgamation of deep Uzumaki red, Brown, and Blond. Naruto had even grown an inch or two!
"Good morning son." The father gave his son a megawatt smile, getting ready to ask his son a question before a third voice interrupted.
"Although I would love to allow you to continue cuddling, Breakfast has been prepared. If that is not pertinent enough, Naruto-kuns training begins today." The shocked duo turned to see Shi standing a foot away, smiling sweetly.
Naruto hopped off his fathers lap, and was almost instantly out the door as he followed his nose. Minato was hot on his tail as the delicious aroma finally reached their noses, leaving a surprised  and laughing Shi.
  As the pair reached a large room, they paused, only just remembering their manners. They looked around and saw that Shisui was talking to Hagoromo with the older man sporting a small smile in one corner. In another corner, Hashirama was meditating silently. Yami sat at the right hand of the Table, with Kami at the head.
  As the siblings caught sight of the two blondes, Kami stood and rung a small bell, calling all of the residents to the table. As they sat in their chairs, the food was passed around.
  As they filled their plates, they all began talking and laughing. Naruto looked around to them, and tears began to escape his eyes.
  "Naruto, are you ok?" Hagoromo was the first to react, he placed his hand over Narutos from across the table as he spoke.
"I-I'm sorry... I-It's just... I've n-never had a f-family.." tears rolled from his cheeks to his chin. Yet as he looked up he was smiling. Spreading his Megawatt shine.
From beside the boy he felt an arm, and finally, he was pulled into a hug. "Naruto... if we are truly your family... we will all do everything we can to protect you.. to make you strong.. and.. I'm sorry I wasn't there for you... when I was alive..." it was Shisui who had hugged the boy.
"It's... it's ok Shisui-nii!!" The boy exclaimed and smiled at the shocked boy.
As Shisui was getting ready to respond they all heard a haughty laugh, "guess that means I have someone to call me Jiji now!" They turned in shock to the normally calm sage at his sudden outbreak.
"Of course JiJi!! And I have another JiJi too!!" Naruto exclaimed as he pointed to Hashirama.
"What?! ME!!" Hashirama smacked his head to the table with anime tears running down his face.
After a few laughs the group began eating again. Soon after they had finished their delicious meal (and Naruto had finished his seconds and thirds) Yami lead the youngest to the training grounds and sat him down.
"Naruto, today you begin your training. Today, you begin your destiny. You will start by sitting and following my lead." The pair sat down, Naruto staring intently at his sensei, and training, began.

~~two months later~~

Naruto Uzumaki-Namikaze was sitting in a field, meditating. He felt the air around him blow, the earth beneath him breath, and the trees around him sigh.
He had been there for an hour, training his spiritual energies. Soon the young boy stood, looking around the field before beginning his daily exercises, supervised by Shisui of course, consisting of a two mile jog and an amalgamation of many other types of work outs. On his legs and wrists were seals, upping the effect of gravity by a small 2 percent, yet it was enough to feel.
As Naruto ran, he felt the air flowing past him, and looked to the sky, to the future, to hope, and smiled.