xXtoDeathXx: Ok as I said I was gonna rewrite the story so here's the story.
Summary: After the battle on the Valley of End Naruto mysteriously disappears the rookie 9 misses him but after a few years of moving on Orochimaru appears with a mysterious girl saying that she "was" Naruto.
DISCLAIMER: I REALLY DON'T OWN NARUTO SO DON'T SUE ME.
It was raining hard that day.
Kakashi was speeding his pace as he went through the forest in search of his students with his summon pakkun by his side.
"They're close Kakashi" said Pakkun.
As they went into the clearing they only saw Sasuke unconscious with supporting only bruises.
They saw a trail of blood being washed away by the rain.
"Pakkun can you find Naruto's scent?"
"I can't, the scent is being covered by the rain."
They hurriedly brought Sasuke to the hospital to be treated by his minor injuries.
At the Hospital
Tsunade was treating the Sasuke-retrieval team. She was now doing the surgery of Neji the boy really pushed himself to chakra exhaustion.
After the surgery she ordered the nurses to put Neji in a room to rest. Then quickly left to see Sasuke.
As she entered his room he saw that he was already sitting on his bed covered with bandages and holding a Konoha headband. She saw that he was wearing his but it has a slash on the leaf symbol.
"Sasuke who's headband is that?"
Sasuke mumbled something but she didn't hear it.
"What?"
"I said this was Naruto's he gave it to me before he left me unconscious after the fight"
"Excuse me did you just say 'before he left'?"
"Hn"
She suddenly ran out the room looking for Kakashi. She found him in the lobby reading.
"Kakashi! Where's Naruto?" she asked worriedly.
"Hokage-sama I only Sasuke at the Valley of End I didn't see Naruto anywhere." he replied.
-LINE BREAK-
Naruto is currently at the headquarters of Orochimaru. He was the one who went with Orochimaru not Sasuke.
"Hello Naruto-chan I see that you took my invitation instead of Sasuke."
"I just saved him from being driven by revenge and you know that I'll come instead of Sasuke because of my thinning patience left." he said boredly
"Ku Ku Ku remove the henge on yourself Naruto-kun you know you can't keep it up yourself."
"Hai"
There was a poof and the place were Naruto was standing was a girl with black hair that reaches the waist with onyx eyes like the Uchihas
"There can you now tell me you're real name?"
"You can call me Mikoto. I was told that I was named after my aunt."
"Anyways can you start training me?"
"First you need to change your clothes then we can start training."
Orochimaru's plan was to transfer himself to the Kyuubi container because of it's power and the sharingan Mikoto had then he can dominate the world.
But he had another plan to turn Mikoto to impregnate Mikoto with his seed so that he can use the offsprings body as his next body.
After Mikoto had changed she was instructed by Kabuto to follow him into the training grounds of Orochimaru.
No one has really known that she has the sharingan except for Orochimaru during their fight at the Forest of Death.
Sasuke was out at that moment and Sakura was hiding Sasuke. They didn't even know that she has the cursed mark too.
She hid a lot of secrets from her teammates even her sensei.
-LINE BREAK-
At Konoha
After a few days at the Hospital all of them were discharged and immediately called at the Hokage Tower.
The rookie 9 except Naruto and their respective sensei's were with them.
"Can someone tell me where that Naruto-baka is?" asked a very mad Sakura.
"Yeah where is Naruto-kun anyways?" asked Ino
Everyone in the rookie 9 didn't know where Naruto was except for Sasuke.
"Everyone quiet I will now explain why Naruto isn't here" said a very depressed Tsunade.
Everyone did what she said then tried to listen to what their Hokage was gonna say.
"Naruto left Konoha."
They all were to shocked by the news and asked again if they heard it right
"What did you say Hokage-sama?"
"I said Naruto LEFT Konoha" emphasizing the word LEFT.
All of them were having different thoughts about why Naruto left.
But they were thinking one thing in common. They all didn't acknowledge Naruto as teammate or friend.
Cliffhanger for now
Signed
xXtoDeathXx