Chapter 1: Confronting the Traitor/Awaken Jikugan!

'I can't believe the old man doesn't want me to pass. I finally get the shadow clone, thus finally making me 'rookie of the year', and he wants me to be the bait to bring in a traitor,' Naruto complained in his head. After Naruto's second attempt the Shodamie told Naruto of the Shadow Clones. Throughout the year he has been using it to pull pranks, much to the ANBU's anoience, and studying. When he was at the library one time, he ran into Hinata, and the two started getting close to each other. 'Even if I hid my newfound smarts all throughout school, I would still be able to be rookie of the year through the test.'

*Time skip (Because I'm lazy) to the forest*

"NARUTO!" Iruka shouted, "What are you doing here with the forbidden scroll!?"

"Shh, Iruka-sensei keep it down, you'll blow my cover."

"What are you tal-" as Iruka started to ask, the two heared shuriken coming towards them. Iruka tried to push Naruto away and get hit himself, but the young blond grabbed him and pulled him out of the way along with him. They heard laughing from the tree the shuriken flew from, and saw Kabuto (yes I'm having him get confronted with beforehand) standing on a branch.

"Good job Naruto. You brought me the best tracker and the scroll," Kabuto told him, "For that you gain a prize. You'll finally know what happened to your clan 12 years ago."

"My clan?" the orange clad teen questioned, not expecting it.

"Don't you dare Kabuto! That information is forbidden!"

"Oh but Iruka, surly you know by now that I'm not truly from the Leaf. I only surve Lord Orochimaru!" Kabuto exclaimed, "Now where was I? Oh yes, the Uzumaki clan, known for their large chakra reserves, long life spans, rapid healing, and fuinjutsu. They were wiped out 32 years ago, your mother being the last." (I'm not going to be adding Karin, and Orochimaru didn't know of Nagoto's decent).

"No! Stop It!" Iruka shouted, knowing where the story was going.

"She was sent to konoha before Uzu's downfall to become the next jinchuriki of the nine tails. 12 years ago the Kyubi was sent out by a masked man to destroy this pathetic village. So the Yondaime sealed it into the only child that could hold it. You Naruto Uzumaki, are the Nine Tailed Fox that attacked Konoha!"

Naruto stood there processing everything when his right arm twitched and jerked up, bringing static electricity down his arm, and coursed through his body. Kabuto saw this as his chance to kill the kid, and sent a giant shuriken at him, which Iruak got in the way of.

Meanwhile in Naruto's mindscape, the kyubi woke up and looked to see the sewer/bunker become a giant replica of Konoha (or did he shrink?), with a yellow ball of lightning becoming a lamp on top of the Hokage Tower. The lamp shot electricity at the seal on the lock of the tailed beasts carrier, shocking the fox inside. The fox then felt himself becoming whole and remembering everything more clearly. After a second the seal spat out a blond ninja in a jounin vest, and white cloak that fell to the inside of his knees. "Yondaime!" Kyubi shouted, getting the man's attention, "No time to explain everything. You need to take over your son's body quickly so his teacher doesn't get worried."

Doing as he was told, Minato opened his son's eyes in time to see a Chunin's blood drip down onto his cheek. "I was just like you Naruto… all alone, nobody to look out for me. I'm sorry you couldn't know about your mother's heritage, but you're not alone anymore. I'm here for you… little brother."

"Save your energy for when my son gets back into control, Chunin. Right now I need to deal with whoever did this to you," the young boy possessed by Minato said, as he crawled out and looked up at the medic nin, "You! You're going to pay for doing that to my sensei. Shadow Clone Jutsu!" He crossed Naruto's fingers hoping his chakra was enough to make four solid clones. However he ended up making hundreds of copies of his son (all of which have Naruto's personality, being his body and all).

"Wha-what is this!" Kabuto shouted, being petrified.

"What's wrong? Aren't you going to fight back?" one of the clones asked.

"If not, then we're going to beat you easily!" another shouted. As all of the clones attacked, Kabuto managed to snap out of it and started using his chakra scalpels. However, the sheer number of clones ended up overwhelming him. When all the clones dispersed, the medic was barely standing.

"I'm impressed. To pull off such a feat. Why don't you come with me and join Orochimaru?"

"I don't think so," Minato stated as he started forming his signature move, "Take this, trator! Rasengan!" Minato thrust the chakra ball into the nin's stomach, making him crash into a tree and get knocked out.

"Good work Naruto. I saw the whole thing. Impressive work with the shadow clones," Mizuki told him, coming out from the shadows and picking up Iruka.

"If you saw the whole thing, why didn't you help?" Minato asked.

"Didn't you start off with the clones?"

"... He was here before that. And also you have the wrong blond.. Sort of. I'm Minato Namikaze, the Yondaime Hokage. I don't know how I got into Naruto's body, but I need to talk to the current Hokage. Kakashi, could you stop staring at me slack jawed and collect the traitor? I'm heading to the office." With that he left with a flash of yellow. When he entered the Hokage's office, he noticed the multiple Flying Thunder God formulas that covered the place.

"Naruto? How did you use the forth's jutsu?" Hiruzen questioned.

"Hiruzen, I'm not my son, and I don't know how, but my Flying Thunder God formula is everywhere."

"Minato? You're back? Wait… what do you mean? I don't see anything."

"Hmm, do you happen to have a mirror?" The wrinkly old Hokage (Ow! What!? You know it's true Saurtobi!) pulled out a mirror from his desk, you'd be surprised by how many times this used to happen with the Uchiha. Minato looked into it to see something similar to the Sharingan, except it had the symbols for the Flying Thunder God in place of the tomoes, and the red was replaced by blue. "It seems my jutsu has turned into a dojutsu. Though I'd like to keep this out of the council's knowledge. Knowing them, they'd most likely try to enact the CRA."

"Agreed. Though this is a strange occurrence. How did it awaken? How did it become a dojutsu?"

"Well if I remember correctly, it must've been created after Obito died. I was using my Flying Thunder God jutsu to burn off my anger, when all the sudden I started crying and feeling guilty. The trauma must've been so bad that it turned my most recently used jutsu into a keki genki, or in the Flying Thunder God's case, a dojutsu. The look must be simulating the sharingan because the center of my grief was Obito. Which explains my son's activation to the trauma of the fact he never knew he had a clan, and how his mother was the jinchuuriki before him."

The Hokage took out his pipe and lit it up. This day was a roller coaster of crazy events that should never have happened. "Speaking of your son, I need him to take control for now. I need to give him his mission pay for the one he was just on. And even though it was you who defeated Kabuto, I have to give him a field promotion seeing as his target was at least mid to high Chunin level. Maybe even Jonin."

"All right, I'll switch over now." He closed his kid's eyes and went back into his son's mindscape. When Naruto's eyes opened again, the dojutsu was deactivated. "Old man? What am I doing in your office, is that guy still out there, Where's Iruka-sensei?"

The Hokage sighed as he put down his pipe. "Naruto, tonight your father did an incredible job. He was able to take down Kabuto with two jutsu, one of which you will need to learn, and has discovered that you've unlocked a new dojutsu, which I think should be called Jikugan, or "space time eyes"."

"Wow! Realy!? How do I activate it!? What does it do!? Can I see through Objects!? Or do I control space time with my mind!? Tell me! Tell me! Tell me!"

"Calm down Naruto. I guess even if this jutsu affected your process of thinking, you're still going to be a hyperactive ninja."

"Wait, did you just say I was a ninja?"

"Yes Naruto-kun, you have gained a field promotion to Genin. Now that that's out of the way. To activate your dojutsu you need to send cakra to your eyes. Apparently they activated when you found out about your mother and her clan. Her name was Kushina Uzumaki, and your father was the Yondaime Hokage, Konoha's Yellow Flash, Minato Namikaze."

"..."

"..."

"... And?"

"I just told you your father was The Forth and you just expect more right off the bat?"

"If people looked, they would've seen that I'm basically a carbon copy of my father. But what I want to know is who is going to teach my father's other jutsu. The one that isn't a dojutsu."

"I could help with that," Kakashi told them as he walked in, "I was a student of his." The Hokage nodded and brought out two water balloons, two rubber balls, and two regular balloons. "These will be your training. First you have to pop the water balloon by rotating the chakra." Kakashi explained as he showed the knucklehead.

Naruto tried it and got it right in two attempts. "..."

"..."

"..."

"..."

"... What's next?"

"How did you do that so fast!? It took me weeks to get that down."

"When I couldn't do it at first I thought I had to bounce my chakra around all over the place."

"... I don't know how to feel about this. Next is the rubber ball. You'll need to push more power in, but still maintain the single strand. Now don't get disco-" The cyclopes was interrupted by a chakra wind explosion.

"Let me guess, the last one is about form?"

"... Yes… Just make sure you don't pop the balloon this time." Naruto tried and held it for five minutes. "... I'm calling it a knight. Catch you later Naruto."

"'Night Cyclopes. I should probably get back to my apartment. Later Old man." When Naruto went to his apartment, he went to his bed and immediately fell asleep.

In Naruto's mindscape, he woke up to find the Forth above him and a carrier at the man's feet with a fox in it. "So, did you come for a visit? Or are you just sleeping?"

"A little of both. Mind explaining the Jikugan? Am I able to time travel? Can I freeze time? Or can I only teleport?"

"Uh… I don't really know. Though I believe you might be able to freeze objects and people in time. Maybe you can even slow them down to deliver a faster punch in a sense."

"Oh great they're getting started on jutsu theories. This is going to be a long night."

I saw a story that had this main idea, and I decided I would try it out. Just so you know, I'm going to add a secondary completed version, where Naruto does control time on objects and people, but won't unlock it until sometime later.