Disclaimer: I do not own Naruto, or anything associated with the manga, or anime. I only own this story.

Hey all, thanks for reading. I can't believe how well this story has done after 6 chapters. Thanks for the support on the last chapter, you guys rock. Another quick update. 40 reviews, 74 favorites, 114 followers, and 4,963 views. I was also placed into my first community, "Cool Bloodlimit Crossover Naruto" Thanks for all of the support, it really means a lot to me. Never thought this story would take off the way it has.

Fallencrt: Thanks for the idea, I agree it would be a great team. I'll put this into the vote. This story will be a Naruto-Sasuke-? Team.

Guest: Thanks for the vote and the review, I will put them I the poll.

Joe: Thanks for the support.

LegionZX: Thanks for the vote I'll add it in the poll.

InnocentxPsycho: Thanks for the vote, I'll add it I the poll.

Michu-92: Thanks for the review. I love how Itachi was an Anbu so young, just shows how awesome he is. Thanks for the vote, I will add it in. I think Shikamaru is awesome as well.

The poll is doing well, So far there have been 40 voters. Here are the standings so far.

Yakumo 15

Shikamaru 15

Hinata 13

Sai 6

Shino 6

Ino 5

Sakura 5

OC 5

Kiba 1

Choji 1

Other 0

If you don't like who is in the lead then please vote. All voters get 2 choices when they vote. The poll will close June 15th. Thank you for participating. Today is your last chance. Poll closes at midnight. I will unveil the winner when I split them into teams after graduation.

Short time skip here, 2 years. Naruto and the gang are starting at the academy. How will they deal with the slow start? Yamato gets an unexpected mission form Hiruzen. How will that affect his future? I hope you enjoy the chapter. Please review.

A Hero's DNA

Chapter 6: Academy Days: A problem Rooted.

Naruto stood in front of the building where he would spend the next four years. In front of him was the Konoha ninja academy. He had been preparing for this day over the past two years and finally he was old enough to join his friends as they began their journey to become shinobi of the hidden leaf.

Naruto had grown over two years and in that time he had adjusted to his new life quite well. Sasuke remained his best and closest friend. He could relate to the fame that Naruto had learned to deal with. Naruto also grew closer with Shikamaru, and both would just sit and watch the clouds at times. Sasuke couldn't sit still for too long to keep up with them. Shikamaru also seemed to be incredibly intelligent and good with strategy. His favorite game was Shogi, and Naruto would play with him. Shikamaru almost always won, save for a rare few instances where Naruto made a strange or unpredictable move that threw Shikamaru off. Naruto wasn't as close with his other friends though, but still hung out with them all occasionally.

About a year ago, Tsunade began to teach Naruto in the art of the shinobi. She began with basic chakra control lessons and had him study the various histories of different shinobi cultures and he soaked up the information like a sponge. She even told him that if his control was good enough she would try to teach him some medical jutsu, if he managed to test into her extra class, which would be starting during his first year at the academy. Naruto found that he had trouble with chakra control and deduced that it was due to his large reserves as well as Kurama. He knew that he would have to work almost triple what anyone else had to on his control to be at a similar level. But that also meant he would have even more chakra at his disposal.

Naruto had also been spending much of his free time learning calligraphy and Fuinjutsu. He found that his hands seemed to be able to almost effortlessly glide across the page when he would practice, but as he learned that the Uzumaki clan were Fuinjutsu specialists, it made sense that he would be a natural. One of the first things that he did was create a set of training weights, with Jiraiya's help, as his uncle had been helping him with Fuinjutsu. At the moment each weight was about fifty pounds. Naruto felt that he should update them soon, as he could barely notice them anymore.

In the present, Naruto walked forward through the main entrance to the academy with Tsunade right behind. All of the new students had their parents with them. Naruto received his class assignment form a nearby Chunin and walked back to his mom.

"Ok, are you all ready?" Tsunade asked him.

"Yeah mom. Don't worry about me. It's just the academy."

"Well do your best, and behave. I don't want to hear that you're slacking off."

"I'm not Shikamaru, I'll make you proud mom." Naruto said with a smile.

"Ok I will see you later. I just wish Yamato was here to see you on your first day."

"He is off doing real shinobi work. That is where he should be." Naruto told her.

"Well your right, of course. Have a great day."

"You too mom."

Naruto turned around and walked towards the classroom he was assigned too. As he entered the room he saw only three other people in the room so far. One was Sasuke, who waved him over, the other two were an indigo haired girl with lavender white eyes, and Shikamaru who sat in a seat next to the empty seat Sasuke reserved for Naruto.

"Hey Sasuke, het Shikamaru, so I guess that we are in the same class together huh."

"Looks that way Naruto." Shikamaru answered.

"I just hope that this academy isn't as much of a joke as some of my clansmen say it is." Sasuke said fearing for the worst.

"Just think of it was a chance to show off that Uchiha pride." Naruto joked.

"Loser."

"Jerk"

Both of them started laughing. Naruto knew that Sasuke had already started his ninja raining as well. They had ever trained together several times. Sasuke was strong and fast for their age group, but Naruto was no slouch either. Naruto turned around to see the girl in the back again. She was fairly quiet so he figure he would say something to her.

"Hey, you're a Hyuga right?"

The girl looked startled but she met his eye and then turned away.

"Y…yes."

"What's your name?"

"H….Hinata…and y…you are?"

"I'm Naruto. You know that you stutter allot right?"

She looked down as if she was ashamed.

"Hey don't worry about it. You just need to have more confidence in yourself. Why don't you come and train with us sometime." Naruto offered.

"That….that sound good." She answered.

"Ok and we will work on that stutter."

She blushed and then looked away again. The rest of the class filed in shortly. Kiba, Choji, and Shino also happened to be in their class. There was also a girl with green eyes and pink hair, and a blonde girl who sat next to her. In the very back corner sat a boy with black hair and incredibly pale skin. Then two teachers walked in and stood in front of the class. The first had brown hair that was in a ponytail shaped like a pineapple. He had black eyes and a scar that went across his nose. The second teacher had light blue hair that went to his shoulders. And both of them wore the standard Chunin attire, completed with their flak vests.

"Hello class my name is Iruka Umino, and this is my partner Mizuki. We will be your instructors for the next four years. I look forward to working with all of you and I know that you will be great Hidden Leaf Shinobi. Now let's get started with a history lesson."

Yamato walked into the Third Hokage's office after the old man sent for him. He was dressed in his Anbu attire and had on his mask. Newly placed on his back was a short tanto sword that he had recently begun learning how to use. The past few years had really made him strong, and his control over the Wood Release increased exponentially, so much so that it was close to being comparable to the first Hokage. His mission success rate was almost as good as Kakashi's.

"You called for me Lord Hokage?"

"Yes you may take off your mask Yamato."

Yamato did as he was told and sat down across form Hiruzen.

"I have to ask you to do something for me that you will not like."

"What is it Lord Hokage?"

"I assume that you have heard of my ex-advisor Danzo and his root Anbu."

"Yes sir."

"Two years ago I ordered his force to de disbanded, and I have reason to suspect that Danzo is up to his old tricks again. What I need you to do is, infiltrate hi ranks and keep close tabs on him for me."

Yamato's face broke out in surprise. A solo infiltration mission into the ranks of the personal Anbu sect led by, a Konoha elder, or ex elder. He immediately understood that this would be the most dangerous mission he had ever gone on.

"Why me lord Hokage?"

"Danzo is a collector. He wants what he perceives as the greatest weapons Konoha has as his own. And after all of your work these past two years, you have proven yourself unique."

Yamato didn't know what to say. He couldn't exactly turn the mission down when he was handpicked for it, but he also didn't know if he was skilled enough to do it.

"Yamato, if I didn't know that you could handle this, I wouldn't have chosen you. Danzo is a man that needs to be watched. He will stop at nothing to get what he believes is due to him. He even tried to turn the councils against your brother in hopes of turning him into a weapon. He is a dangerous man to just leave alone."

Yamato's face changed when he heard about Danzo wanting his brother. He knew that he couldn't let that happen no matter what.

"I'll do it sir."

"Excellent Yamato."

"So, Lord Hokage, what do I do?"

"Just keep up your everyday life, and missions the same as always. Trust me when I say Danzo will get in touch with you. And when he does join him. After that we shall play it by ear. That is all Yamato you are dismissed.

Naruto sat in class taking notes on everything Iruka sensei said. He found the whole lecture rather boring, ad wasn't sure exactly how this would help him as a ninja, but he wanted to learn everything he could just in case he needed it. It had been three months since the academy started and Naruto was starting to feel a little antsy. All they had done so far was history lesson, shinobi customs and rules, and chakra theory. He wanted to put it into practice. Iruka noticed that Naruto, who was one of his best students, was starting to fidget around more and more each day.

"Ok guys that's enough for today. Go home and study because I will be testing you all on this material tomorrow." Iruka said to the class.

He watched as one by one all of the students began to leave in a hurry. Naruto was never in a hurry though and he would always wait to leave until just about everyone else was gone. It intrigued Iruka to no end.

"Naruto can I talk to you for a moment?"

"Is there something wrong Iruka sensei. Did I do something wrong?" He asked as he approached Iruka's desk.

"No Naruto, of course not. I just wanted to speak with you for a moment."

Iruka pulled a chair over to the desk for Naruto, and the blonde sat down.

"Is there something bothering you Naruto? In class I mean. I've noticed you're getting a little stir crazy."

"It's nothing important Iruka sensei." Naruto said, not wanting to overstep any boundaries.

"No, Naruto, I would like to know."

"Well…" Naruto was hesitant to say anything in fear of disrespecting his teacher.

"Don't worry Naruto, you won't get in any trouble."

"It's just, all of the history lessons are interesting and all, but I don't see how they will help me be a ninja. It's been three months and we haven't done any Taijutsu training besides everyday normal workouts, nor have we gone past chakra theory to actually chakra control exercises." He said without looking into Iruka's eyes.

"I'll answer all of your concerns ok Naruto."

Naruto just shook his head yes to Iruka.

"There is a saying that history will repeat itself if we don't learn from it. All of the lessons are to teach you about the problems of our past, so that maybe we won't make those same mistakes. And trust me, shinobi have made more than enough mistakes. As for the slow pace at physical and chakra ability, Most of our students do not come from shinobi families, so while you and the other clan born children have been conditioned for ninja training the others have not. Because of this we need to build them up so that they can handle the harder training we will eventually do. Does that all make sense."

"Yes sensei."

Naruto looked down to the ground and he thought of how Iruka just explained everything and he realized that his wants were not fair to the other students. H felt bad for being slightly selfish, and made a vow to himself that he wouldn't leave anyone behind ever again.

"I'm sorry Iruka sensei."

"There is no need to apologize Naruto. That's what teachers are here for, to help students understand things. And if you can take what I just said to you to heart and learn from it then I have more than accomplished my duties as your teacher."

Naruto smiled up at Iruka and decided that from now on he would take what his sensei taught him to heart more, because Iruka really was there to teach him, not only how to be a good shinobi, but how to be a good person.

"Naruto have you thought about applying to Tsunade's medical training class."

"Yes, mom is going to be great teacher."

"I almost forgot that she was your mother." Iruka said while chuckling a bit. "Well you can get going Naruto, and remember to study for the test tomorrow, I expect to see your same great marks."

"I'll see you tomorrow Iruka sensei."

Naruto ran out of the room and headed home to go over all of his notes.

Yamato was on his way back to the village after completing a mission. He could see the village gates about a mile up ahead. His thoughts drifted to the mission that the Third had given him. It had been three months and he had not been contacted yet. He wondered if Hiruzen was correct about this Danzo guy. When he reached the village and checked in with the gate guards, he began to head to turn in his completed mission. He felt like someone was following him, but when he looked around there was no one.

After turning in his mission Yamato decided that it was time for a little R&R so he went looking for a nice secluded spot in the woods. When he found it he got into his meditative position and began to feel the nature around him. Everything was still, and he knew that it meant he wasn't alone. The sound of shuriken chopping through the air alerted him to a hostile three and a tree burst from the ground to stop the thrown stars.

Two masked figures jumped from the trees and began to engage him with their kunai knives. Yamato drew his tanto and blocked the oncoming strikes. The attacking shinobi slashed and weaved through Yamato's defenses and impaled him with their kunai. As it bled the body turned into wood.

"That would be my Wood Clone Jutsu, I can keep this up thirty times over." One of the ninja said.

"Wood Style: Binding Roots Jutsu!"

The roots from the surrounding tress began to break through the ground and wrap themselves around the shinobi bodies. They attempted to use the Replacement jutsu but found it wouldn't work nor would the Body Flicker, or any jutsu.

"You can keep trying all you want. Those roots are absorbing your chakra and feeding the trees. Now unless you want permanent chakra exhaustion, or worse death, you tell me what you're doing here, and why you attacked me."

"Well, that was an interesting fight. I must say I am impressed that you can use the Wood Release jutsu so effectively when you aren't of Senju descent. Orochimaru really knows what he's doing doesn't he?" An elderly man with a bandage covered eye and a scar on his cheek said as he approached Yamato.

"Who are you?"

"My name is Danzo, and I have come to offer you a lace at my side as the weapon which will destroy all who oppose us."

"And why would I do that?"

"Because I know you. You seek peace above all else, but you know that true peace, in this world of ours, is impossible. If you want peace you must enforce your will on all of those around you. If Konoha was to take over the other villages, as is its destiny, then we would have peace. I offer you the chance to help make it a reality."

"And if I say no?"

"Then I shall leave you alone, for now."

"I'm in. Show me this peace you wish to create." Yamato said to Danzo.

"Very good. Now if you would please release my ninja."

Yamato made a hand sign and the roots recede into the ground.

"That technique will be far more accurate for you soon enough." Danzo thought to himself.

Naruto walked home with Sasuke, and Shikamaru. They had just finished their test over shinobi principles and the First Great War. Sasuke had a 94%, Naruto had a 95%, and because of Naruto making sure he didn't just sleep through it, Shikamaru had a 100% on the test.

"Well it looks like the great Uchiha clan got beat out huh Shikamaru." Naruto said trying to goad Sasuke.

"Naruto just shut up ok, a 94 isn't a bad score." Sasuke defended. "It is still an A."

"Sasuke you're right a 94 isn't a bad score." Naruto began.

"But a 95, and a 100 is better." Shikamaru finished.

Naruto and Shikamaru laughed at Sasuke's misfortune. You could see his ivory face go red from embarrassment, and faux anger.

"You two just wait until we get into some real ninja stuff, then I will make you eat your words."

"Maybe Sasuke, but for now your still third best." Shikamaru responded.

"By one point!"

The three friends joked and laughed on the rest of their walk to their respective houses. Unbeknownst to them a black haired boy was following and watching for a distance.

"Welcome to your new home Yamato."

Yamato looked around at the underground base of Root. He memorized every detail that he could so that he could relay the information the Third Hokage.

"Is something the matter Yamato? Are things not to your liking? Or to Hiruzen's?"

Yamato paled, there was no way this man knew was there.

"What are you talking about?"

"You know full well what I am talking about. I am no fool, unlike the Hokage. I know that you were ordered to infiltrate my organization and relay information back to Hiruzen. It would have been a good plan, except that I have already done it."

Yamato knew that he needed to get out as soon as he could. But then he heard a strange sound behind him. He saw ink animals crawling across the floor as a black haired pale boy walked towards Danzo.

"Hello Sai, are you keeping tabs on the boy?"

"Yes Lord Danzo. Naruto Namikaze is under watch. We await to see what power he may bring to root."

"You leave my brother out of this!" Yamato felt his strength fail him as he was grabbed from behind. It was as if his chakra was stolen

"Silence you fool. That boy and yourself are nothing in this world but tools. Tools to be used as the tool masters see fit. He will join root I will be sure of that. And as for you. Sealing Art: Mind Snare Seal!"

Danzo placed his hand upon Yamato's head and a mark appeared. Yamato fell forward and when he raised his head all emotion was gone from his eyes.

"You will be the foundation of the new Leaf. Fitting with whose powers you were granted." Danzo turned away from his new puppet.

"Now for our first target."

Thank you all for reading. Please continue voting on the poll. Today is your last chance. Poll closes at midnight. I was happy with the results so far but I want to know everyone's opinions on the matter. Please review, I love hearing from you guys, and it makes me want to update faster. Until next time.

Next Chapter: Family Ties: Root rising.

Naruto Senju-Namikaze: 8 Academy Student

Sasuke Uchiha: 8 Academy Student

Shikamaru Nara: 8 Academy Student

Hinata Hyuga: 8 Academy Student

Sai: 8 Academy Student (root Anbu)

Tsunade Senju: 47 Sannin

Yamato Senju (Mori): 15 Anbu (Jonin)

Kakashi Hatake (Inu): 22 Anbu Captain (Jonin)

Iruka Umino: 18 Academy Instructor (Chunin)

Mizuki: 18 Academy Instructor (Chunin)

Danzo: 64 Root Commander (Ex-Advisor)