Disclaimer: I like to think of Naruto the same way I think of my uncle's new Mustang. I don't own it but it's still cool to take for a drive.
"Human talking"
'Human thinking'
"Demon or Summon talking"
'Demon or Summon thinking'
Jutsu will be underlined
Naruto hated Danzo for more than he had just made him do. Two years ago he had taken the shady man's offer only at the fox's insistence. He hated the caged bird seal variant that Danzo had applied to the small of his back, interwoven with the nerve endings of his spine. He hated (albeit to a lesser extent) the seal on the bottom of his tongue that kept him from speaking of Danzo or Root. He hated how, when pitching his proposal Danzo had decided not to mention the seals and upon Naruto's acceptance of becoming Danzo's apprentice (he never agreed to become a root agent) he was placed under a sleep inducing Genjutsu and awoke a slave 24 hours later.
But despite himself he had allowed his hatred of Danzo to fade into a strong disliking/grudging respect for the man. After all Danzo had never once used the seal on Naruto's back to discipline him. Instead he would just train Naruto into the ground pushing him past his limits and causing him incredible amounts of pain. But it was a type of pain that Naruto was glad for. A type of pain that allowed him to gain power at a ridiculous rate.
However as he looked down at the slain body of his first sensei, the first person who he had ever formed any kind of bonds with he made himself a rage influenced promise. Danzo Shimura would die by his hand.
"Well done Naruto, remove his mask." Danzo ordered from the now opened doors of the chamber. Naruto knelt down and took his teachers mask surprised by how young he was maybe 16 or 17 years old. "Now rise, new Crane of Root." Naruto looked at Danzo with surprise and outrage clear on his face, unable to conceal his emotions after everything that had just happened. "Do not forget your place." Danzo warned raising his hand in the half ram seal. Schooling his features Naruto simply replied "Hai, Danzo-sama" and slid his dead sensei's mask over his face. "Crane, follow me."
Atop the Hokage monument 10:04 Hrs
Naruto landed on top of the head of the Nidaime seconds after Danzo not at all surprised the supposedly crippled man could move so quickly. What was surprising was the slight but unidentifiable emotion present on the mans face as he looked down on the village below. " Crane when you look down on this village what do you see?" Danzo asked. "I see civilians and shinobi going about their day." Naruto answered not understanding where Danzo was going with this.
"I see those that walk in the light with happiness and hope and the will of fire in their hearts. I see what I must protect by any and all means even if it means giving up my soul. I had you kill your predecessor to see if you could do what was necessary for the betterment of the village i…" "I killed Crane-sensei because he would never have disobeyed you! I killed him to survive!" Naruto interrupted. "Yes, your survival is important not only to you but to this village." Danzo informed.
Naruto, lost once again simply replied "What?" "I was not lying to you when I said I wanted you to be my apprentice. When I am gone you will lead Root and as its leader you will have to commit atrocities far greater than killing a sensei. Root exists for this purpose, to spread our roots in the darkness so that the great tree that is Konoha can grow strong in the light." "But why choose me? Most of the people of this village hate me and I hate them right back." Naruto asked.
"Look at that little girl eating ice cream in front of Haruno's convenience store. Do you hate her? Of course not. People are stupid, panicky, easily influenced animals. They abused you because they believe you are the Kyuubi or are being influenced by it but it is not you, Naruto Uzumaki that they hate. Just as it is not the people of this village that you truly hate, but the pain that you have suffered at there misguided hands and your own weakness that prevented you from stopping them. I know that you have grown close to Hayate Gekko and Yugao Uzuki no matter how much you deny it. They will not be only people of this village that you will hold dear. Despite this hatred will always be what drives you and it is hatred that will always keep you from walking in the light. It is for these reasons that I choose you to be my apprentice. From this moment on the training wheels are off and you will bare witness to the horrors that this shinobi world has to offer. Welcome Crane, welcome to Root."
Industrial district 21:12 Hrs
Naruto sat on top of the abandoned chakra conductive metal factory the tallest building in the industrial district thinking about all the things that Danzo had said to him. Some of which he had taken to heart but mostly, he chalked up Danzo's little speech as an attempt to manipulate him and placate his fury. 'I'll take over Root when he's gone and it will be sooner than he thinks.' Naruto thought to himself. It was a few minutes later that he sensed someone approaching.
"Naru-kun no time no see." "Uzuki-san how many times have I asked you to stop calling me that?" Naruto asked sighing, to tired to put up his usual protests of the overly affectionate nickname. Mistaking his fatigue for brooding Yugao decided to ignore his question and cheer up her little brother figure. "I have some great news for you. Hokage-sama pulled some strings and found a teacher willing to give you a chance. Next year you'll be going back to the academy instead of that dreadful alternative school. Isn't that great!" Yugao exclaimed far to excited for Naruto's liking. 'The alternative school is run by root if I get transferred back to the academy my training will be set back. I'll have to see if Danzo can get me out of this.' "Sure Yugao-san, I can't wait to catch up with my old classmates." Naruto lied with a very convincing smile on his face.
It turned out that Danzo and his allies on the council where unable to stop Sarutobi from placing Naruto back in the academy. For this reason Danzo decided to bar Naruto from going on any more missions despite promoting him to full Root Anbu Status. He spent the next 9 months training Naruto even harder than before determined to capitalize on the time he had left with him. He put together I team of instructors with various skill sets and assigned them each an army of Naruto clones to train.
He was even able to get Naruto to cast D-rank Genjutus to standard and use his tenketsu seals to sense when someone was trying to cast one on him. Danzo also discovered that Naruto possessed a high aptitude for Fuinjutsu but that was one talent he couldn't afford to nurture at least, not until he was sure the boy had come around to his way of thinking. After all, he was forging the greatest weapon the world has ever seen. A monster of a shinobi, allowing said monster to figure out a way off its leash could prove disastrous.
Night before Naruto's return to the academy:
Naruto was running through the residential district, a place that he usually avoided but needed to cut through tonight if he was going to make curfew. When on active status in root he could stay away from his apartment for weeks at a time thanks to the highly talented Chameleon who created some sort of special henge that was nearly imposible for even Jonin to detect. But because of the Hokages renewed interest in him Danzo had changed Naruto's status to sleeper agent.
Naruto was forced to stop running when a training kunai was implanted into the ground a few feet in front of him. Looking to his right he saw none other than Sasuke Uchiha preparing to launch another. "What the hell is wrong with you Uchiha?" Naruto asked. "Fight me." Was Sasuke response. "Look I don't have time for this if you want to fight we can do it tomorrow after class." Naruto offered. "So the rumors are true, you're returning to the academy?" Sasuke asked. "Yeah, later." Naruto took off even faster than before. 'Faster than a academy student should be able.' Sasuke thought to himself.
Next morning 7:55 Hrs Academy Courtyard
Ino was waiting for Sasuke-kun to show up hoping that he would maybe walk her to class today. Deep down in her heart of hearts she knew that he would just blow her off but a girl had to hope right? After all nothing worth having comes easy right? As she was scanning the courtyard for her crush she noticed something that drew her attention, a fellow blonde. None of the rest of her clan's youth were currently attending the academy being either to young or having already graduated.
Upon closer inspection she saw a boy of slightly above average height but definitely above average build walking towards the building. He was wearing an unzipped black track suit jacket with a burnt orange muscle shirt underneath and a pair of slightly baggy shinobi shorts with kunai and shuriken holsters on each leg. Upon looking at his face she couldn't help but think the boy handsome.
Maybe not in the obvious, in your face way Sasuke was but with his near shoulder length spiky blond hair that seemed to glow in the morning sun and framed his angular baby fat free face he was definitely a looker. It was when she noticed the whisker like marks on his face that she realized who this kid actually was. "Naruto?" Ino asked. Despite being seemingly out of ear shot Naruto looked at her and nodded and then walked past her not stopping for conversation. Forgetting about Sasuke for the moment she walked behind him all the way to their nearly empty classroom and sat in the row behind him completely entranced.
She was so entranced that she only noticed Sasuke when he walked up to Naruto with a group of fan girls behind him something that should have bothered her but for some reason didn't. "Don't forget our fight later today." Sasuke reminded him. "Kami, class hasn't even started yet, why do you want to fight me anyway?"Naruto asked. "You remind me of someone that I hate." Sasuke informed. For some reason Ino didn't like the idea of Naruto and Sasuke-kun fighting so when their Two new instructors walked into the classroom and had everyone take a seat she couldn't help but be relived.
"Hello everyone my name is Iruka Umino and this is Mizuki well be your instructors for the remainder of your time in the academy. These final two years will be more intense than your last three and a third of the people in this classroom won't even make it pass this year. That's why its important that you take your training seriously and ask for help when you need it." Iruka lectured.
"This year while the class is so large you'll be split into two groups, I will be the primary instructor for A group which will consist of those whose last names beginning with A-M. Everyone else will be in B group. You will all receive instruction from both of us but when you need extra help and are turning in your test papers come to your group's instructor that way we can keep up with all of you… Oh that reminds me tomorrow when you come to class A group will sit on the right side in alphabetical order." Mizuki said. "Um… everyone in B group will sit on the left side of the classroom but I'm pretty good with names so your order doesn't matter." Said Iruka.
Many of the students such as Choji Akimichi were upset about not getting to sit with their friends. Others like Sakura and the rest of Sasuke's fan club that weren't in his group were absolutely outraged. This outrage led to the class becoming acquainted with Iruka's Big Head Jutsu.
The rest of the day passed unremarkably with the students taking a few assessment tests so that Iruka and Mizuki could see where they should start off. When class was over Naruto left to see everyone gathered in the courtyard deciding to get this out of the way he walked into the group and squared up with Sasuke. "Glad you decided to show I would have hated to have to hunt you down."Said Sasuke. "Let's skip the banter and get to the fighting." Naruto replied.
Not wasting any time Sasuke started going through a set of hand seals Naruto recognized completed faster than the Uchiha. "Great Fireball Jutsu" Naruto exclaimedsending a ball of fire at the Uchiha. Sasuke was undeterred and to Naruto's surprise launched the Jutsu's fire chakra enhanced version that seemingly absorbed his jutsu and continued right for couldn't help but feel a small amount of fear at the trouble he'd get in for setting the blond on fire but when the flames receded he found himself looking at a burning log instead of a burning body. "Substitution" Sasuke smirked excited at the prospect of finding a worthy opponent.
Sensing an incoming attack from behind he spun around to defend himself. Had he acted a split second sooner he might have avoided being hit with the strongest punch he had ever taken in his life. It was so powerful it lifted him the ground but recovering quickly he managed to roll away form Naruto and get to his feet. Feeling something dripping from his mouth he wiped it with the back of his hand to discover he was bleeding. His opponent had drawn first blood.
Deciding that engaging Naruto in straight Taijutsu (given his powerful punches) would be a bad idea Sasuke generated three regular Bunshin and channeled a small amount of chakra to his legs hoping to confuse and overwhelm Naruto with his speed. It was not to be however, as Naruto simply ignored the intangible clones and blocked 80% of Sasuke's attacks.
Those watching the fight couldn't believe what they were seeing. The former dead last was now winning a fight against Sasuke Uchiha how could he have gotten so strong in alternative school? Sasuke was asking himself the same thing after all this was the most intense fight he has ever been in. He might actually get hurt. It was this realization and the small fear that came with it, combined with the speed in which Naruto, who was now on the offensive was attacking that did it. Sasuke's Sharingan awakened.
It was like someone had slipped a pair of glasses over his eyes and then slowed time down to a crawl. He now able to deflect more of Naruto's punches and having his reaction time greatly improved grabbed one of his opponent's wrists and twisting his body flipped Naruto over his shoulder and onto the ground. As he prepared to unleash a heel drop on Naruto's face he managed to stop himself when two words he didn't expect hear came from his target. "I give." Naruto loudly but calmly said.
For his part Naruto had been holding back the entire fight after all a jump in skill could be explained by two years of being tutored by Hayate and Yugao but actually beating the Uchiha would cause to many waves. What happened next began a friendship that would end in tragedy Sasuke extended his hand and helped Naruto to his feet. "Good fight dobe." Sasuke complemented with a smirk.
"You too teme, although you could have mentioned being able to use the Sharingan." Naruto replied mirroring the smirk. "That's because I couldn't before now." Realizing how valuable having someone like Naruto as friend and rival he swallowed his pride and asked Naruto a question. "Would you like to come by my place later and train? The compound I live in has its own training ground and equipment." "I don't have anything better to do." Naruto answered deciding the Uchiha could prove to be a valuable ally in the future.
In the time that followed Naruto and Sasuke could be found walking through the village or just hanging out at Ichiraku's ramen shop. Naruto's friendship with Sasuke combined with him taking the number 2 spot in the class standings led to many things that Naruto didn't expect. First he developed his own small group of fan girls despite their parents telling them that he was dangerous and to stay away from him. After all who doesn't like a bad boy? Second the some of other males in the class started to challenge both Naruto and Sasuke thinking that if they put up a good fight that they'd be allowed to hang out with the 2 coolest kids in school. Needless to say they were all fairly unimpressive.
But the most surprising thing to Naruto was how some of the villagers seemed to be more tolerant of his presence. They weren't exactly nice to him but he was able to by goods and equipment at regular prices in some places. Naruto was even starting to feel a small amount of optimism about things improving for him. But upon entering the industrial district one night after a training session with Sasuke his reality check came in the form of a masked female assassin managing to get the jump on him and plunging a kunai into his chest.
A/N: Alright I know I did a lot of things that people may not agree with (Sasuke awaking his Sharingan early and forming a friendship with Naruto. Making Ino into a possible love interest.) But just remember that this story is labeled as a tragedy for a reason.
Ps. I feel like I'm still rushing so now that the story is getting closer to the events of cannon I'm going to take more time between updates and try to put together longer more thought out chapters. If you want to speed things up just share your ideas with me in a review or PM. Next update should be 5-15-12