Chapter 1: Genin

A/N: Hello all, first crack at a Naruto fic I'm hoping I can manage to write the level I expect of myself. This story is basically an AU where there are some rather big changes that completely change the story in comparison to canon. We'll start from the very beginning of Naruto (Well, more like episode 3 or 4 but whatever) here but we won't spend too much time on this time period where the characters are in the early stages of being Genin… I promise.

But I'd rather not sit here and discuss spoiler topics in the FIRST author's note lol… Hope you enjoy

UPDATE: 1/4/16 This chapter has been renovated, it's possible in the early chapters there will be A/N statements that don't match up because I've fixed a thing or two in addition to adding to the length. Please keep in mind that early chapters are not an accurate reflection of the quality of writing as you get further in. So I ask everyone to be patient in the beginning. Thanks

*DISCLAIMER* I do not own Naruto, or characters from Naruto… obviously. I own nothing but the storyline in what you read throughout Re-Alignment and that I cannot profit… this is and will be the only disclaimer, cause I always forget to post the fucking thing.

Shikamaru sighed as he passed through the doorway of his class in the academy, hands in pockets, looking less than excited even though this was the big day. Iruka-sensei was going to reveal the squads each ninja graduate was assigned to by the Hokage himself. He passed by Sakura and Ino practically ready to beat each other to a pulp arguing over who was going to be on Sasuke's team… as if they really had any idea how they were divided up. Women… Willing to fight over what they don't know anything about. Unlike his female classmates, Shikamaru had absolutely no interest in being paired with Sasuke… hell he'd rather be paired with Naruto than the last member of the Uchiha.

Yes Naruto was exuberant… zealous, mouthy and overbearing most of the time despite not even being able to make a simple clone properly. And despite his reputation, lack of popularity and history of causing trouble for civilians throughout the village… He was at least a nice person for the most part. There was a lot left to be desired in the skills department there, but Shika acknowledged the blonde Uzumaki would at least work hard and stand with his team, whereas Sasuke hardly struck him as a team player.

Sasuke sat idly with his hands folded together, not aware of the eyes gazing at him due to being preoccupied with ignoring several fangirls. Shikamaru held disdain for his attitude and tendency to put off the 'I'm better than you' vibe, which was bound to harm his squad's teamwork compatibility. If he was paying either of the two crushes arguing in front of him, there was no evidence in his expressions. Of course, he typically only spoke when he had to… or to berate losers… which were usually Naruto. Although, in Sasuke's defense, Naruto usually started their verbal engagements.

The sight of orange stopped the Nara cold on his way to a seat by his best friend, Choji. "Naruto? What are you doing here, this is for people who graduated… You can't be here right now."

"Oi, you see this?" Naruto tapped his headband with the Leaf insignia. "I passed!"

Shikamaru momentarily raised an eyebrow but shrugged it off and proceeded to his seat, putting the Uzumaki and Uchiha out of his mind to consider other potential teammates he could possibly be paired up with.

Sakura or Ino in his opinion would be extremely annoying. Especially if Sasuke was his other teammate. Then there was Shino, the Aburame prospect. Shikamaru didn't have anything against him, but found him rather cryptic and odd; he would rather have a nice average and simple balance on his team with no eccentricities or dramatic tendencies.

He scanned the room eying each classmate that graduated and decided that the only one he truly felt his that description was the one he beside him, Choji. Perhaps Kiba, though arrogant and prideful… Hinata's shyness was his only concern with him. All in all, he knew that no matter what… it was highly likely that the transition from students in the academy to four-man Genin (plus a Jonin-sensei) squad would wind up a total drag. He sighed again as Naruto got smacked by both Ino and Sakura after he attempted to interfere with their pointless argument taking an opportunity to take a shot at Sasuke… which the females predictably didn't like.

"Settle down everyone. And take a seat if you haven't already," Iruka ordered as he suddenly appeared in the center of the room in a poof of smoke.

Naruto, Ino and Sakura complied… though there was somewhat of a battle between the latter two over who got to sit with Sasuke. So annoying… if I get Sasuke AND one of them, I'm going to apply for civilian status before the training even starts.

Iruka began going through a mini-speech about the squads but Shikamaru didn't feel the need to listen until he announced the actual squads. As a Nara, Shikamaru was well exposed to concepts far beyond something as simple as the purpose and need of operating in squads. It didn't make sense that anyone in the room wouldn't know that much at the very least. Can't we get on with this already.

"Now, I will announce each of the squads, one member of your squad will be handed a piece of paper that gives the name of your Jonin, as well as the time and place to meet with them," Iruka declared.

Everyone in the room, including Shikamaru was now on the edge of their seat. Please pair with Sasuke! Sakura inwardly obsessed.

Anyone but Sasuke, anyone but Sasuke! Naruto thought in contradiction.

As long as they don't put me with Naruto I think we'll be good with whoever. I can't believe that fool graduated. Kiba suppressed a snort.

I wonder if I'll be teamed with… Naruto… Hinata meanwhile considered.

Funnily enough, every soon to be shinobi in the room had at least one person they didn't want to work with, but ultimately held no control of the matter.

"Squad One: Hinata, Choji, and Shino," Iruka named off a few more squads before reaching the one the Nara actually cared about.

"Squad Six: Shikamaru, Naruto and Kiba."

What a drag… Shikamaru thought.

Of all the people why did it have to be him!? Kiba thought as his eyes narrowed on Naruto.

But Shikamaru's sooo lazy! Naruto inwardly complained.

"Squad Seven: Sakura, Sasuke," The pinkette's eyes twinkled in victory and she actually cheered aloud to the Uchiha's immediate annoyance who just huffed. "—And Ino."

"WHAT?" Ino/Sakura blurted. Shikamaru couldn't help laugh at that one.

Unbelievable… Sasuke groaned in his head, glaring at Iruka as if it was his fault.

Iruka handed Naruto the slip with the directions to meet their new sensei, and then another to Sasuke before he finished naming off the other squads. The newly assembled team six rallied together interested in where things would go from there. "Anko Mitarashi," Kiba voiced aloud. "I'm not familiar with that name," he then added.

"Me either. But if she's a Jonin she must be highly skilled," Shikamaru mused. Naruto watched his companions in silence having nothing to say. He wasn't thrilled with the teammates that were chosen for him, but at least he didn't have to deal with Sasuke every day now.

Kiba glanced at the clock. "That's twenty minutes from now," he realized.

"Then we better get going. Come on Naruto," Shikamaru invited.

"Right," Naruto nodded, slightly surprised neither of his fellow Genin had a sarcastic complaint about being on the same squad as him.

Naruto and Shikamaru… Kiba grumbled in his head. The two class leaders in falling asleep, how lame.

Elsewhere…

"You really shouldn't be seen here out in the open like this sensei," Anko advised.

Orochimaru, standing tall in a black cloak with a formation of red clouds dispersed through its fabric and a leaf handband with a slash through it to signify being a 'Rogue ninja.' He merely chuckled at the suggestion. "This relay will only take a moment my dear," he assured. "There are no shinobi nearby at this time." Orochimaru had used a shadow clone and transformation jutsu to send a snake across the Hidden Leaf searching for clues that lead him to the whereabouts of his former pupil. It took time, but proved fruitful in the end. "It's come to my attention that Saratobi-sensei has convinced you to finally take on students of your own. Anko my dear, you're making me feel old," he joked playfully.

It was the information that he stumbled upon about Anko becoming a squad leader to a group of newly graduated Genin that gave the Snake Sannin a hunch he could find her out in this particular training ground, the very same that he had once brought her to for training years ago.

Anko smirked. "I admit I'm not really the model choice for a mentor, but Lord Hokage has been encouraging me to try and leave my mark on the next generation. If me having students makes you feel old… that's just a bonus."

Orochimaru chuckled again. He missed his former student, his assignment was proving to be well worth it, and he knew very few leaf shinobi other than him were equipped for the task, but it was frustrating to deal with being exiled from the village hidden in the leaves, mission or not.

"Those Genin will be here soon; sorry but we don't have any more time for chit chat sensei."

Orochimaru's hand went through his long dark strands of hair, moving them out of his way and he nodded his face portrayed a more serious expression. His other hand pulled a scroll from inside his Akatsuki cloak. "This scroll contains all the information I have to deliver this time," he stated, holding it out to Anko.

She reached out to grab it but Orochimaru didn't let go. "After Sarutobi-sensei and the others read the scroll, I need you to deliver a special piece of information to be kept between you and him only," he emphasized.

She raised an eyebrow after he released the scroll from his grip. "Why?"

Suddenly, the Snake Sannin ducked for cover behind a tree and Anko realized that the Genin were just a couple paces away from clearing the forest. They're early. She thought.

"Hey!" An adolescent shouted out. "Are you Anko Mitarashi?" It was unmistakably Naruto, the ninetails' Jinchuriki in his unique orange outfit. All three of the new shinobi were scrutinizing the figure they believed was their new sensei.

After a strange and awkward pause she regained her composure. "Yep!" She shouted back. "Kiba Shikamaru and Naruto I presume… a pleasure." What the hell do we do… Knowing she couldn't expect them to just stay as distant as they were and felt it was best to not act strange she decided to just invite them over and waved for them to get closer. Orochimaru is more than capable enough to remain hidden from a bunch of Genin. She reassured herself.

Her eyes moved from squad six to her mentor who was giving her hand signals that the two of them have been using for many many years.

"Uh… Anko-sensei… what are you looking at?" Naruto asked.

Anko watched Orochimaru finish and then his shadow clone transformed back into a snake. She then turned her attention back to her students barring what his hand signals said in mind. "Oh uh… nothing, don't concern yourself with it," she replied.

Akamaru barked twice. "What's that boy?" Kiba whispered to his four legged companion.

Naruto appeared skeptical, gazing at her with a squint. "Nothing huh..?" He muttered, deadpanned. "Sure seemed like more than nothing! People normally don't choose to stare at a tree when they're meeting someone new."

"Hate to side with Naruto but Akamaru told me he detected a second scent," Kiba announced.

Damn. Forgot about that Inuzuka shit. Anko thought, recalling his lineage.

Anko narrowed her eyes on the three of them. "It is none of your concern. I am aware that I chose the time and place of our meeting… but I'm afraid this will have to wait. Meet me here again same time tomorrow. Then we'll get down to business."

"Tomorrow!?" Naruto flustered. "That's pretty lame, having a sensei that just brushes off her new team right after we all just met!"

Shikamaru studied her throughout this conflict. Something was going on, something of importance that she couldn't talk about with the Genin. It was much like the times when his dad, Shikaku would either ask certain people to leave the room or he would excuse himself to talk alone with a high ranking Jonin or an ANBU.

"Not to mention she's already hiding things from us," Kiba added.

"Guys," Shikamaru interrupted. "Drop it. She's a Jonin," he reminded. "If she could include us in whatever it is that's going on, she would do so… Let's not forget we're the lowest of all the ninja in the village. Genin on our first day."

Kiba and Naruto registered his point and conceded. Anko smiled at the Nara. Having him on her squad was a blessing. "Like I said, same time tomorrow. It can't be helped," she waved and took off.

Orochimaru's signals indicated the four Hokage. Which can only mean his clone will await me at the four carvings. She smiled at that. Her sensei didn't make it too complicated of a riddle for her to interpret, she would arrive long before the clone ran out of chakra and dispelled.

The three Genin decided to get some ramen at a place Naruto suggested. It was the same place he had recently been introduced to by Iruka. "Hey, Shikamaru?" Kiba started.

"What is it?" His lazy teammate replied without looking up from his food.

"Aren't you at all bothered that Anko-sensei just sort of… brushed us off?" Naruto looked up from his second bowl interested in where this conversation was going.

"Nah… It's something we just have to get used to. We've made ninja, that is true... But the higher ranking more experienced adults will still keep things from us just as they have throughout our whole lives. Even someday many years from now, if we were Jonin, there would be things we're left in the dark about. It's a drag… but it's common in the ninja world. My dad taught me as much," He explained.

Naruto considered what he said and immediately thought of the ninetailed Kyuubi sealed inside him. He had only so recently found out about that… even though it directly involved him. Shikamaru's right, if the old man and every ninja in the village can hide that I have a demon inside me for twelve years… Who knows what kind of stuff they keep from the village for all kinds of different reasons.

Kiba sighed in understanding. "So I guess we should just call what happened today bad timing?"

"Pretty much yeah; whatever involved her wasn't expected or she wouldn't have chosen that time to meet us, that's why I think we should just lay off of her, because I don't think it's her fault."

"All right…" Kiba agreed. "What do you say, Naruto?" Naruto's mouth was full of ramen so he just nodded in agreement and silently noted that Kiba actually included him even though he was pretty sure Kiba wasn't one of his biggest fans. Over the years the two had done all sorts of pranks on one another and when that got old they had competitions of who could prank other people better than the other but they weren't anywhere near friends.

Swallowing Naruto decided to throw in some input of his own, "It's probably not a good idea to start everything out by being mad at our sensei for doing her job."

"Yeah I guess you guys are right… Well, I think we're gonna head home," he indicated Akamaru. "See you guys tomorrow…" he paused and smirked. "Team six." Naruto and Shikamaru smirked back and with that and bid them farewell.

"Naruto…"

The blonde pushed his third empty bowl aside and dragged the next one closer as he replied, "Yeah?"

"What changed? How were you able to graduate?" Naruto's new, curious teammate asked.

Apparently, Naruto took it the wrong way because he glared at Shikamaru as he shouted, "Why? Wondering why you have to put up with the dead last?" The offended Naruto emphasized.

So defensive over a question… This whole new team stuff is going to be such a pain… "Whatever, don't answer if you don't want to… I was just wondering," The Nara neutrally replied.

Naruto blinked and softened a bit, he wasn't used to people asking him something out of curiosity. There were only a handful of people he had in his life that were nice to him and had his trust. That thought made him realize he needed to answer… This was one of his teammates now, and he needed to make friends, even though he would probably need some time to trust them that way.

The Hokage and a small group of his most trusted Jonin gathered around the scroll Anko delivered to him. Anko and the third Hokage stood in the middle, with Asuma Sarutobi to their left. Ebisu, the Jonin instructor of the 'honorable grandson' Konohamaru stood to the right with Hiashi, clan leader of the Hyuga as the final shinobi among the group.

"This is most troubling…" Sarutobi broke the silence.

"Yes, the acquisition of the terrorist bomber Deidara bolsters the threat even more." Ebisu agreed.

"What bothers me," Asuma started, releasing some smoke. "Is that since they operate in twos, we don't actually know all that much about what the other members on the Akatsuki's roster are capable of. And with Orochimaru's 'partner' being Itachi… that is pretty unhelpful to that matter. A list of names and some bingo book reviews are only going to help us so much…"

"Indeed," Hiashi agreed. "It will be more difficult to stop such a powerful organization of rogue shinobi without with limited information on their capabilities. And if Orochimaru's claim that they wish to capture all of the Jinchuriki is true we are facing a much more serious problem than we previously believed."

"Speaking of Jinchuriki…" Hiruzen brought up. "Naruto is a member of Anko's team. I'm putting his safety in her and Orochimaru's hands. It seemed like the logical move having the former apprentice of our spy and his primary contact within the village be our Jinchuriki's overseer. The others nodded in understanding.

"What about the rest of the village, are we ready to tell them about the Akatsuki?" Anko asked.

"Hmm… if we do, we do not tell them about Orochimaru," Sarutobi replied thoughtfully.

"It would be hard to explain how we got the detailed information without admitting we had a spy…" Ebisu argued.

"That is true," Asuma backed him up.

"So we all agree for the time being, we keep our knowledge of the Akatsuki a secret?" Hiashi offered.

All agreed and Sarutobi dismissed them. Each of the shinobi filed out with the exception of Anko. "Is something the matter?" The Hokage asked, grabbing his pipe.

"Orochimaru had a separate message to convey to you that he requested be kept between us alone."

Sarutobi scratched his beard in thought. This was a surprise to him but he gestured her to go on. "He wished to warn you that both he and Itachi would be visiting the hidden leaf soon."

"What!?" The Third Hokage cringed.

"He told me he'd be sure to secretly contact me while in the village and said he has a plan to bring Itachi after Danzo. Apparently Itachi has an arrangement with Danzo but doesn't actually trust him, and he is going to use some of the lies surrounding his exile to direct everything to Danzo being the man who exposed Orochimaru's 'illegal activities' that we staged."

I better watch my tongue… neither Orochimaru nor Anko know the sad truth of Itachi Uchiha. The third Hokage reminded himself.

"A good plan… Though you don't understand, Orochimaru is trying to use his current affiliation with the Akatsuki to solve the problem Danzo poses for the hidden leaf."

Anko blinked. "What?"

"Danzo is a power hungry village elder that we suspect is preparing to make a push for becoming the next Hokage… even if he has to have me assassinated or perhaps even make a deal with a rival village to enact war on our village. Orochimaru sees Itachi as a tool to solve that problem even if Itachi doesn't realize what's actually going on."

"Isn't allowing Itachi kill a village elder an extreme method? Not that I'm all that surprised my sensei would come up with a scheme like that."

"We don't have to allow it. Orochimaru is giving me a set of cards to play with. Some people are born with a true gift at manipulating people. Such a gift is what makes your sensei so good at infiltration missions like the one is on right now." Sarutobi smiled. "Even while being technically exiled, he is trying to solve a problem back home."

"Oh… I thought the idea was that Itachi would be in our village and we could take him out," Anko suggested.

It would pain me so much for that to happen… Sarutobi thought inwardly, knowing everything Itachi had truly gone through. "That option is there as well, but Orochimaru likely accounted for the fact we could hit two birds with one stone if we choose. He kept this quiet not only so the others would not know about his idea to deal with Danzo but also to make sure his and Itachi's arrival in the village truly was a surprise to everyone. His cover would likely be blown otherwise," He explained to the young Jonin.

"Not to mention," The Hokage scratched his chin. "Orochimaru doesn't know who to trust when it comes to Danzo. Loyalties between him and I are divisive throughout the village."

Two tall men donning black cloaks with red clouds on them walked side by side in a forest in silence. Orochimaru's clone had dispelled three hours ago, and in those three hours no words had been shared between himself and his partner. Itachi Uchiha was on guard, although he was content with silence, it was unlike his partner to not comment on a single thing for that long. After awhile, he concluded Orochimaru was up to something, it was only a matter of time…

"Why don't we pay Danzo a visit, Itachi?" The two of them halted their leisurely slow walk as he voiced that idea, and Orochimaru awaited some form of a reaction. "Well?" He stated impatiently.

Itachi slowly rotated to face his Akatsuki partner and to the Snake Sannin's shock he found himself staring right into the Mangekyou Sharingan. Caught in Itachi's genjutsu, there was little the Sannin could do but try to break free. This, was the Tsukuyomi.

"What is the meaning of this?" Orochimaru rasped, prepared to fight.

"Relax." Itachi told him. "I did not perform a Genjutsu on you to attack, but to talk privately."

"What do you mean?"

"I believe Zetsu is watching us at this very moment, and I do not want him to hear this conversation… The Akatsuki do not trust me."

Orochimaru chuckled. "Need I remind you of your clan?"

Genjutsu-Itachi did not respond, staring at the pale man emotionlessly.

Outside of the Tsukuyomi, "What is happening?" "It would appear Itachi has decided to turn on his partner. Not good." Black Zetsu replied his other half.

"Should we intervene?" White Zetsu prompted. "No, there is little we can do against a ninja of his caliber. We would only embarrass ourselves. We will watch and see what happens… and report back to Pein and Madara."

"No need to take it too personal Itachi, after all we're all S-Class criminals. I'm sure Leader trusts you as little as he trusts me."

"There is no escape from this jutsu, Orochimaru. Someone like yourself, who is so intrigued by the Sharingan, its history and jutsu of any kind with as much power and stature as you once as you, should know of Tsukuyomi."

"I am aware of that," Orochimaru frowned. "You said this was for a conversational purpose, not an attack," He reminded, not understanding the Uchiha's actions.

"That is true, but I will do as I must… If I am in fact wrong about you," Itachi elaborated only slightly.

Orochimaru said nothing, just staring back at Genjutsu-Itachi, awaiting a question of some kind. Had Itachi figured out he was a spy? Was he not careful enough when he dispatched a Shadow Clone to the Leaf this time?

"You were one of the Hokage's students, one of the closest people to him out of all the Hidden Leaf; But even you were not told the truth about me, were you?"

Orochimaru raised an eyebrow. "The truth?" He repeated out of curiosity.

"The truth about me is a secret. A secret I will not reveal without learning the truth about you."

"My my Itachi… As often as you speak, it's curious how you're able to talk in riddles. I'm impressed," Orochimaru mocked. "Seek your truth… I have nothing to hide."

"Is that so?" Itachi stated, ignoring the bulk of his comment. "Then you're not a spy for the Hidden Leaf?"

Orochimaru's heart skipped a beat, but his face betrayed no emotion. "An interesting accusation, but I do not believe you are stupid Itachi. You are well aware of the bounty on my head as well as my official exile."

"In the ninja world…" Itachi began, locking his eyes shut. "Things are rarely as they appear…" When his Mangekyou shot back open the two of them found themselves in a Genjutsu version of the Leaf village. It was a residential section of the village the Sannin was less familiar with, and he was momentarily confused before seeing a familiar symbol on a nearby door.

The Uchiha clan emblem.

Orochimaru followed Itachi into the building, passing by the sentries oblivious to their existence and the Sannin found himself in a crowded… rally? Of some sort full of Uchiha. Fugaku Uchiha, Itachi's father and Clan head stood before the entire assembly of members.

What is this, an Uchiha clan meeting? Why would Itachi— Then Orochimaru noticed something, most of them carried a look in their eyes he was all too familiar with, having fought in war. Their eyes, Sharingan inactive… carried malice as they listened intently to their leader who was spieling hatred for their treatment by the village, the suspicion on them revolving around the Kyuubi and where their rightful place in the Leaf's standing should have resided.

Orochimaru was not a fool. He understood exactly what this was, but that meant…

The Sannin stared at Itachi with an incredulous gaze, which the former ANBU captain took as his cue to skip to another memory.

Now they were on the balcony at the top of the Hokage tower. Orochimaru and Itachi stood to the side in their Akatsuki robes, listening to the younger Itachi and Lord Third, as the old man made promises to Itachi that he would protect Sasuke… particularly from Danzo. Based on the course of the conversation and the obvious remorse that infected younger Itachi's voice, Orochimaru concluded this was a meeting after the massacre took place.

If these were authentic versions of what happened… Itachi Uchiha was a traitor to his clan… but not his village.

A/N:

[1/4/16]

Well, as you can see I intentionally mixed and matched the squads a bit to help diversify things from canon and also looked to change the Jonin leaders up as well though only Anko has been revealed as one.

More importantly… Orochimaru is actually a good guy O.O

As far as characters go on who's more important than who… I use a large cast like the Anime but Team Six is the most common center of attention.