Disclaimer: I do not own Naruto. It is owned by Masashi Kishimoto (hope the spelling is correct and I don't know his last name)

Answers to Reviews:

Mashiro chi1: Yes, Kakashi will be here. I did not add him before because, until he got his team, he wasn't in his right state of mind. Or at least the massacre. So, I kept him away. But, don't worry, he won't be side lined.

Shadowdragondanny: Thanks

Wolvmbm: Thanks. The massacre will be a lot different this time

davycrockett100: Thanks

Immortalman18: Thanks

arcabrad1: He needs to gain control of his powers from the start as his body still needs to adopt to his capabilities.

shadowfang jutsu: Thank you

Guest: Lee hasn't graduated yet. So, he won't.

Guest: Yeah me too.

Guest: Thanks

"Blah" – Normal speech

'Blah' – Thoughts

"Blah"- Kurama and other tailed beasts talking

'Blah' – Kurama and other tailed beasts' thoughts

Shadow Clone Jutsu- Jutsus

Okay guys, without further delay, here is the story

FLASHBACK:

As soon as Sasuke left, all the rest removed their masks. Itachi then said, "I will call for reinforcements to take these ROOT ANBU's away. Can you explain to us how you managed to defeat such opponents?"

Naruto answered, "They underestimated us. Shikamaru used his clan's jutsu to immobilise them and I knocked them out".

The ANBU's were impressed. Itachi then said, "We better leave. And we need a detailed schedule on what you do every day so that we can protect you more efficiently".

Shikamaru answered, "Well, we will come up with one. We don't have a fixed one at the moment. So, Naruto, let's plan a schedule".

Training Ground 7:

Naruto asked, "What kind of schedule?"

Shikamaru answered, "Well mister Orange Hokage, we need to get stronger. I need to get stronger. Duh".

Naruto pouted and said, "Stop that Orange Hokage thing Shikamaru".

Shikamaru smirked and said, "Not until you become the hokage".

The ANBU's smiled at the boys' squabble. It was good to see that the boy who was shunned by most of the villagers had someone he could call a friend.

All of a sudden, ten more ANBU's arrived. The four, who were already present, put on their masks. They, apparently, had come to take away the ROOT ANBU's. The four went to the newly arrived group to inform about the situation.

Shikamaru took advantage of the situation and said to Naruto in a hushed voice, "Let us not discuss about what we will be doing. We can do it once we get to that training ground of yours. Let us now discuss about at what time we will meet".

Naruto nodded and started thinking about the schedule and how it should be as Shikamaru did the same.

The four ANBU's returned after the ROOT ANBU's were taken away. They once again removed their masks. Itachi then asked, "Have you decided your schedule yet?"

Shikamaru answered on behalf of both of them, "Yes, we have. We will leave our house at 6 AM and go for a jog around the village. Then meet up behind the hokage monument. Then, by evening, around 4 PM, we will go back".

Naruto nodded and added, "I will probably train for a couple of hours more".

Shikamaru said with a disapproval, "No Naruto, you would better go home too".

Naruto replied, "Why? It's not like anyone will be waiting for me".

A pang of sadness came over the faces of everyone present there.

Shikamaru said, "If you want to, you can come with me to watch the clouds. Chouji will be there too".

Itachi added, "And maybe, Sasuke would also like to join you two. If you want to, I will ask him".

Naruto brightened up at this, and happily exclaimed, "Really? Thanks Shikamaru. Thanks Itachi-nii-san".

Everyone smiled at the boy's happiness. Itachi was surprised that Naruto had called him brother, but it didn't feel bad. So, he let it pass.

Itachi then said, "Very well then. We will be within 50 feet of you two all the time until our job ends. And, during your training behind the hokage monument, we will set up a barrier and a perimeter around the grounds so that no one can attack you. And don't worry, we won't spy on you. We don't know why, but it seems like lord hokage trusts you two a lot. So, we trust you too. That is all. Now, we will get to our posts".

Both the boys nodded as the ANBU's vanished and Naruto sensed that they had got to their positions. Then, both the boys separated as they promised to meet up the next day at 6AM near the main gates.

The Next Day- Konoha's Main Gates:

Naruto had already arrived at the main gates and was now waiting for Shikamaru to arrive, rather impatiently. After waiting for some minutes, which seemed like hours for Naruto, Shikamaru arrived with a very big yawn, and with a very lazy expression. There was no end to Naruto's anger towards the lazy genius. It was further aggravated by the fact that Kurama was rolling on the ground due to laughing inside his mindscape.

He shouted towards the lazy boy, "WHERE THE HELL HAVE YOU BEEN SHIKAMARU? I HAVE BEEN WAITING FOR WHO KNOWS HOW LONG. YOU ARE LATE".

Shikamaru sighed while holding both of his index fingers to his ears. He then said, "Have you seen the time Naruto? It's still 2 minutes to 6. You say I am late. In fact, you are early. Besides, you can pick up the habit and annoy your sensei maybe".

Naruto was both annoyed and happy at the same time. He was annoyed because, in the end, as pointed out by Shikamaru, he was early and the lazy boy was not late. He was happy because, he had finally found a way to annoy his sensei, even though he knew the reasons for the lateness of his sensei. Maybe, adding the woeful explanation as a revenge would also annoy him, he thought.

Naruto, after calming down, said, "Okay, Shikamaru, we will jog through the training grounds 3, 4, 5 6 and 9 and from there go towards the grounds behind the hokage monument. That should be enough for now. It will probably take us one to one and a half hours with our present stamina and strength".

Shikamaru replied, "What a drag. Okay, we will. Hopefully, by the time we graduate, we will be a lot stronger than before".

Then, they both set of jogging. Along the way, they passed through the empty training grounds 3, 4, 5 and 6 and also through a rather loud training ground 9. The noise was from Gai sensei, who himself was going through his daily exercises. When he saw the two boys, he rushed at them, cried happy waterfalls while shouting something about their flames of youth and had finally given them tips on physical exercises before letting them go. After an hour and fifteen minutes, they reached the grounds behind the hokage monument.

Naruto sensed that the four ANBU's had scattered, most likely to set up a perimeter and a barrier to keep away the ROOT ninja's. Naruto, heaved a sigh of relief, knowing that they won't be nosing into their training and also that they would be safe from Danzo and ROOT as long as the ANBU's were near.

Training Ground behind the Hokage Monument:

Naruto and Shikamaru made their way towards the place where the hokage had made a waterfall and a cliff with his jutsus. Shikamaru was stunned by seeing this. Naruto chuckled at this. Even he had to agree though, that jiji's jutsu totally overshadowed the one that Captain Yamato had done in the previous timeline.

Recovering from the awe, Shikamaru said, "Okay, we both need to get strong to change the future. But, getting strong without a plan is useless. So, we need to make sure we grow in all areas rather than one or two. Getting more jutsus is as important as mastering the one's you have. So, first, let us begin with telling each other what our present situation is with our abilities. Naruto, you begin. Tell me your chakra capacity, abilities, control and the jutsus you know".

Naruto replied, "Okay Shikamaru. My chakra capacity is definitely above Kage level. It is 5 times as much as jiji's. Add Kurama's chakra too and it becomes like 150 or so times. I have like mid-chunnin level chakra control. It's really hard to better it thanks to my already huge capacity and Kurama's chakra. I will never be affected by Genjutsu thanks to Kurama and old man Sage's chakra. My taijutsu is my own style and I am still starting to develop it. Even super fuzzy brows sensei also said that it is really effective. I can't cast Genjutsu unless it uses huge amount of chakra. As for my Ninjutsu, It's my strong point. I can use wind release, water release, earth release, lightening release and fire release, in order of affinities. I can also use yin release, yang release and yin-yang release. Then, I can also use magnet release, coral release, lava release, steam release, acid release, scale release and ink release".

Shikamaru's jaws dropped to the ground. After recovering, he said, "I have never heard anyone with so many releases. Most of it, I haven't even heard of. You really are something else Naruto".

Naruto smiled as he rubbed the back of his head and said, "Well, I am the pseudo jinchuriki of every tailed beast. So, I get their powers as well. And, there is old man sage's chakra as well. Anyway, as for the jutsus I know, I know the academy two and Shadow Clones. Then, I know Wind Release: Gale Palm and Wind Release: Great Breakthrough for wind release and was starting to work on Wind Release: Drilling Air Bullet. I know Water Release: Wild Water Wave, Water Release: Gunshot and Water Release: Water Prison for water release and was about to learn Water Release: Water Formation Wall. I know Earth Release: Double Suicide Decapitation Jutsu and Earth Release: Hiding like a Mole Jutsu for earth release and was about to work on Earth Release: Multiple Earth-Style Wall jutsu. Then, I know, Lightening Release: Electromagnetic Murder and Lightening Release: Lightening Beast Tracking Fang for lightening release and was to work on Lightening Release: Conductive Shock jutsu. I know Fire Release: Fireball Jutsu and Fire Release: Phoenix Sage Fire Jutsu for fire release and was about to begin on Fire Release: Flame Bullet jutsu. I was also about to work on Body Flicker Jutsu. Then, I can use Rasengan and many of its variants. I can't use either Rasenshuriken or its variants yet. And I haven't tried sage mode yet. I can use, Lava Release: Lava Bullet,Steam Release: Unrivalled Strength, Steam Release: Erupting Propulsion Fist as other release moves. And I can utilise version 1 form of jinchuriki transformation and have already mastered one tailed state. And I will begin to master the two and three tailed state of my version 1 form. Also, my fuinjutsu is at intermediate level. I can make exploding notes, paralysis notes, flash bang notes and storage scrolls. I need a fuinjutsu master to get to a higher level. That sums it up".

Shikamaru was at awe of the blonde's jutsu knowledge and growth. He said, "Well, that is a lot. As for me, my Genjutsu is non-existent even though I can both cast and release them. My chakra capacity is at low-jonin level and chakra control in my present state is non-existent. My taijutsu is only up to the mark. My jutsu are mostly clan based, which include, Earth Release: Practice Brick Jutsu, Shadow Clutch Jutsu, Shadow Gathering Jutsu, Shadow Imitation Shuriken Jutsu, Shadow Imitation Jutsu, Shadow Sewing Jutsu and Shadow–Neck Binding Jutsu. That is all".

He continued, "We both have lot to work on. Even though you have grown a lot stronger, it isn't enough. So, first, learn the moves you said you were working on. Also, master every chakra control exercises so that your chakra control can keep up with your chakra capacity. Then, learn to do the academy jutsus and body flicker and also the shadow clones without hand seals. Then, master the Rasengan and learn to do it single handed. That should keep you occupied for some time. And also work on physical aspects of your body, shuriken and kunai throwing and taijutsu".

Naruto nodded and said, "Okay. What about you?"

Shikamaru answered, "I have to start from scratch. Lucky for me, at my chakra capacity, I can do about 5 shadow clones. I will have them work on the chakra control and elemental affinity mastery for the next six months and I will work on my physical body. That should do it for now".

Both boys nodded, did a fist bump and got to training. It would be a long six months, till the massacre day, for them.

Six Months Later:

During the six months since Shikamaru's arrival, both the boys had trained on a regular basis. Naruto had been to the Nara clan compound and the Akimichi clan compound quite a few times, thanks to Shikamaru's and Chouji's invitations. He had also become good friend with Chouji, in the meantime. Sasuke had also warmed up to the three boys, eventually enough to call them his best friends, especially Naruto. To Sasuke, Naruto had become a friendly rival. He proclaimed that in front of the group, surprising the two time-travellers, who questioned themselves whether this was the same emo-king of their previous timeline.

During weekends, the two time-travellers would train basic chakra control exercises, taught in the academy, with the two other boys. The blonde and the lazy genius, when questioned about how they had mastered the exercises, replied that they had been doing that for quite some time. Luckily, both the boys had bought the story. So, their secret training was still a secret.

Shikamaru's chakra capacity had grown from low-jonin level to mid-jonin level. He was now using 10 shadow clones instead of the initial 5. He had already mastered the leaf sticking exercise, tree walking exercise, water walking exercise and their variants. He was now working on extending the time doing those. At the moment, each of his clones could stand for an hour sticking to the tree and for thirty minutes on the water. He was hoping to extend those to five and three hours respectively.

He was also making good progress in the elemental manipulation exercises. He had mastered the first stages of the exercises and was now working on the second stages.

As for Naruto, his chakra control had increased from mid-chunnin to high-chunnin level. His chakra capacity had also increased. He had learnt all the jutsu he had been working on and had managed to do the academy jutsus without hand seals. He was now working on doing the shadow clones without the hand seals. He had finally managed to do the Rasengan single handed and was now trying to do it in his left hand without the sage mode.

Naruto had found out about the 'promise', that the old man sage had asked whether Shikamaru would like to keep. It was a memorable talk for him as a matter of fact –

FLASHBACK:

It was about 2 in the afternoon and both Shikamaru and Naruto were taking a break from training. They were totally exhausted, and now, they were watching clouds. It had been two months since Shikamaru had come 'back' from the future. They were both peacefully watching the clouds.

Suddenly, Naruto remembered about the talk with jiji. He remembered that Shikamaru had said something about a promise and ever since that day, it had started to bore through his brain. Shikamaru had not elaborated about it, and that had made it so suspense filled promise that he wanted to know about it at all cost. So, he decided to ask the lazy boy.

Naruto got up and took up a sitting position with legs crossed. He asked, "Shikamaru, that day, you said something about the old man sage asking you whether you would like to keep your promise. What was that promise?"

Shikamaru, at this, lifted an eyebrow and sighed. He then said, "Leave it Naruto. It is just a drag".

Naruto wasn't silenced by this, he pressed on, "Come on Shikamaru. Tell me the truth".

Shikamaru sighed again and said, "What a drag? Why do you need to know the truth?"

Naruto's mood dropped at this. He said with a little sad voice, "I have been lied to, half of my life. I have been hated for the truth I had been denied. I was left without a family for a truth that was hidden. That, Shikamaru, is why I wish to know the truth".

Shikamaru noted the apparent sadness hidden underneath the anger in the blonde's voice. He sighed to himself knowing that he had no other option but to tell him. So, he said, "That day on the battlefield, when you saved my life by giving Kurama's chakra, I figured out something. You are just like the first hokage. You are stupid and jolly goer. But unlike him, you don't have an intelligent younger brother to guide or advice you. In your childhood, you were lonely. I made a mistake by not being a friend of you. I regret that. I didn't want to you to be lonely anymore. So, I promised myself and my dad that when you become the hokage, I would be with you as your chief advisor and guide you as a brother, just like the second hokage was to the first, because no one is better advisor to you than me".

Naruto sat there dumbfound as a couple of teardrops escaped his eye and fell to the ground. He then said, "Thank you Shikamaru. You don't know how important those words are for me. It's good to know that there is a friend to rely on, no a brother to rely on. Thank you again".

Shikamaru sighed and said, "What a drag. You don't need to thank me Naruto. I just want to correct my mistakes."

Naruto looked at him and held his right fist out for a fist bump and said, "If so, we will both correct our mistakes together, dattebayo".

Shikamaru looked at him, smiled and did the fist bump and said, "Okay then orange hokage, let us do it together"

He was really happy for finding such a friendship. He knew that this time, he wouldn't be lonely. That thought alone gave him massive confidence boost. But, for now, he had other things to concentrate on. It was only a week till the Uchiha massacre. He hoped that it would go as planned.

A Week before the Massacre:

Itachi was bothered. Recently, the upper members of his clan, the heads and advisors, were planning a coup against the hidden leaf village. They had thought that the village had betrayed their trust and so, it needed to be thought a lesson and also the leadership of the village should belong to an Uchiha, which, they thought was their rightful inheritance. Even, Shisui had been bothered by this. They thought that these were absolutely stupid ideas, but couldn't do anything about it.

But, more than anything, what bothered them was, a man in a spiral face mask. Surprisingly, the third hokage had already warned them about the man, and that he should be avoided at all costs. And, so, they had managed to stay away from the man, who was definitely playing a major role in the coup.

But, recently, things had taken a violent turn. The two pacifists were invited two a clan meeting, which, neither of them attended. So, they were confronted by some stuck-up Uchihas, only to be beaten up by the two prodigies. They, however, did attend another meeting as they didn't want the repeat of the incident. But, they regretted the decision soon. Because, they had to endure the arrogant Uchihas' high-headedness. The only exception was Fugaku Uchiha, the clan head and Itachi's father.

But, the actual reason they had to regret their decision was because they had been assigned a mission. Specifically, a mission to assassinate the third hokage. Only the clan head, Fugaku Uchiha, looked sad at this, and they instantly knew that he had failed to convince the others that it was a bad idea. So, they also couldn't say anything about it. This was the thing that was bothering Itachi as he waited to see the third hokage with Shisui.

As they were invited into the hokage's office, they saw that the hokage looked gloomier than ever. It was as if the hokage knew what they were about to tell him.

As if on cue, the third hokage spoke up, "I know why you two are here. Isn't it about the assassination mission?"

Both, Itachi and Shisui were surprised by this. Itachi, who was first to come out of the surprise, asked, "How do you know lord hokage?"

The hokage answered, "I knew all along that I would be targeted eventually. So, what do you two want to say about it?"

Both of them answered at the same time, "It is utterly stupid. They won't succeed".

The hokage just nodded and then said, "Will you two accept a secret S-ranked mission?"

They were surprised that the hokage was giving them an S-rank mission at such a time. But, for them loyalty towards the village and duty came first. So, they said, "Of course, lord third. What are the mission details?"

The hokage nodded and said, "To assassinate everyone involved in the massacre".

Both the Uchihas were shocked by this. But before they could interrupt, the hokage continued, "I know this is sudden, but a problem should be solved before it goes out of hand. The innocent Uchihas will be sent to somewhere safe and only the ones who are involved in the coup shall be killed. Will you accept?"

Both of them thought about it. If they could just assassinate the ones involved, they could prevent unnecessary bloodshed and loss of lives. Most of the Uchihas would be safe too. The pros outweighed the cons. So, they said, "We accept, lord hokage".

The hokage smiled and said, "Very well then. Shisui will most probably become the new clan head, because Itachi's mission will not end there".

This surprised both of them. So, they asked, "What do you mean lord hokage?"

The hokage answered, "Shisui's involvement in this affair will be kept a secret, whereas Itachi's will not be. He will instead be branded as an S-rank missing ninja. His mission, from there, will be to join the organisation known as Akatsuki. Once you do so, you will send important information of their activities to Jiraiya. He will be informed about the mission. He will then send the information to me. Of course, these are only if you accept, Itachi".

Itachi thought about it for a while and then asked, "What is so special about this organisation, lord hokage?"

The hokage answered, "It is an organisation, consisting only of S-rank missing ninjas. According to Jiraiya's reports, they are after all the tailed beasts".

Both, Itachi's and Shisui's, eyes widened at this. Both of them came to the same conclusion. This was a dangerous organisation, plotting the destruction of elemental nations. But, one important thing crossed their mind and Itachi voiced it, "They will come for Naruto-kun".

The third hokage nodded his head in a grave way.

Itachi, after weighing every information, said, "I accept lord hokage. We won't disappoint you. How long will the mission for my part be?"

The hokage replied, "As long as it takes to delay them or till I tell you to abandon the mission".

Both of the Uchihas nodded and said, "We accept lord hokage".

The hokage nodded and said, "Very well, your mission will begin in a week. Every innocent Uchiha will be transported to a safe location. There is a chance that Danzo will try to manipulate you to kill the whole clan. But, don't pay heed to him. Because, he plans to extract Sharingan eyes of the dead Uchihas. So, dispose of the bodies as soon as you kill them while I will make a small squad to kill Danzo. Itachi, as soon as you finish your first part of the mission, leave for the second part immediately. If you meet your brother, tell him that you will explain everything to him when you get the chance. Now, you two may leave".

The two Uchihas nodded and left while mentally planning for the assassination.

The Night of the Massacre:

Assassinating the clan elders and those who were involved in the coup plan was easy for Itachi and Shisui and they had carefully disposed their bodies. The only person left to be assassinated was the current clan head, Fugaku Uchiha. Itachi had already sent away Shisui, so that his involvement would be kept a secret and the innocent clan members were at a safe location. His father was most likely to be at their house. So, he went there first.

As expected, Itachi found his father inside their home. His father sensed him but did not fight him. Instead, he sat, where he was, still. Itachi moved forward with an unwilling heart to kill his father. Sensing his predicament, his father said, "Don't hesitate Itachi. You are fulfilling your duty towards the village. That is a great honour indeed. I just hope that the Uchihas name shall regain its pride as an important and loyal clan of Konoha after my death. Hopefully, Shisui will make sure that it happens. Remember son, no matter which path you take, I am proud of you".

Itachi, for his part, was at a loss of words. He said, "I am sorry for doing this father" as he ran his sword though his father's heart while tear trickled down his face. A searing pain shot through his eyes, which he thought was a cue to the fact that his Mangekyo had been activated. He left the clan compound to run away soon after disposing his father's body. He chose not to visit his brother, as he could not bring himself to do so.

Meanwhile:

Danzo had been very angry. Both Itachi and Shisui had not listened to him and Hiruzen Sarutobi had managed to send all the 'innocent' Uchihas to safety too. At least, he would get Sharingan eyes for himself. Shisui had managed to evade him, so he had to do with normal Sharingans. Thinking so, he made his way towards the Uchiha clan compound.

But when he saw what the two Uchihas had done to the bodies of those who were assassinated, he was beyond angry. He had lost his chance to get the Sharingans for himself. But, it seemed as if it was just the beginning of his plights, because just then, a team of four shinobis – Maito Gai, Kakashi Hatake, Asuma Sarutobi and Tenzo, also known as Yamato, just appeared out of nowhere and surrounded him.

Kakashi stepped forward and said, "Shimura Danzo, you are to be executed for charges of treason. There is no means to escape for you".

Danzo, not looking even the slightest bit intimidated, asked, "What happened to Fu and Torune?"

Tenzo answered, "They are dead. Assassinated, because, they could prove to be quite a risk. Soon, you will join them in the afterlife".

Danzo, for his part just laughed and said, "Do you kids, seriously think that you could kill me?"

Asuma replied, "Don't underestimate us. Because, it could well be the end of you".

Danzo suddenly did some hand seals and said, "Wind Release: Vacuum Wave". He took a deep breath and started spinning and compressing it and finally exhaling it as blades of winds in different directions.

Tenzo, did a hand sign in response and said, "Wood Release: Wood Dome", as a wooden doom rose up to protect them from Danzo's jutsu.

Kakashi then jumped out of the dome, did some hand seals and shouted, "Fire Release: Grand Fireball Jutsu" and shot out a giant fireball towards Danzo.

Danzo knew that using wind style jutsus against fire style jutsu at such close proximity would only bring trouble. So, he backed down a bit. Gai and Asuma, taking advantage of this, jumped out of the dome and engaged him in a Taijutsu fight.

Danzo noticing this, passed through several hand-seals, said, "Wind Release: Vacuum Spheres". He took another deep breath and then exhaled several small blasts of wind chakra towards Gai and Asuma.

Luckily, just in time, Kakashi shouted, "Earth Release: Earth Style Wall" and created a wall of earth with faces of dogs to block Danzo's attack.

Asuma, using the cover charged his trench knives with wind chakra while Gai opened five of his eight inner gates. Gai was the first to attack giving no time for Danzo to perform any jutsu. He jumped up into the air, shouted "Asa Kujaku" and started punching the air which caught fire due to friction and speed of his punches. The fireballs hit Danzo injuring him in the process.

As soon as Danzo got a little away from the dangerous attack, he took out a kunai and exhaled wind infused chakra to make it into a makeshift sword. Soon enough, Asuma attacked Danzo with his wind chakra infused trench knives. They kept on trading blows for some time.

Even Danzo had to admit, that fighting against four jonins was not easy. Especially, if they were prodigies. They were not letting him to remove the seal on his right arm to use his wood release abilities. Close combat against two taijutsu experts was not easy either.

All the while he was thinking about the fight, he failed to notice Kakashi charging up his Lightening Cutter or Tenzo making hand-seal for his wood release. Danzo was taken by surprise when a tendrils of wood latched on to him, binding him to the place. But, before he could recover, a lightening chakra infused jab, ran through his heart, killing him immediately. Danzo, died there that night, at the hands of four exceptionally skilled shinobis of the leaf.

After the four jonins disposed of his body, they left to inform the hokage that their mission was a success. The next day, news of the assassination of the leaders of the Uchiha clan spread like wild fire and Itachi Uchiha was officially labelled as an S-rank missing ninja.

There you go guys, after a long time of three weeks, maybe?, an update. Sorry about that because, my laptop broke down and I received it back after repairs just two days ago. So, I gave you a very long chapter. Hopefully, updates will be back to frequent from now on. Thank you.

Read and review guys.