Naruto and Madara were currently walking through the Land of Fire. It had been six years since the two left the village hidden in the leaves. During this time, lots had happened. The Uchiha clan was slaughtered by Itachi Uchiha, leaving only Sasuke and Mikoto Uchiha alive. This, in turn, made Sasuke become a very person in the village and it created a sense of entitlement that Mikoto was ashamed of.
Naruto and Madara encountered clan killer Itachi and they learned the truth behind Danzo's actions and the two promised to have him eliminated. They also learned of the akatsuki's plans to capture all nine of the tailed beast. However, they wouldn't start moving for another four years.
Kirigakure's fourth Mizukage snapped as he started the bloodline purge and brought his village into a bloody civil war. During the training trip, Naruto fought against Juzo, Kisame, Zabuza, and even his student, Haku. Naruto fought against many powerful shinobi and had encountered both Iwagakure ninja and Kumagakure ninja that wanted the head of Minato Namikaze's child.
The young blond also changed greatly. He no longer wore the mask of a loud idiot. In fact, he became calm and collected. This was created by Kurama's genjutsu and Madara's Tsukuyomi. Though he became cold and ruthless, when it came to Kurama and Madara, his heart was pure as ever.
Naruto's nature affinities were Wind and Fire, he was originally a pure Wind user. However, thanks to being a Jinchuriki, he gained a powerful Fire element. This excited Madara as her student was able to learn some of her most destructive fire jutsu.
Along with Naruto's growth, Madara also grew stronger. Her body also became more developed as the nineteen year old woman was quite the looker. During their journey, they located the mask of the Shinigami and had called fourth the reaper. This allowed Madara to sacrifice a bandit boss who was kidnapping innocent girls to satisfy the reaper. Naruto was able to speak with his father and he grew to truly respect the man's sacrifice. Also, Naruto was able to have the full power of Kyuubi now that he had both Yin and Yang halves.
Instead of signing the Toad contract like Jiraiya wanted him to, Kurama had his Jinchuriki sign the fox contract. Naruto's ability to call fourth Kurama at anytime was great for crushing multiple enemies and to allow Kurama to enjoy the real world instead of his cage inside of the blond's mind.
As Naruto explored more of the world, he met a few others that were just like him. He met the two tails Jinchuriki, Yugito from Kumo and the eight tails Jinchuriki, Killer Bee. He also met both Han and Roshi from Iwa, the Jinchuriki of the five and four tails. However, unlike the Kumo ninja, Naruto engaged combat against both of them. It was a sight to be seen as it forced Madara to step in and save her student. While he didn't win, neither Han or Roshi could believe that such a child could have so much power.
Naruto went to Suna and met the Fourth Kazekage and his children. Naruto and Gaara had a mutal respect for each other after Madara and Jiraiya adjusted the seal on him. For the first time in the red head's life, he had a real friend and promised to always value Naruto's friendship. Temari and Kankuro also became friends with the blond.
The final Jinchuriki that Naruto met was Utakata from Kiri and Fu from Taki. Utakata was an uptight man who didn't care much for other people. However, when he learned that Naruto was just like him, the six sails Jinchuriki became more friendly and even sparred with the blond.
To Madara's annoyance, Fu was just like her student. The two were happy go lucky idiots who loved a good fight. Unlike many of the others, similar to her feelings towards Gaara, Madara felt pity towards Fu to her upbringing. Naruto promised he would visit her again someday.
Madara also had Naruto learn his father's rasengan. However, instead of the basic rasengan, Naruto developed the second stage and called it the Kaze sphere which was a simple rasengan with the wind element. Naruto managed to perfect the jutsu and create the Wind Release - Kaze Shuriken. The blond also master the Nine Tails Twister and Shockwave, along with the Nine Tails Beam. Madara hammered her two moster powerful fire release jutsu being the Great Fire Annihilation and Great Fire Destruction.
Jiraiya had visited them quite frequently and informed them that Naruto needed to be able to produce a clone. However, because of his massive reserves, Madara taught Naruto the Shadow Clone Jutsu. During one of their spars, Naruto had awoken his Uzumaki bloodline and had used the Adamantine chains that were used to subdue Madara and go on the offense. Though they were strong, Madara was able to get free from her constant experience from battiling with Hashirama.
The last thing Naruto wanted to learn was his father's Hiraishin. This required great knowledge of fuinjutsu and like his parents, Naruto was a natural. He learned the basics of transporting both matter and energy. This allowed Naruto to learn how to create his own seal. It didn't take much longer to place his seals on his kunai to use the Flying Thunder God - Second Step. The blond even learned his father's guiding thunder varient to redirect powerful jutsu.
Having seen the benefits from the Shadow Clone Shuriken jutsu with his Hiraishin kunai, Naruto learned how to multiply his weapons like he did when using the shadow clones. As a reward for his hardwork, Madara taught him the Exploding Shadow Clone Jutsu that Naruto learned first hand why it was an advanced jutsu. It was deadly. The last thing Naruto developed before the training was over, was mixing his two strongest jutsu. The Hiraishin and Kaze Shruiken.
"Hard to believe its been six years already." the blond haired boy said as he wore the traditional anbu uniform that Jiraiya got him along with the blood red scarf Madara got him when they went to the Land of Iron. The Uchiha woman also came to respect the boy. Some would even say she's taken a special liking to him.
"Yeah. Now remember, don't reveal your full strengths." Madara said to the blond.
"What's the point of hiding it?" Naruto asked.
"At least wait until we confront Danzo. The last thing we need is that damn council trying to control you." the Uchiha woman said as they entered through the gate and were met by Izumo and Kotetsu.
"Huh? Naruto? Is that you?" asked Kotetsu.
"Hello, Kotetsu. We're returning from our six year training mission." Naruto said in an emotionless tone.
"Yeah, go right ahead." Kotetsu said as he stared at the boy in shock.
Naruto and Madara walked through the village streets as the people were giving Naruto glares of hatred and disgust. One of the civilians had the nerve to try and throw a glass bottle at the blond. "Die, you demon!" shouted the man.
However, Naruto flicked a kunai and knocked the man out from a single chop to a pressure point in his neck. Madara was just as ruthless with Naruto's knowledge. She refused to have a muscle head student without a brain. The two went up the stairs and arrived in Hiruzen's office.
"Well, its been sometime, Naruto, Mara." Hiruzen said with a chuckle.
"Hello, Lord Hokage." Naruto said emotionlessly. During the trip, Naruto realized the hokage considered him nothing more than a weapon, a tool to defend the village. To say Naruto was hurt, would be an understatement. It was thanks to Madara that he didn't lose control and let the Kyuubi take over.
Hiruzen frowned slightly. He missed being called grandpa by the blond. "Well, I'd like to hear your progress. Would you like to get some ramen, Naruto?" asked Hiruzen.
"No, Lord Hokage. I've come to take my graduation exam. I'm sure you're busy with your paperwork." Naruto said.
"Well, to tell you the truth, you made genin about two years ago. I don't believe you'll need to take such an exam. However, I've been having trouble finding a genin team to put you on." Hiruzen said.
"Lord Hokage, I do have a suggestion." Madara said sternly. "Put Naruto on the same squad as the Uchiha. I believe Hatake would be an ideal teacher. Especially since he was Naruto's father's student. I would like to request being placed in the anbu black ops." Madara said.
"The anbu black ops? Do you think you're ready for such a thing?" asked Hiruzen.
Madara sighed as she created a privacy and silencing barrier that not even the anbu in the room could listen in on. "Lord Hokage, it's time I reveal to you the truth of who I am. My name is Madara Uchiha. I'm from a different universe than this one. The last I remember, I was fighting against Hashirama. He killed me and when I used my Izanagi, something happened. I was brought to this world and I'm thirteen again. From my understanding, your Madara Uchiha is a guy. So, as for a backstory that I want the people of the village to know, I'm the great granddaughter of Madara." Madara said.
"I see. I figured something was off about you. I will allow it. Would you like to move into the Uchiha compound?" asked Hiruzen.
"No. I will be staying with Naruto at his apartment." Madara said.
Hiruzen said. "Unfortunetly, I couldn't save it. When people learned that Naruto left, they went to burn his apartment down... Nothing was able to be recovered." Hiruzen admitted with shame in his tone.
"That's fine, Lord Hokage. I would like to have access to my parent's house." Naruto said.
"Yes, of course. And Naruto, please feel free to come visit me anytime. Also, here is your headband." Hiruzen said as he handed the blond a black headband. Naruto bowed and informed Madara that he would be going to the estate and that he needed some of her blood to add to the security seal.
"See you later, Naruto." Madara said. Naruto vanished in a yellow flash.
"So, he's learned the Hiraishin... Tell me, how strong is he?" asked Hiruzen.
"Without the power of the fox, easily high jonin. Naruto could be an anbu captain. With the fox, I'd say he could take you and your students on, all at once." Madara said with pride in her voice.
"Are you serious? So, why am I giving him the rank of genin?" asked the hokage.
"You want your weapon under control, right? Besides, I think it will be good for Naruto's peers and the village to see their demon. Anyway, we have more important matters. I spoke with Itachi in regards to the Uchiha clan massacre. I would like to receive an S rank mission to kill Danzo and eliminate his entire root." Madara requested.
"Huh? Madara, I've been trying to disband root for the longest time. I cannot seem to do it." The hokage admitted shamefully.
"Trust me. give me a single day, and I'll have every root ninja brought to Ibiki. Also, I'll let you view Naruto's skills by having him kill Danzo." Madara said.
"I don't know about this... Danzo may be old, but he's still a force that won't be taken down easily." The hokage said nervously.
"And my Naruto doesn't go down without a fight." Madara shot back.
"Your Naruto?" Hiruzen asked with a slight smirk. This forced Madara to blush as she glared daggers. "I'm kidding. Alright, let's see what you two can do." Hiruzen said.
Namikaze Compound
Naruto was inside his parents house. As he looked around, the blond was unsure of what to feel. He was sad because his parents weren't alive, but he was happy to see they didn't abandon him like many of the villagers told him.
"Hello, Madara." Naruto said.
"Are you ready for your first misison?" asked the Uchiha.
"Yeah. What is it?" asked the blond.
"Your job is to kill and bring the head of Danzo Shimura. He's going to be a problem in the future. I just assume have him eliminated now." Madara declared.
"Okay. When?" Naruto asked.
"Now. I told the hokage we'd meet with him tonight." Madara said.
"No problem. I'm on it." Naruto said as he left the compound.
Danzo's Office
Danzo Shimura, the old war hawk. He was currently going through his plan to get both Naruto Namikaze and Mara Uchiha. He wasn't an idiot and cknew she had deep connections with Madara. "I wonder..." said Danzo as a kunai cut across his neck.
However, he appeared in the doorway while a particular blond was sitting in his chair. "So, Namikaze. What do I owe the pleasure of this visit?" asked Danzo.
"Well, I came here to originally kill you. But now, I'm curious. How and why do you have all those sharingans?" Asked Naruto.
"The village needs strength. As you know, Hiruzen has greatly weakend us." Danzo explained.
"I agree. But that doesn't answer my question." Naruto said emotionlessly. He gazed daggers at the olderman before him. Naruto learned about the Inazagi as it was how Madara survived her battle with Hashirama. "With ten sharingans, minus one. He can only survive death nine times. However, what if I cut the arm off?" Naruto thought.
"Why don't you and your girlfriend consider this offer? Join me and we can overthrow the hokage." Danzo declared. However, he qucikly found himself on the floor with his arm being no longer attached to his body. "What the hell? How did you do that?" asked the old war hawk.
"Madara taught me all about the Inazagi. I was just curious to see how fast your reactions were. The first attack was to try and kill you. I also marked your body as a way of insurance. Afterwards, I had a clone perform the Hiraishin and strike you with my Kaze Shuriken Barrage. I knew you'd perform the Inazagi again. However, I was curious to see if you could do it again. That answered my question. While you have the power to use it multiple times, you don't have the stamina as you once did." Naruto pointed out.
"You little bastard! I'm doing this for the greater good of the village! Hiruzen will only drag this village down!" Danzo spat at the blond.
"Oh, I agree. I'm planning on having Madara take over as Hokage. But now I'm interested in something. Lord first was the only known user of the wood release. How come you have it too?" asked Naruto.
"I was able to mix some of Hashirama's DNA within my body. Once I saw the conditions were right with one of my former ninja. I applied the same process and it worked out." Danzo said.
"Gaki, If you take some of his DNA, you may be able to have the same power as the first hokage." muttered Kurama
"No thanks. I rather use my own power. I don't even like using your power if I can help it." Naruto said.
"Who are you talking to?" asked Danzo.
"Oh, just Kurama. He told me if I took your DNA, I could have the power of the first hokage. While it would certainly benefit me greatly. I rather have pride and honor in using my own power." Naruto explained.
"Yet, you use the power of the fox, do you not?" asked Danzo.
"Only when absolutetly needed. Now, Danzo. This has been fun, but I need to report to the hokage's office with your head." Naruto said.
"Haha! You fool! By the time I die, this entire underground base will be obliterate and nothing else will survive!" Danzo said as he laughed at the blond.
"Then I guess I should take it now." Naruto said as he charged at Danzo. However, as he declared, a massive explosion occured and everything was about to be obliterated. Unfortunetly for the old war hawk, Madara used the Inazagi with one of her eyes and removed Danzo's head from his body.
"Damn it, Naruto. You costed me one of my eyes." Madara growled at him.
"Here you go. I snatched this one from him before everything. I was surprised to not have needed a genjutsu. He was so focused on killing me, he failed to realize that I had a clone take his arm." Naruto explained.
"Not bad. Not bad. I've gone ahead and eliminated root. It seems that our mission is done. Let's return to the hokage's office." Madara said as both Naruto and her left the underground base.
Hokage's Office
"Thank you, Naruto and Madara. Now that Danzo is gone, I can run this village without having to worry about him running around in the dark. As requested, Madara. You're being placed in the anbu black ops as its commander and chief. Your nickname will be Raven." Hiruzen said.
"Yes, Lord Hokage." Madara said.
"Naruto, you will be meeting Kakashi and your teamamtes at training field seven, at seven am." The hokage told the blond.
Naruto bowed. "Yes, Lord Hokage." Naruto said as he and Madara vanished in a Yellow Flash back to the Compound.
