I do not own Naruto, this is a fan fiction.
I gave plenty of warning, so by popular demand here is my promised story, enjoy.
Ten years before the end of the third shinobi world war, a crime was commited a crime that to the man who did the evil deed, wished it would never come to light. Minato Namikaze so named because the head of the Senju clan refused to accept that he was in fact his illegitimate son. The clan head even went as far as falsely accusing Minato's mother of treason and causing her to be executed. Mjnato grew in the poorest of orphanages, and then through great difficulty he became the strongest of ninja field commanders.
This bring us to his own crime. In the dead of night he sneaked into the tent of one Mikoto Uchiha, wife of his own executive officer Fugaku Uchiha. Their he did something that later he would wish he had not done. While being just recently married to Kushina Uzumaki. He brutally and with no hesitation raped Mikoto, every night that she was stationed at his camp. She was only removed from the front lines when it came to light that she was in fact pregnant. Fugaku was probably the happiest man alive when he found out.
Seeing her husband so happy she decided to never reveal the truth, the truth that Minato was the father of the child she now carried. Nine months later Mikoto gave birth not to one child but twins. Fugaku named the youngest Itachi and Mikoto having been reading a book by the toad sage, Jiraiya named the eldest of the twins Naruto after the main character of the book.
The twins were stronger than Fugaku could ever imagine. They both did what was considered impossible. Having activated their eyes at the age of five, they mastered their elements. Itachi mastered his lightning element and Naruto mastered his wind, lightning and fire element. Even being able to summon the dark flame of their clan. In a matter of seven years they both graduated from the academy with honors. Having such amazing abilities the two were sent to join the elite of the elites, the were both ordered to join ANBU.
The brothers would do many of the most difficult and most dangerous missions during the war. They both became captains of their own ANBU teams. Itachi wore the weasel mask for he liked to do sabotage missions more than any other. Naruto wore the jackal since he loved to do assassination missions more than anything. As the war came to and end the two did what two bored young men did. They trained to become stronger each and every day.
They first did this out of sheer boredom true, but they had another reason. They both hated how lazy and egotistical their clan had become thanks to the belief that their eyes made them invincible and worthy of worship. They both consider these supposed clan members little more than garbage. "Brother are you not sick and tired of seeing how pathetic our once powerful clan has become!?" Naruto looked at his brother and glared at the clan district. "Indeed I am, brother. But the second we get permission we will cleanse our clan and make it what it should have been all along."
Seven years after the war and the brothers continued to do the same boring missions, and continued to train till they could barely make it home. One a warm day they were told that their mother had been pregnant all along, and that she was about to give birth. Fugaku ordered the twins to help her move to the hospital, which they did.
As it turned out, Kushina also was giving birth to Minato's child. Kushina had a healthy baby boy who she named Menma. She loved that ingredient in her ramen it seems. Mikoto also had a boy and she named him Sasuke. The two brother happily greeted their little brother. They hoped that he would follow in their example, but not all hopes become reality. Sasuke liked to play with flowers, ribbons and dolls more than training. To make matters worse his favorite color was bright pink.
The two brothers began to call him their little sister. "Give me a break!? Even Orochimaru, that filthy traitor, hid his sexual preferences better than Sasuke!?" Naruto clearly was very upset at seeing how feminine his little brother was. "What is even worse he does not train and father tells him he does not even nerd to, because his eyes made him all powerful. I swear if I have to listen to that drivel one more time, I am going to lose my lunch!?" Itachi was very upset how Fugaku was not training him properly.
Danzo had at long last found the two that would be key in his plans. He asked them to meet in private at a local bar. "So nice for you to come, weasel, jackal. I can tell you hate how much our once powerful clan has become so weak. I am going to cut to the chase, the Hokage has ordered me to find two capable men and spy on the secret meeting your father is having. I think you two are perfect for this mission."
Itachi accepted out a sense of duty, but Naruto knew there was more to this mission. "So what is the pay?" Danzo looked rather shocked that Jackal would even ask for money. "Look old man, it is true we are not happy about what our clan has become, but if you think we are going to spy on our own clan and do it for free, think again!? When the shit hits the fan we will more than likely will have to run, and we will need the money. So pay up or shut up!?"
Danzo flat out called jackal a killer for hire, he even said that he was as bad as the bounty hunter Kazuku. Naruto smiled and thanked him for such high praise. In the end he did decide to pay them five times the pay for an S rank mission. When they both agreed Itachi looked at his brother with a glare. Danzo is the right hand man of the Hokage, why did you have to be so disrespectful!?" Naruto glared right back. "Because the old man already knows what our dear father is up to and is just using us to do his dirty work!? If I am going to be treated as a thug, I want it to be a well paid one!?"
The two brothers did the mission even if they complained and argued while doing it. In the end they learned that Fugaku wanted to kill the Hokage, and take the position for himself. When they reported the mission to Danzo, he indeed gave Jackal the money in a storage scroll. He even told them that he double it if they killed all the members of their clan. Itachi told him to keep his money. He told him they would do it, if he promised that no harm would come to Sasuke! Naruto as much as he liked the money, had to admit Sasuke was innocent.
As the two were getting ready to do the mission and escaping the village. They both met with a strangely masked man. He introduced himself as Madara Uchiha. They both told him that was impossible, Madara's death was well know fact. He died fighting the first Hokage at the valley that was now called the valley of the end. Masada told them it was a lie, that his own clan betrayed him and that it took years for him to recover enough to get his revenge.
"What is in it for us?" Madara laughed as he heard Naruto ask.. "Power, money, and fame. Once you two boys finish your killing of your clan, you will need a safe haven, a place to earn a living, and a place to accomplish great and magnificent deeds. I am forming a group that you two would feel right at home."
They both agreed if he told them how to unlock the next stage of their eyes. Madara laughed like a maniac. "Oh, that is as simple as breathing. You just have to kill the person most precious to you!" With that Madara vanished and left the two brothers to decided. Naruto would kill Mikoto, and Itachi would kill Fugaku. With the use of the shadow clone jutsu they sent 20 shadow clones to slaughter their clan. Naruto and Itachi went yo kill their parents themselves, it was a rather personal thing after all.
Sasuke saw as his brothers killed the Uchiha guards outside their home, and how Naruto cut Mikoto's head off with his Katanga,and Itachi stabbed his father through his heart. He then saw them cut out their parents eyes and place them in a jars in a strange liquid. Their parents had awakened the magenkyou sharingan during the last war after all. "Brothers why are you killing our clan!? Our family!?" Naruto walked over to him and smiled a rather sinister smile. "Foolish little sister, we are just taking out the garbage, now don't you worry you pretty little head. You are the last one we have to kill."
Sasuke tried to run but Naruto was quicker thanks to his training, he hit Sasuke hard and knocked him out. Leaving him right next to the bodies of their dead parents. "I knew you could not kill him, you loved our precious little sister so much." Naruto told him he was no better, to stop wasting time. They both left th village and that is how Sasuke became the last Uchiha in the village and how the journey of the twins brothers infamy began.
As the two brother left the village,Madara attacked the Hokage's home. He killed Kushina causing the Kyuubi to be released. He placed th fox in a genjustu of the village killing her children over and over again. This made the fox go mad with rage and attacked the village. Madara figured that this was the perfect distraction to allow the twins to reach the agreed upon meeting place. If the fox destroyed the village well that would be a nice bonus. Minato tried his best to reason with the fox, but the fox was simply so mad that she was not able to listen to reason.
With the help of the third Hokage they managed to seal the fox in Menma, but at the cost of his own life. His last dying words was that he be forgiven for all the wrong he did, and that his son should be treated as the hero he was. The trauma of having the fox sealed inside him caused Menma to forget his parents, his life with his family, even the two Uchiha twins that he loved as his own brothers. Menma was placed in an orphanage, he was not alone though, the fox's attack caused many children to lose their parents and they all hated the fox for doing so, all except Menma who did not even remember having the fox sealed inside himself.
The twins finally reached the cave, and Madara was waiting for them. He told them he had to hideu his true identity and pretend to act like an immature crazy person that went under the name of Tobi. He placed his orange swirl mask to hide all but one eye. He took a deep breath and got into character. "Okey dokey, just follow Tobi! Okay!?" The twins felt like he should receive an award for his acting skills, but he followed him none the less.
"OK, we got our boss god Pain, and his priestess Konan. Next we have the blonde with the mouth on his hands, Deidara. I forget what he does. Oh well. Then we have the zombie duo, Hidan and Kazuku. Don't ask Hidan about his religion or we will hear about it all week, and nobody wants that. As long as they pay him. Kazuku will kill anyone and anything." Itachi decided to interrupt and smiled at Naruto. "See brother coming to his freak show was not so bad after all. You finally met a man after your own heart. He loves getting paid just like you."
Naruto glared at Itachi, " And don't think I forgot your loan. You better pay up or my interest rates will eat you up!?" Kazuku laughed and asked what was the interest rate on the loan? "650% I took it down form my usual 700% he is my brother, I had to give him a discount." Kazuku hold him in a rather tight hug. "I think your brother is right, we will get along just fine. Put it there brother!" Tobi continued his introduction.
"This is Sasori, he loves to play with his dolls. And finally we have the great big white, the man that looks like he was the lovechild of a shark, likes to bite and so does his sword. And I am Tobi, so you got question for Tobi!?No!?okey dokey." Pain decided to welcome them by presenting each with a ring and told them in which finger to placed them and to never removed them. Itachi and Naruto did as they were told. They were given a pair of cloaks by Konan but was seen blushing when Naruto whispered something in her ear.
Itachi pulled his brother to the side, and demanded to know what he said to her. "Just told her she was a hot looking woman, and that if she wanted to have some fun to just call me." Itachi could not believe he was hitting on her when they just met. "Hey, you only gay brother is back in Konoha, I see a beautiful woman like her I am not wasting time and letting someone else get her before me!?" Pain could see that he was going to have many headaches in th future.