A few years later in the village hidden in the leaves a new tragedy is in the makings . Itachi Uchiha the greatest and strongest Uchiha currently in existence is assigned a mission by Danzo to exterminate his entire clan and in return his brother Sasuke wont be harmed . Itachi after the death of his best friend Shisui Uchiha of the body flicker awakened the Mangenkyou Sharigan and has gained a level of mastery over it that would shock even Madara Uchiha . "I have no choice to protect Sasuke but I cant let this event cause Sasuke to sink into madness . I need to do some recon and examine Danzo's plans and see if theres some other way or am I doomed to destroy my clan" he thought . Later that night Itachi successfully locates a high level root anbu named Hyo and manages to put him under his control and extract the location of the anbu root bases and the file locations. Itachi changes into his anbu gear which is black pants,black combat boots,black shirt with light armour built into it before he leaves to find the information he needs .
Itachi using a mixture of Genjutsus and stealth manages to infiltrate the base and reach the files and what he finds shocks even him but he knows he cant do anything to Danzo without revealing what he did which could cause Danzo to go after Sasuke in revenge. The files show that Danzo has samples of Hirashima's cells and has a sample in a safe that will merge hirashima's cells and give him the mokuton plus allow him to implant Sharigans into his body without suffering ill effects. It also states that there will be several teams sent in to collect all sharigans after the massacre of the Uchiha Clan . "I must stop him and I have to protect the Sharigan and not allow him to gain the mokuton because with those abilitys Danzo could overthrow the hokage" . Itachi successfully manages to steal the sample of hirashimas cells but has to figure out what to do with it .
A few days later Itachi is assigned to watch the five year old Kyubi Jinchuriki Naruto Uzamaki who to his disgust is treated like utter trash by the village hidden in the leaves . Itachi has had to stop assignation attempts,beatings, and a multitude of other things the village has tried to do to the young Naruto . Unlike most people Itachi cares for the young Jinchuriki and knows the truth of Naruto's lineage and knows that Naruto is the only thing keeping the Kyubi contained . Itachi also knows once he has to leave things will get much worse for Naruto since very few people care for him and actually protect him from the village .'I think I know what I can do to protect the Sharigan ,Hirashima's sample and young Naruto but I will need the kyubi to cooperate with me at least to manage the implants on young Naruto" he thought carefully . Naruto look into my eyes and as Naruto looked Itachi put him asleep with Genjutsus and using the Mangenkyou entered the seal to speak with the Kyubi . As Itachi arrived in the seal the first thing he noticed was it looked like a sewer and had many different pipes running thru it with a giant cage in the back . He slowly approached the cage and Kyubi I need to speak to you . The Kyubi roared damn those accursed eyes you will not control me again I will kill you and tried to blast his way thru the cage but the seal held . Itachi spoke carefully to the Kyubi "Look I know you hate the Sharigan and everyone due to being trapped in this seal but I have found out that Danzo has bad plans for your container and if what master Jiraya said is true there is a group that is being formed to collect all the bijuu and they plan to seal them into a statue permanently . The kyubi says I don't care I will destroy all of them but Itachi plants subtle cues in the kyubi's mind and eventually the kyubi asks him why does he want to stop them from destroying him . Itachi replies I really don't care about you but I want to protect young naruto and the best way to do that is with your help . I have a plan Kyubi but I need your help to accomplish this and if you help you will have a strong young container that you can be proud of and with your help he can become the strongest ninja the world has ever seen before .The kyubi hesitantly agrees but says on one condition Itachi must fully reveal his plan to the Kyubi and as a means of trust reveals that the kyubis real name is Kurama and that the kyubi is a female . Kurama listens carefully as Itachi explains that soon he must destroy his own clan besides Sasuke and that Danzo wants sharingan and to have the Mokuton and that Itachi believes if the Kyubi will assist he can successfully implant the Sharigan and Mokuton into Naruto giving him two powerful blood lines plus give Sasuke someone to be friends with and to prevent sasuke from going to the dark side. The kyubi says all right I will help merge those but you must get the sharigans first before you implant the mokuton into naruto and I will merge both blood lines at once into Naruto .Hai itachi replies and exits the seal looking down at naruto " I may not be here for you much longer kid but at least this way you will be protected".Stay safe Naruto as he switches out places with his relief anbu.
A few days later its time for Itachi to destroy his clan and to protect naruto . Itachi carefully consults his map and equiptment one last time. He checks his suit to make sure no color can be seen and that his katana and kunai are sufficiently blackened and prays please don't let anything go wrong this is the only way I can save the village and Sasuke. As he leaves his hiding spot he senses a powerful presence and is shocked when a man warps out of no where and begins to talk to him . Young itachi so you accepted this mission your going to destroy that ungrateful clan who turned its back on the Great Madara ? Itachi replies who are you and how do you know? Itachi activates the mangenkyou and readies for battle but the masked man replies calm down I am Madara Uchiha and I will help you destroy the clan but in return you must join a group called Akutsuki . "Akutsuki that's the group Master Jiraya was talking about… I must accept and see what their plans are" he thought carefully . Madara I accept your help and I will join . Examine my map and these will show you where the patrols are and everything else . be here at this location in 5 minutes itachi orders.
Meanwhile at the Uchiha clan district almost everyone is in bed besides the patrols that guard the district and young Sasuke who is currently training in a distant training ground . The Uchiha coup was planned soon and everyone was staying low so not to draw attention to themselves .Everything was peaceful but not for long as Itachi approached the first Gate guard and quickly immobilized him with Genjutsu before slicing his neck . Madara appeared exactly where itachi told him and Itachi ordered leave my house to me but everyone else besides my brother is fair game . Madara replies we shall do it your way but form shadow clones we don't have much time before the village reacts . Madara and Itachi both produce 10 clones and the slaughter of the Uchiha begins . Unnoticed by Madara Itachi sends a clone to get Naruto and while they destroy the Uchiha clan the clone brings Naruto to a hideout and puts him in a deep sleep and prepares him for the sharingan implants and the Mokuton implant. Itachi's clan takes a few food pills before activating the Mangenkyou and telling the kyubi be ready before disappating . Meanwhile Itachi and Madara have successfully killed almost the entire clan besides Sasuke and his parents . Itachi orders Madara to wait for him at the valley of the end and to allow him to kill his parents his way . Madara says do whatever but be there by day light.
Itachi enters his house and notices complete silence and draws his Katana and enters each room till he locates his parents . His Mom and dad tells him that they knew and that they are proud of him for standing up for himself and that he needs to protect sasuke and that they were sorry . Itachi slashes his moms throat and notices that his dad eyes changed and quickly before his dad can utilize his new mangenkyou sharingan he slices his throat and kills his dad .Itachi quickly removes his dads Mangenkyou sharingan eyes .Then Itachi stands there crying because he just slaughtered his whole clan and his parents .Meanwhile Sasuke approaches the compound tired from his training where he finally completed the fireball release but quickly notices the guards body and enters the Uchiha compound at full speed and notices the bodies every where . Sasuke quickly enters his house yelling mom and dad and hearing no response enters their room and sees something the completely traumatizes him . He sees His big brother standing over his parents bodies holding a katana dripping blood off of it while crying . Sasuke asks Itachi why did you do this ? Itachi replies I needed to test my power to see how strong I was and tells sasuke your too weak for me to kill foolish little brother and begins to walk away . Sasuke's sharingan activates and he begins to chase itachi and throws a kunai and knocks off itachi's headband before Itachi grabs him and pokes him in the forehead before using Tsukuyomi to torture Sasuke with images of the clans destruction . Itachi says im sorry before using shunshin to Naruto.
Itachi quickly finishes the preparations for the implants and enters the seal and tells the kyubi get ready im about to put the implants in . The kyubi replies im ready do it quick and fast and I will merge them to young Naruto . Itachi first using medical Ninjutsu removes Naruto eyes and implants his dads Mangenkyou Sharigan's eyes into Naruto and then injects the Hirashama sample into Naruto . Meanwhile inside the seal the Kyubi begins pumping Chakra into Naruto and using its Chakra binds the Mokuton to Naruto's Dna and Then assimilates the Sharigan into Naruto's eyes . "Thinking quickly the Kyubi manages to turn Naruto's eyes back to blue and add a few modifications to the Sharigan and makes it so Naruto will have to unlock his sharingan before he activates it so that naruto will have to earn his abilitys" .The Kyubi says to himself I will have to keep these abilities secret so no one shall know . The kyubi finishes the merger and as it finishes a huge burst of power is released and a tree begins to grow around Naruto . Itachi sensing the power outburst looks on in surprise and flees before the sensor nin can get their because the power outburst was off the charts.
The 3rd hokage was in the office battling the greatest enemy of all hokages everywhere paperwork when he sensed a great outburst of power . Hiruzen quickly summons a guard of Anbu and tells them quickly secure the village and orders Kakashi and Yamato to accompany him to see what the outburst is . Hiruzen with his guards quickly locate the power outburst and break thru the tree to find Naruto unconscious . Hiruzen quickly removes Naruto and summons medical ninja to examine him and finds nothing wrong with him before he has him transported to his home and guarded by anbu while he tries to figure out whats going on . "I don't understand whats going on I sensed hirashima's chakra along with a sharingan presence emanating from Naruto.. I will have to have Jiraya and Kakashi investigate this to figure out whats going on" Hiruzen thought . Hiruzen returned to his office and dismissed his anbu as he pondered what happened tonight . A crow appeared and brought Hiruzen Itachi's report.
Hiruzen,
I successfully completed the mission Danzo assigned to me to destroy the entire Uchiha Clan besides my brother Sasuke . Please protect him from Danzo and watch over him . Also I transplanted with the Kyubi's help the Mokuton blood line and the sharingan into young Naruto so I could protect him even when I was gone . I'm sorry Hiruzen I tried to peacefully resolve this but it was the only way . If any thing ever happens to Sasuke I will reveal what happened tonight and who ordered this massacre and ordered the destruction of the Uchiha clan. Also I have a request Have naruto spend time with sasuke . I think they can be friends and rescue each other from their darkness and due to naruto's lineage and new abilities he will be a good rival for sasuke
Itachi Uchiha
Hiruzen quickly summoned the anbu and sent them to the Uchiha distract . As Hiruzen gazed on horrified at the bodies of women,men,and children that covered the district .His killing intent began to flare until even the closest Anbu were afraid . Hiruzen yelled to the Anbu bring Danzo to my office and the other counselors . A anbu approached Hiruzen and says we found one survivior . Hiruzen locates Sasuke and after sending him to the hospital for treatment shunshin's back to his office to punish Danzo and the counselors. Danzo begins to speak what have you before hes quickly shut up by the amount of killing intent Sarutobi is releasing. Every Shinobi and civilian in the village can feel the killing intent being released by Sarutobi . Hiruzen quickly reins in his intent when its silent and says I don't care what reason you had to do that but If you ever go against me again I will kill you and destroy every bit of your organization . Now get out of my sight before I kill you. Danzo quickly leaves . The 3rd then summons the village council and explains the Uchiha massacre and the effects it will have . He also announces Naruto has two bloodlines that will change the world . The civilian council quickly calls for the demons death because with two bloodlines like the mokuton and sharingan he could be unstoppable while the ninja council ponders the situation and begins to change their opionions of Naruto .The 3rd quickly tells the civilans to shut up or die and that the council is over .
Jutsus
Tsukyomi-one of the ultimate genjutsu of the Sharigan where the user can make time pass by however fast he wants to and do whatever he wants in it