Author's note:the Jutsu chosen by what is said to be taught in the academy
Two years later
Naruto Uchiha
Naruto was nervous for today, today was graduation and Naruto was nervous to take the exam. He had done pretty well on the physical parts like the weapons portion, but he had trouble with the writing portion. He however thinks he passed it. He HAD been studying for it with Mikoto. So now he had been ready now was time for his Jutsu test. He got nervous when Iruka said "Naruto Uchiha, you're up now" as he got up Hinata said "good luck Naruto" Naruto then gave her a thumbs up and went down to the front. Iruka then went down the list "Body replacement Jutsu" Naruto then did it and then Iruka nodded "Cloak of invisibility Jutsu" Naruto then turned invisible and back. Iruka then said "Transformation Jutsu" naruto then turned into Iruka and lastly he said "clone Jutsu" naruto then concentrated hard and made one clone. Iruka then nodded and said, "you pass". As Naruto went up to his seat Sasuke said "good job Brother." Naruto then smiled and said I hope you pass
Sundown.
Mizuki went up to Naruto before he left and said "hey Naruto can you do something for me, go and meet me near the Hokage tower with a scroll labeled the scroll of sealing and I will teach you a new technique. Naruto then said "ok meet you there" he left and Mizuki thought "this is easier than I expected.
Flashback
Mizuki went to Danzo's root headquarters, when he approached he said "Lord Danzo, what is it that you wish of me. Danzo responded "I want you to trick the Jinchuriki with your previous plan and then you will cause him to run rampant after you do this go to Orochimaru, he will have accommodations for you. Mizuki then said "how is it that I will be able to do this. Danzo the ordered him "come with me I have a gift for you"
End of flashback
Naruto had got the scroll and was waiting at the tree at the appointed time, Naruto was waiting for Mizuki when he thought to himself "well if I am going to be waiting for him I am going to start reading the scroll. "So the first one is called shadow clone, wonder if that is anything like the clone Jutsu, I hope it is easier to do, so the next one is called the eight trigrams seal, hey I am pretty sure I saw that before." Naruto thought "I think I saw that on my chest once before, or maybe I was imagining thing" Naruto then looked down the list and said "most of these are sealing jutsu, well better start quickly"
Elsewhere in Konoha
Fugaku had been wondering where Naruto had been when he heard that he had taken the scroll of sealing. Fugaku had been rushing around Konoha for he knew what might happen if Danzo was able to get his hand on Naruto. Fugaku met up with Itachi and told him "I believe Danzo may be using this to seize power, Itachi I want you to locate Naruto." Itachi replied I agree, this is too convenient to be a coincidence, I have asked Shisui to keep an eye on the edges of the village in case anyone is being sent in to take advantage of the situation." Fugaku then nodded and went their separate ways. Fugaku went towards the Hokage tower and went to Hiruzen. Fugaku said, "Hiruzen, what is the news on the search, have they been able to locate Naruto yet." Hiruzen then replied, "I do not believe they have, however it appears he has entered the forest around the Tower, you should go find him, let's pray it is a friend, for if he is found by someone unfamiliar you know what could happen." Fugaku then said, "that we both agree on." Fugaku then began to head towards the forest thinking "please be safe, and don't let him find you first."
Naruto
Naruto looked up and saw Mizuki looking at him and said "there you are Mizuki sensei, I was doing some of the techniques in this scroll, hey Mizuki sensei why are you covering one of you eyes" Naruto then grinned at the man who then responded with a twisted smile and said, "good you got it, this will then take the next step so much easier." Mizuki then removed the covering over one of his eyes revealing a transplanted Sharingan. Naruto then got up and was on edge. Naruto then in a very angry tone said "where did you get that, only the Uchiha clan, my clan has Sharingan, DID YOU TAKE IT FROM SOMEONE" Mizuki the laughed at him, saying "what scared little Naruto and I wouldn't exactly say you are an Uchiha." Mizuki then took the enlarged Shuriken off his back and threw it at the child. Naruto then jumped away to dodge the shuriken and said "what do you mean I am not an Uchiha, even if I am adopted Dad says I will always be his son. Mizuki then laughed at Naruto, he then said "oh please Fugaku doesn't care for you, you are just a tool for him, a political tool, for there is a secret in this village no one has told you. Naruto then yelled "OH YEAH WHAT IS IT, YOU BETTER TELL ME" Mizuki then ran towards him and kicked him in his chest and said, "you are the Nine-tailed foxes host, your it's Jinchuriki." Naruto then froze in fear and confusion Naruto then with utter terror in his eyes and in a scared tone "what, I am what" Mizuki then thought "yes, keep it up" Mizuki then said "your "father" Fugaku only let you live there because you are a Jinchuriki" Mizuki then transformed his transplanted Sharingan into a Mangekyo and turned it on Naruto. After this Naruto began to have orange chakra form around him. Mizuki then said, "well time for me to leave, with the scroll." Mizuki then went to grab the scroll when he saw Fugaku approaching. Mizuki then thought "if I try to escape with the scroll, they will pursue me more than if I am without" he then went towards the exits of the village.
Fugaku then got to Naruto with a two-tailed chakra cloak thinking "this is bad, if I don't get him out of this he may transform." Fugaku then used his Sharingan to reach Naruto.
Inside Naruto's head
Naruto looked around and said "hello, is anyone here, hey what is that cage for" Naruto the got a little closer to the cage and saw something in it Naruto then saw something in the cage and said, "Hey you in the cage are you the kyubi." The fox then looked at him and said "Yes I am, I have been watching you Naruto, you appear to be consuming my chakra now as we speak." Naruto then said "so, how do I stop that?" the Kyubi then said, "I cannot stop it, due to this prison made by your fourth Hokage, all I can do is let small bits of my chakra out at once." All of a sudden Fugaku appeared in this mindscape and said "Naruto there you are." Fugaku then looked and saw the nine-tailed fox in its cage and said "so your the kyubi everyone fears" the kyubi then responded, "your the Uchiha, that has been raising Naruto, your Sharingan are impressive, the last person who was able to do this was MADARA UCHIHA". Fugaku then said "hm, Naruto lets get out of here" Naruto then took his hand, and then Naruto saw he was back in the forest and saw Fugaku in front of him. Naruto then said, "Mizuki told me everything, he said that I am a Jinchuriki and he also said that you only adopted me because I am a jinchuriki, is that true." Fugaku then said to him "this is not how I wanted you to find out about this, what he said is partially true, yes it is true you are a Jinchuriki and yes I originally had taken you because of that I took you in and raised you, however, that is not how I see you today, I love just like I love Itachi and Sasuke, now come home, your mother misses you." Naruto then gave Fugaku a hug and said "I love you dad" after he let Fugaku said in a surprised tone "Naruto your eyes, they have transformed." Naruto then looked and saw they transformed into one Tomoe Sharingan. Naruto then in shock said "wow" he then smiled as they walked home
Danzo
Root headquarters
"So, it appears Mizuki has failed." Danzo told his subordinate, the root member then said "yes, and in addition, his escape was almost thwarted by Shisui." Danzo then said "call the Aburame and the Yamanaka, I want to speak with them. Danzo then began to think "this was supposed to be easy, Mizuki would get him to transform with the Mangekyo and he transforms and then I use that to isolate the Uchiha, it appears we may have to go with Orochimaru's plan." Then while he was thinking Torune Aburame and Fu Yamanaka appeared in front of him. Torune then said, "what is it that you want Lord Danzo." Danzo then said, "I have set it up so you two will be placed on the teams of the Uchiha boys, it will be your mission to observe and report back on those two." Fu then responded "it will be done, lord Danzo. The two root members then left the area. Danzo then went back to his room to see Kabuto waiting for him there. Danzo then said, "what is it that Orochimaru wants this time." Kabuto then smirked and said, "Oh I am here for your response, I believe and Lord Orochimaru believes it is time for you to make your final decision, will you assist us in the invasion or stay out of it." Danzo then responded, "I have decided that we will assist you in the invasion if it truly comes to pass." Kabuto then proceeds to leave by using the body flicker Jutsu.
Uchiha compound
Naruto had been home for a while so he decided to go to his father and ask him what had been worrying him since Mizuki had attacked him. Naruto then said, "Hey Dad, I wanted to know, do you know anything about my birth parents ." Fugaku then said, "Hiruzen would probably know more on the subject, however from what I've been told your mother was a member of the Uzumaki clan, they were famous for their fuinjutsu skills, in fact, many of the Jutsu on that scroll you had taken was from the Uzumaki clan." Naruto then responded, "wow, that's so cool do you know any Uzumaki, like do any of them live in the village." Fugaku responded by saying "they used to have a village of their own, however, it was destroyed in the last shinobi world war, many fled." Naruto then asked, "do you know anything else about them." Fugaku then said, "we know that they have extremely large chakra reserves and that many fled to the surrounding villages like the leaf and the grass village." Fugaku then continued by saying "I know about your father that he was of Uchiha ancestry, that Sharingan of yours is proof of that, I also believe that with the proper training due to the aforementioned chakra reserves you will be a great shinobi." Naruto then grinned saying "I will Dad, I will make you proud and I will honor my Uchiha and Uzumaki sides." Fugaku then said "now remember why we always wear our crest on our back" Naruto responded, "because we are proud and none can hide from the Sharingan."
if anyone wonders how what he wears is different than the main story is his jacket is dark blue and the back has the Uchiha symbol on it