Naruto, the Hidden Genius of the Leaf

Hello world! I'm back with a new story that after reading one where Naruto had over time managed to gain knowledge on all the clans, I don't remember much else besides that as of this writing. I liked the idea so much that I wanted to have a go at it myself

A couple of notes before we start however-

There will be bashing of certain characters, some more so than others

Naruto is smarter than in cannon and knows a lot more jutsus at the start as well

Naruto doesn't have the rinneagan, nor any elemental bloodlines

Naruto has Wind, Water and Fire Natures

The Kyuubi is good and helps Naruto

Kakashi is a better teacher than cannon

Naruto gains kitsune powers eventually

Naruto x Hintata as all of my Naruto fanfics will be at some point or another

Hinata is slightly stronger at the start thanks to Naruto actually noticing her and helping her

May gain the Sharingan at some point

And many more surprises to come!

Chapter 1

Twelve years ago a great tragedy befell the great village of Kohonagakure, or better known as the Village hidden in the Leaves. What was this tragedy? Simple, the Nine Tailed Demon Fox suddenly appeared and attacked the village in a rage. However this came as a shock to some as they knew that the fox was sealed away in Kushina Uzumaki and that the fox wasn't was evil as everyone thought it was, so for it to suddenly show up and start attacking in a rage was rather suspect and a source of worry for Kushina's condition as well as those that were with her

And worry they should for shortly after Kushina gave birth to her and her husband Minato Namikaze, otherwise known as the Yellow Flash and the Fourth Hokage's first son Naruto Uzumaki Namikaze a strange man in a orange spiral mask appeared and killed everyone else and managed to separate Minato from his wife by taking Naruto hostage. This allowed the man to forcefully remove the Kyuubi from Kushina, however the Kyuubi knew what was going to wind up happening due to this and quickly sent a message out to the realm of the summoning foxes to relay what's going on to the monkeys, turtles, dogs, toads and any other summons that Konoha uses in hopes of making things better for Naruto after everything blew over

Not that the Kyuubi minded being sealed into the poor boy as while Minato and Kushina were working on a plan to safely free the Kyuubi as he wasn't a threat to Kohona and was going to go live in the summoning realm and run the fox clan

That's not to say the Kyuubi didn't do his best in fighting against the mind control and tried to break free, he did, but who ever the man was knew exactly how to control a tailed beast effectively. Something that bothered the Kyuubi greatly as only very few people have ever managed to succeed in controlling a tailed beast, let alone him. Only Mandra Uchiha being the first to ever fully control him, and he died some years later as the last person to know how to truly control a tailed beast, so how did this person know how to control him was confusing and frustrating

The noble ninja of Kohona knew non of this as they valiantly defended their home from the mind controlled fox. By the the time Minato got Naruto ready for the regrettable sealing that he was about to do on him, nearly half of the village's forces were wiped out. Of course the Kyuubi used the situation to his advantage to take out Danzo and his Root with a massive Tailed Beast Blast, Minato noticed where the Kyuubi was aiming and let him fire his attack. To everyone else that didn't know about Root or where it's base was located only saw the Kyuubi blow out a massive hole into the side of the mountain right next to the Hokage Mountain

Danzo didn't know what hit him as he was vaporized along with his ambitions and schemes. He was not missed

After the Kyuubi fired it's attack Minato used the short recharge time to teleport the Kyuubi away from the village and to where Naruto was to preform the sealing, knowing that due to circumstances it would cost him his life. Minato hoped that Kushina would make it so that Naruto wasn't alone in the world

"Forgive my son" Minato told Naruto as he flew threw the handseals needed for the sealing

As soon as he was done Minato shouted "Reaper Death Seal!" summoning the shimigami, or the death god, who started pulling the Kyuubi's soul into Naruto, breaking the control the masked man had on him

"Minato, I wish that things didn't have to come to this" apologized the Kyuubi as he was being sucked into Naruto

"I... know... I only wish... is that the villagers see Naruto for who he is... and not a monster... for having you sealed into him" said Minato with heavy breaths

"I can't guarantee that he'll stay fully human due to me being sealed into him so soon after he was born" said the Kyuubi

"Any child that is born to a biju's female container will have a high amount of their energy in them, but it'll fade away by the time they can walk and talk. However if that child is around other demons or has that same biju sealed into them there is a good chance that they'll become a half demon" explained the Kyuubi after seeing Minato's horror struck face

Soon the sealing was done and the death god took Minato's soul with him, but a higher power forced him to let Minato go to the pure world as they knew about a certain event that was going to happen within the next two decades

The Third Hokage, Sarutobi Hiruzen arrived to scene shortly to find Naruto crying on the alter that Minato summoned to preform the sealing on as well as Minato's fallen body

"Hush now Naruto, everything will be alright" soothed Sarutobi as he picked up the poor babe

"ANBU please bring the Fourth's body with" said Sarutobi "And see if you can find out what happened to cause this to happen"

"I can't believe he's gone" said Inu, one of the ANBU that was there

"Tell me have you found Kushina?" asked Sarutobi

"Yes, she's with Jiraiya and Tsunade at the moment" replied Inu "However I don't know how well she is currently"

"That's good to know, hopefully she'll pull through" said Sarutobi "Now lets move out

Hiruzen Sarutobi soon got himself ready for the emergency council meeting, after conferring with the Fire Dynamo, who just so happened to be in the village during the attack, beforehand to make sure that the council didn't try anything funny like take more power than they should have

"Alright, lets get to business" said Hiruzen as he entered the room carrying a sleeping Naruto in his arms

"Is that the demon container?" asked one of the civilian counselors

"Indeed he is" started Hiruzen

"Then kill it! And finish what the Forth started!" yelled the counselor

All of the civilian and some of the shinobi counselors agreed loudly as well, how Naruto slept through it all the Third had no idea

"Silence!" roared Hiruzen as he let out a large amount of his KI out at the counsel, making them shut up

"If I may Lord Third, just who is the child, and who are his parents?" asked Hiashi Hyuga, head of the Hyuga clan

"His name is Naruto" replied Hiruzen "And he is the son of Minato and Kushina"

"Where is Kushina? I saw Minato's body on the way in, but didn't see her anywhere" asked Tsume Inuzuka, head of the Inuzuka clan

"With my apprentice currently as she is currently in a coma" answered Tsunade who was worried for both Naruto and Kushina

"Any idea when she'll awaken?" asked Tsume

"Sadly no" replied Tsunade

"You're not planing on leaving after this are you?" asked one of the counselors

"I am, I only came back for Kushina and make sure Naruto was healthy" answered Tsunade "But I'm going to take her with me as I don't trust anyone but me to take care of her"

"But what about Naruto?" asked Hiruzen "He's going to want his mother when he finds out her condition if she doesn't wake soon"

"That's a good point sensei, I guess until he's old enough have him grow up in the apartment complex that the Uzumaki's own and when he asks about his parents tell him that his mother is still alive, but is in a coma at the time and that is why she's not around" suggested Tsunade

"I'll stay for the first year or so, before heading back out to the field" added Jiraiya "Just to make sure he's properly taken care of, I am his godfather after all"

"You better not try to turn him into a pervert Jiraiya" threatened Tusnade

"Kushnia would kill me, or worse if I did that!" exclaimed Jiraiya as he paled just thinking about what she would do to him for turning her sun into a pervert

"Alright, until Naruto comes of age or Kushina wakes up Naruto will be raised in the Uzumaki Apartments" said Hiruzen "Further more no one is to speak about Naruto having the Kyuubi sealed into him or his parentage under penalty of death. We don't want our enemies to know what became of the Kyuubi or Minato's enemies trying to kill Naruto for being his son"

"Also NO harm is to come to Naruto, physical or mental, doing so will result in sever punishment" warned Hiruzen

"Now lets move on to assessing the damages and counting the dead" said Hiruzen

"Well here's your home for the foreseeable future Naruto" said Jiraiya as he arrived at the Uzumaki Apartments

The Uzumaki Apartments are two five story buildings that are towards the center of Kohona (Leaf) that were at right angles to each other on a street corner. Both were white with oak wood frames and low wall separating the grounds from the road with the gate having the Uzumaki swirl over the entrance. The second building was further back with the entrance of the building lining up to the wall of the main one.

When the people who lived in the buildings heard that Naruto was going to live there almost all of them moved out saying that they don't want to live with the demon container. Much to Jiraiya's ire, though there wasn't anything he could do about it, as he was hoping for Naruto to make friends with the children that lived there

"Well since Naruto owns this place what ever he wants to do with the extra rooms is up to him" noted Jiraiya "I should probably set up my own room at some point for when I'm in town seeing how my apartment was destroyed in the attack"

"With all my research!" cried Jiraiya as he crumpled to his knees and began anime crying while still holding Naruto in his arms

Well that's it for now hope you liked it. Know of any Jutus please let me know as it'll be a big help as Naruto will slowly gather a large number of jutus from all the clans. That said I'm going to add three original clans picked from your suggestions!

Here are some rules about those suggestions-

First I want to know their specialty, what type of jutus they use

Second how do they feel about Naruto, do they hate him or not

Third I want some names of the clan members and a little of their personality traits