The Neglected Genius

First Contact

A few years later, we find a 9 year old Naruto seated behind Tsunade's desk, going through some documents as Tsunade was training him in strength enhancement, patience, and even medical ninjutsu, something neither of them could believe was possible. The way they found out? Not one either of them like to remember...

*FLASHBACK*

A 7 year old Naruto was walking aimlessly through the streets of Konoha after another bitter moment at the Uzumaki-Namikaze Compound. During dinner, Minato, Kushina, and Menma were happily eating, unaware of missing family member from the table. As they talked, they heard the door to the compound opening and closing, causing them to become alarmed, because that seal only allowed those with the blood of the Uzumaki and Namikaze in. 

As Minato and Kushina reached for a kunai each always had prepared in case of an attack, they found guilt grasping their throats.

Walking through those doors, was one Naruto Uzumaki-Namikaze.

"Is something wrong?" Naruto asked, sensing his parents sending chakra to their hidden kunai.

"N-Naruto! Where were you!?" Kushina asked as anger settled in her, realizing Naruto hasn't been inside the house for who knows how long.

"I was at the Academy studying for our upcoming quiz..." Naruto informed them as he looked at the ground, feeling the animosity within Kushina's chakra, and slight disappointment coming from his father. For some reason, this was something he was able to sense ever since he was a toddler. He was aware of what people were feeling as well as their chakra levels, despite the attempt at hiding.

"How do we know you're not lying?! For all we know, you could've been out there pranking someone!" Kushina accused, not realizing what she was doing. Unknown to the both of them, there had been some seals placed on them both, making them express artificial feelings without their knowledge, as well as other seals that were serving their purpose constantly.

"I'm not! The one who pranks is Menma-"

"Don't try to blame your brother!" And just like that, another resounding slap, just like the one two years prior to this one, was given. And just like the first one, Naruto's cheek began to swell, redden, and ache, while Kushina's hand began to burn, releasing Kushina from the seal that had been placed on her while Minato's eyes widened at the occurrence. 

"N-Naruto! I'm so-" 

And just like last time, Naruto ran away from the compound, his destination? The Senju Compound, leading him to walking this path, with the thought that this had been the worse night of this life, unaware that something far worse was in store for him. 

Just as he rounded the corner to the Senju Compound, a strong hand had grasped his face, clogging his mouth to prevent him from screaming. The owner of said hand, a member of the Kurama clan, known for their powerful genjutsu, some said to cause actual damage in real life.

"So, here we have the little demon." The man whispered with a crazed look in his eyes.

"D-demon?" Naruto's muffled voice asked the man.

"Don't play dumb with me, demon. I saw what the Yondaime did to you, allowing you to take over this body. He wanted the fun of killing you all to himself, huh?" Asked the man.

Naruto had never felt such fear and dread in his life. Here was a man in a Jounin jacket, prepared to end his existence. However, he knew that the man was not going to go easy on him. No. This man was prepared to torture and kill him.

As such the man threw Naruto to an alley, head first into the wall, rendering Naruto unconscious.

When Naruto came to, he was standing in front of a red, glowing door, enticing him to approach and investigate just what it was. As such, his hand immediately grasped the handle and twisted as he pushed the door to enter.