Meanwhile, at Naruto's home...
The night went through as normal as everyday. Naruto finished his meal as he finished the bowl of Miso soup. He then did the dishes for a moment, and continued training at the basement. To most of the villagers, Naruto was still in his apartment. But little did they know, Naruto was already inside his true home that he had discovered eight months ago. Back then, the Hokage was still inside a meeting that Danzo set up to handle the situation with the Kurama clan. Naruto entered the Hokage's office to find no one, so he tried finding the allowance that Hiruzen was supposed to give him. He searched everywhere. Then, when he opened the safe behind the Fourth Hokage's picture, he discovered a letter, three scrolls and a Flying Thunder God Kunai in it. The moment Naruto looked through the letter, he couldn't believe it: turned out, the Fourth Hokage was his father, and his whole legacy was kept hidden away from him. Not to mention, the letter also mentioned of an older sister, but for some reason she wasn't seen in the village. So Naruto quickly took the scrolls, the letter, and used the kunai to teleport back to the Namikaze compound. From that day, Naruto lived three lives: a quiet boy to the village, a brother to Yakumo and Sai, and a kid secretly learning Fuinjutsu inside his family's compound. Which lead us to the present, where a seal he set up that he didn't want to be triggered, has just triggered. He heard every single word, from Sai's report about him, to Danzo's order.
"No..." Naruto crouched down as tears started filling his eyes.
The cold stone floor of the basement felt unnaturally heavy under his trembling hands. A single, silent tear broke free, splashing into a faint, glowing seal drawn on the wooden floorboard in front of him.
It was a specialized eavesdropping tag-a sophisticated branch of Namikaze-style Fuinjutsu that he had spent months perfecting from his father's scrolls, linked directly to a subtle ink mark he had placed on Sai's collar. He had built it to protect Sai, to give them an early warning system if Danzo ever tried to hurt him.
Instead, he had just listened to his best friend's mind being completely erased.
"Kid, I'm so sorry." Kurama sighed. "But just sitting here won't solve any problems. What are you gonna do?"
Then, slowly, he stood up.
Naruto: "You want to play in the dark, Danzo? Fine, let's play."
In the next couple of weeks, the tension had risen amongst the group. Sai's expression had become, faker, which instantly caught even Yakumo's attention. And his fighting style, despite having improvements that Naruto helped building, still had some mechanical in it.
So one day, as they were alone, Yakumo brought Naruto to a corner, and asked. "Naruto, what happened to Sai? He isn't like the ones we know recently, he is more like the Sai we first met. What happened to him?"
Naruto stood in the shadow of the tall pine tree, his arms crossed over his dark shirt. He looked toward the clearing where Sai was practicing his ink techniques-his movements clean, precise, but completely devoid of the quiet warmth he had slowly built over the past year.
"Danzo found out," Naruto said quietly, his voice dangerously calm. "He used a high-level Genjutsu on him weeks ago. Overwrote his mind. Right now, Sai thinks he's playing me, waiting for Danzo's command to strike me in the back."
Yakumo gasped, her hand flying to her mouth as her eyes widened in horror. Her chakra spiked violently for a fraction of a second, the air around them growing cold as dark illusions flickered at the edges of the clearing.
"No..." Yakumo whispered, her voice trembling with rage and heartbreak. "That monster... after everything Sai did to break free? What do we do, Naruto? Can't we break the Genjutsu with my kekkei genkai? I can dive into his mind, I can-"
"No." Naruto interrupted softly, placing a firm, steady hand on her shoulder. His touch instantly grounded her, smoothing out her chaotic chakra. "If we force our way into his mind right now, Danzo will know instantly. The seal on Sai's tongue and the mind-control tag in his brain will kill him before we can even undo the damage. We have to play along."
Yakumo: "Then, what are we gonna do?"
Naruto: "For now, you don't do anything suspicious in front of Sai. I will handle the rest. Got it?"
Yakumo nodded.
After the day was over, Naruto instantly made his way. Sai was about to follow him, but...
"Sai?"
The black haired kid turned to see Yakumo behind him.
Sai: "Oh, Yakumo, is something wrong?" 
"Nothing, I just want some ice-cream, that's all." Yakumo said as she tried keeping her composure, avoid any suspicions.
"Oh, okay." Sai sighed. He wanted to follow Naruto, to see what he was up to. But then again, he didn't want Yakumo to gain suspicious on him. As far as he knew, she still didn't suspect a thing.
Meanwhile, with Naruto...
Naruto made his move quietly towards the Hokage's office, only to find it empty.
"Okay, the coast is clear." Kurama sighed inside Naruto's mind. "But what exactly are we doing here anyway?"
Naruto: (in thought) "The Hokage is the closest to Danzo. If anyone has any clues that can help us taking down Danzo, it's him."
"Okay, then." Kurama sighed. "Just don't come to me when things get out of hand."
Naruto then began searching across the entire archive. He even looked behind the Sandaime's picture, but there was nothing. Until...
"Let's see the safe." Naruto cracked it,  and eventually found a key. "Why is he keeping a key here?"
Kurama: "It the key to the forbidden section in the archive room."
"What did you say?" Naruto's eyes widened.
Kurama: "Yeah, your mother used to be the advisor for your father. They discovered the key, and many nasty stuff that old man hid from the public."
"Let's see where this leads to then." Naruto then left the room in a blur. Later...
The forbidden area was dark, like its secrets was about to swallow a person whole. As Naruto walked through the documents, there was a sudden force that pulled him back.
Naruto: (in thought) "What, Kurama?"
"Look to your left, kid." Kurama sighed. Naruto did so, and froze.
"The Uchiha clan?" Naruto muttered in confusion. He slowly opened the files, and froze at what he found. It appeared that the Hokage and Danzo sent a shinobi named Itachi Uchiha to spy on his own family, and massacred his own family to maintain peace for Konoha when the Uchiha planned a coup. There was another file, containing the information of Danzo eliminating Shisui Uchiha after hearing his peaceful solution, saying he was too emotionally attached.
"They wanted fairness, and justice." Naruto narrowed his eyes at the thought. "And they got silenced the moment they tried to ask for it."
"There's more, kid." Kurama then turned Naruto's head to another corner after Naruto sealing all the evidence into a package scroll.
Naruto froze at the section's name.
Namikaze
His own family.
Naruto checked through the files.
"So that's why..." Naruto clenched the scroll tightly as he read the content. It was about a red-haired young kunoichi named Koyuki Namikaze, and the conditionings that Roots applied on her.
"Nee-chan...that's why you're not in the village." Naruto muttered with a breaking voice. Then, he looked at another file. It was the record of his birth. But according to the record, he wasn't born alone.
"T-triplets?" Naruto muttered.
Kurama: "I forgot to tell you: it was very chaotic that night. Sorry."
Then, he looked at the files to found out that they were separated after the Kyubi's incident. His big brother, Ashuto, got handed to the one responsible for the Kyubi's attack. And his little brother, Djin, was given by Orochimaru. And it all thanks to one name.
"Danzo." Naruto clenched his fist. And then, he discovered a secret cloning program from his parents DNA. "Damn you..."
At that moment, he suddenly heard footsteps occurring. So he instantly packed all the evidence, and used Flying Thunder God to escape back to the Namikaze compound. The moment someone reached the section, there was nobody left. But...
"Some of the scrolls are missing." Danzo commented as he looked around. And then...
"ROOTS!" He shouted as he realized which scrolls were missing.
At that moment, multiple Root Operatives landed in front of him.
"The Kyubi has committed treason. Bring Yakumo Kurama to me at once. We need to do every measure possible to eliminate Naruto Uzumaki, am I clear?"
With that, the Root Anbu squad vanished with swifts of Shunshin.
"Naruto Uzumaki." Danzo narrowed his eyes. "You think that you have won? I will show you the consequences of messing with the shadows of Konoha!"