I feel the need to state that IF there is a pairing at all in this story, it will not take place until the Shippuden timescale.
"I never go back on my word. That's my Nindo, my ninja way."
Everybody in the office aside from Legion whirled around to see none other than a slightly taller (about five two), slightly broader, Naruto Uzumaki standing in a black hooded robe similar to Legion's, but with the hood down. Two things were more different than the rest, though. One, His once cerulean blue eyes were now black with three glowing blue dots spinning slowly in a very Sharingan-esque manner.(1) Two, the mouth that was typically arranged in a goofy and lopsided grin, was now pressed into a stern, thin line reminiscent of Hyuuga Hiashi.
"Naruto? Is that you? How did you get in here?" asked Hiruzen.
"It is. The window was open." Naruto answered before turning to Jiraiya, "You... are an idiot."
A vein popped out on Jiraiya's head, before he calmed down and said, "Listen Naruto, I still don't know why you weren't able to summon a toad. What happened?"
"You dropped me into a pit half a mile deep and practically forced me to either conjure up the Kyuubi's chakra, or die. The demon is immortal. If he dies he simply reforms after a couple of years. He knew this. How do you think he reacted to the situation and my demands for his life-force?" Naruto asked sarcastically.
"I'm sorry, I didn't think the Kyuubi would choose to die rather than give you chakra." said Jiraiya solemnly.
Kakashi walked up to Naruto and asked, "What happened? Why are you so different? What are those eyes?"
"In order. One, I died." he and Kakashi both sent a glare at Jiraiya, "Two, only my brain remains of my original body, and even it has been extensively modified. Three, These eyes allow me to cycle between normal sight, infrared, and electromagnetic vision, which also allows me to see chakra and the flow of energy."
"What do you mean 'extensively modified'? Is there any of the real you left in there?" asked Jiraiya wearily.
"The 'real me', at least as you knew me, was a mask I put in place to hide from the pain of neglect when those who call themselves citizens of this village practically tortured me. People are more likely to cease beating a little boy when that little boy acts like one." said Naruto grimly. "But as you asked, my brain is significantly more refined and faster paced than the standard human brain, as well as having its two most powerful attributes, Telepathy and Telekinesis, unlocked and readily available for me to use."
"But Telekinesis is just a myth. Nobody in history has ever used it." said Jiraiya.
"You are wrong. Hagoromo Ootsutsuki, better known as the Rikudo Sennin, possessed this ability through the power of his eyes, the Rinnegan." said Naruto.
Everyone except for Legion were stunned. Naruto knew the name of the first, and most powerful, shinobi ever to exist? AND he knew about the power of the Rinnegan?
"Naruto, what you are saying is impossible," said Hiruzen, "There's no way to suddenly develop a power like that within the span of a couple days."
Naruto looked at a potted plant next to the old Hokage's desk. Raising his hand, the group watched in awe as the pot gently rose from the ground and floated up to the ceiling before coming back down with a light thud.
"Stop." commanded Legion, "No matter how much we tried, we couldn't seem to erase some of his habits that were unbecoming of a shinobi, such as showing off. His will was -IS- too strong."
Jiraiya stepped forward, "You mean to say you erased some of his personality? You fucking monsters, l'll kill you!" He was just about to launch forward with a full forced punch when he was stopped by none other than Naruto catching his hand, the muscles underneath his skin glowing a faint blue.
"I will not tolerate an attack on my friends, even from my godfather." stated Naruto flatly, "They tried to erase sections of my personality to help me survive in this cruel shinobi world. They were not able to affect it at all however, as my personality is very resilient."
Jiraiya was in shock. Naruto stopped that punch like it was nothing, but with how much force he put into the attack, Naruto's arm should have exploded from the pressure. Yet he held firm as if lecturing a child on a proper attack. Also, godfather? How did he know that? Jiraiya was just about to voice these questions when Naruto beat him to the punch.
"I did some research on myself while my mind floated through the largest information network ever to exist. They have tools that allow me to do studies on my DNA. I compared this to all the available DNA samples that the Hive had in their memory and i found a match.
"Imagine my surprise when I found that the DNA on my cells matches that of the Yondaime Hokage, Minato Namikaze. Who also shared half of his DNA with the Nidaime Hokage, Tobirama Senju."