Plot: Throwing caution to the wind always has consequences. Unfortunately, Naruto doesn't learn this until he is hurled 25 years backwards in time. Time Travel. Rated M for later chapters. Spoilers up to Naruto chapter 535.
Pairing: Naruto/Mikoto.
Prologue
With pure determination in his eyes, Naruto leapt from tree branch to tree branch.
Though he was not using the Nine-Tails Chakra Mode or Sage Mode at that time, he knew exactly where he needed to head to in order to get off of the island where he had been training with Killer Bee.
'I can't believe Granny Tsunade tried to keep me there.' Naruto thought as he glanced down at the note that he held in his left hand. It had been slipped under the metal plate of his forehead protector by Iruka after it had fallen off.
"I'll end this war myself." Naruto promised himself in a whisper.
"Will you, now?"
As soon as the foreign words were spoken, Naruto stopped himself and entered his Nine-Tails Chakra Mode. The instant that he did, he sensed a malevolent chakra that Kisame's paled in comparison to.
Spinning around, Naruto spoke the name of the man before him. "Madara Uchiha." He involuntarily snarled the moment after he spoke the man's name. He saw the change in appearance. More specifically, he saw the Rinnegan in Madara's formerly covered eye.
"Oh, do you like it? I decided to take back what's mine." Madara said with a chuckle. "That's actually what I'm doing now. You contain my old pet, and I'd like it back."
"Fuck you." Naruto said as he dashed forward with the incredible speed that he possessed in that form.
Madara looked slightly amused at the attacking Naruto. That did not put the blond on guard as much as the spinning sharingan in Madara's eye.
In an instant, Naruto's chakra cloak dissipated and Madara held out a hand.
"Shinra Tensei"
'Shit!' Naruto thought, feeling the sudden lack of power in addition to the gravitational powers of the Rinnegan.
He flew back and slammed into a tree before he could process another thought.
As he slid to the branch under the spot that he impacted upon, Naruto heard Madara speak again.
"Really? What would possess you to use my pet's power against me? Weren't you aware that I could completely control it? Maybe you thought that I could only control it and not its power… oh well." Madara said with a nonchalant shrug. "I must thank you for getting out of whatever chakra isolation chamber you were in. I was incapable of finding you until about ten minutes ago. And now, I know where the Eight-Tails is also. It must be nice to know that you undermined the efforts of the entire shinobi world to protect you. It turns out that I won't even have to get involved in the war after all. All I have to do is go to the location where I first sensed you at, and I can get the Eight-Tails. Take comfort in the knowledge that you will live a little longer. I have to seal the Eight-Tails before the Nine-Tails, so you'll have five days left to live. No more… no less."
Naruto's eyes suddenly opened, revealing that they were yellow and shaped like the eyes of a toad.
'I saw that in Zetsu's recording. That's Sage Mode.' Madara thought.
In a matter of seconds, Naruto had a Rasenshuriken in his hand and threw it at Madara.
Madara's eyes narrowed a fraction as he saw the attack. He knew what it could do. Thus, he simple used Shinra Tensei to dissipate the Rasenshuriken.
"So, you're still going to try to fight." Madara said as Naruto dashed towards him with a hand held back.
Madara knew that he could not use Shinra Tensei on Naruto again at that moment. Nagato may have had a five second delay between uses, but Madara had only had the Rinnegan for a few days. As a result, Madara's delay was closer to fifteen seconds.
Madara was by no means defenseless though.
"I'll let you cool off." Madara said as he began to use his Space-Time Migration Technique.
The sensation of spinning in on himself had Naruto disoriented, but his determination to defeat the elder Uchiha was still present.
"I don't think so." Naruto said as he fought against the Uchiha's power with every fiber of his being.
Something unlocked within Naruto as he fought against the power that was trying to teleport him. The feeling of the power unlocking caused Naruto to close his eyes for a brief moment.
When he opened his eyes, Madara gasped in shock.
No longer were toad-like eyes in Naruto's eye sockets. Instead, his pupils were crimson with black shuriken-like emblems in them.
'That's Itachi's Mangekyo… but how?' Madara thought in shock.
"I won't give up!" Naruto yelled as the new power flowed threw him.
Naruto had never been a very intelligent person. If he had, he might have considered the possible consequences of using his own power, natural energy, and the new power within him to fight against Madara's power. The conflicting powers, combined with the fact that one of them was a space-time ninjutsu, could only spell trouble.
With the Rinnegan and Sharingan, Madara was able to tell that something bad was about to happen. Thus, he cut off his Space-Time Migration Technique and focused all of his efforts on becoming intangible.
Madara barely managed to do so before a massive explosion radiated from the exact spot where Naruto stood.
When the dust cleared, Madara found that he was standing in a crater that one of the large toad summons could have sat in comfortably.
Madara's eyes widened further as he regained tangibility and found that he could not sense Naruto anymore. He couldn't sense any trace of the Nine-Tails chakra either.
All that was left in the crater, other than Madara, was the metal plate of a Leaf forehead protector.
For the first time in many decades, Madara found that he had no idea what to make of the situation and even less of an idea as to what his next move should have been.
'I should have had Zetsu record this.' Madara thought as he teleported away. 'I was foolish to send him to watch the Eight-Tails.'
No one would ever learn what happened to Naruto… not in that timeline, at least.