Here's the slightly rewritten prologue. The story begins to differ more from the original version in the later chapters.
Prologue – The beginning of the beginning
Rasengan!
Chidori!
The cries of two shinobi echoed throughout the cavern. Two young men, one blonde, the other raven-haired, called up all their strength and signature techniques. They had been fighting a grueling battle against the ancient leader of the S-ranked organization, Akatsuki
Naruto Uzumaki stood proudly cloaked in the Fox Shroud with crimson Rasengan swirling in his right hand. Sasuke Uchiha was to Naruto's right, smirking there beside him, with a black Chidori chirping louder than ever before in his left hand. The teens smirked as they merged their two jutsu together into an all new jutsu, Rasenchidori, a swirling orb of chirping lightning and wind chakra, whose glow lit up the cavern like the morning sun.
Staring at the duo with his Eternal Mangekyou Sharingan was Madara Uchiha. The ancient Uchiha had initially scoffed at the audacity of the two whelps. Yet, now after fighting them, he was feeling the effects of old age for the first time.
Again and again he had clashed with the blonde Jinchuuriki and his traitorous descendent. The fools just wouldn't stay down and DIE!
As the two came charging for one final assault, the old Uchiha felt a cold chill travel down his spin. He had overused his Sharingan and was low on chakra. He knew he wouldn't be able to get away from the two young ninja charging towards.
A new feeling gripped his black heart: Fear.
Acting quickly, Madara flared his Sharingan and tried to activate his Space-Time Jutsu as the two teens' attacks touched his cloak. But alas, it was a futile gesture. The combined force of Naruto and Sasuke's jutsu and his own low chakra supply rendered the technique useless, allowing their attacks to strike him dead-on.
An explosion of energy rippled through the cavern, kicking up dust and debris…
As the dust slowly settled, the fallen figures of Naruto and Sasuke lay at the edge of a 50 foot crater with Madara at the bottom. The two were fatigued beyond belief and more than a little torn up from the battle and the backlash of the Rasenchidori.
The battle was over, they had won…
Sasuke just stared at the man that was responsible for the destruction of his clan. He couldn't believe they beat Madara. After everything he'd been through, the bastard was finally done. Naruto was happy that they stopped the maniac from enslaving the world.
"HA!" Naruto shouted as he slowly rose to his knees, smiling like an idiot. "TAKE THAT ASSHOLE! " Sasuke turned his head to the upright blonde and a light clicked on in his mind. Slowly his lips began to twitch and a smile wormed its way onto his face. He reached up and propped himself up against Naruto's kneeling form. "He's dead", he gasped out, leaning heavily on Naruto. "…he's dead…" Sasuke muttered this mantra over and over, completely unable to believe that they won.
Naruto looked at the Uchiha out of the corner of his eye. The war was over, the battle was won, and he got his best friend back. All was good in the world. The two suddenly heard a shuffling sound from Madara's "corpse."
The world's strongest Uchiha lay there, mangled from the jutsu and slowly losing consciousness. "How could I have been defeated by these two whelps? How could they have gotten so strong?" These thoughts filled Madara's mind as he slowly lifted his head to stare at the two kneeling boys. He lay there beaten and slowly bleeding to death while his two opponents were celebrating his defeat. Hearing his slight movements, they turned their gazes to the dying Uchiha.
"Listen well you wretched dogs! You think you've won but you have failed!" Madara gasped out as darkness clawed at the edges of his vision. "You've defeated me, yet you've failed in your goal. My dream is complete!" Sasuke and Naruto stared at the dying man with shocked faces. "Yes, I've achieved my goal. There's peace in this country and you want to know why? It's because everything is either dead or dying anyways!"
The two's eyes widened in realization…Everyone was dead?
Madara painfully chuckles as more blood rapidly pools around, while the two teens begin to comprehend his words. "The Gedo Mezo, despite being incomplete, fulfilled its purpose. It brought peace to all by sending them to their graves! I may not have become the God of this world, but at least you two will live 'til the end of days, rotting in this dead world!" With that said, Madara Uchiha died with an insane smile on his face.
The solemn shinobi rose painfully to their feet and stared at the now quiet man. Leaning heavily on each other, they slowly shambled their way out of the cave and out into the world.
Their gloom deepened when they surveyed the barren wasteland that was once the Elemental Countries. Everything was either charred black by wildfire or reduced to rubble from the earth-shattering aftershocks of the Akatsuki's incomplete weapon. The Gedo Mezo had exploded when Madara attempted to use the statue with only eight bijuu contained. The resulting blast had left everything outside the cavern desolate and destroyed all life.
As far as Naruto and Sasuke knew, they were the last people alive…
And that was it... Tell me what you think. I only editted it to my liking, but the story is gonna be changing a lot more in the next chapters.