The Ruins of Reality:
Naruto bit back a moan as his arm snapped back into place, Kyuubi's power flowing through him, forcing his body to mend. Atksuki had won, he was the last and it was only a matter of time before he was found too. He may have kept the nine tails out of their hands, but it seemed it wasn't an issue any more. With the capture of the other eight Bijju, the Atksuki had done the impossible, they had conquered death it's self, and the newly immortal were well on their way to conquering the world.
It has to be here, I know it's here somewhere
Naruto stumbled, and behind him he could hear the Trekidites baying for his blood. Pein had taken to his new powers in unexpected ways, twisting the forces of the universe, creating monsters from animals, demons from people. Faster, Smarter, Harder to kill, and all subservient to only one power. His own. Itachi was the only mortal left, and the Kyuubi the only thing stopping them from becoming truly all powerful in this world. Shuddering Naruto forced his exhausted and burning muscles to move a little faster, he was among the ruins now, and they seemed to burn red under the twisted sky.
On the last day of the solstice as the final light dies seek you the balancer of all things, the one being that none escape. There you shall invoke his name, and there he shall answer you, and the deal shall be struck again, as it was of old.
Beware yea the deal, for what was lost cannot be regained and the deal once struck cannot be struck again. Beware yea, for only a hopeless fool would try to pay his price, and only a hopeless fool can change his flow.
Beware... A fool I may be, and hopeless I am. So it's time to pay the price.
Abruptly Naruto stopped. Around him were twelve tallies scratched into solid stone, Twelve massive columns still proud for the millennium they had stood untouched.
Fitting... a sundial, One the size of a small village.
Shaking and fearful Naruto strode quickly to the center, to the print of a hand sunken into the solid rock. Behind him the Trekidite shrieked, and from across the ruin another answered. Naruto chuckled grimly.
"To late boys, to late."
Taking a deep breath he pulled out a kunai and cut his right hand open down each finger, from nail to palm, working quickly to keep the kyuubi from healing it. The demon, finally realizing what he intended poured out it's power, trying to delay him long enough. As horrifying as being captured by the atksuki was, what the little bastard had planned was just as bad... for him. The Kyuubi was too late though, without wasting a minute Naruto slapped his hand into the indent
"Guardian of time, I demand your presence! Guide me to the truth! Help me right the wrongs! I offer the power of Nine to return and fix what should not have been!"
for a moment there was nothing and then the dial glowed, a curtain of blue power raising out of the ground just in time to lock the mis-shapen forms of the trekidites out, and they wailed their loss, three mouths screaming discord, five sets of razor sharp claws tearing madly at the power that kept it from it's prey. Soon it was joined by a second of it's kind, and then a third, Naruto saw none of this however, heard none of it... in his mind a voice was speaking, a voice older than then mountains, deeper than the sea.
… THE TREATY IS INVOKED, THE PRICE SHALL BE PAID, FOR THE POWER OF NINE THE ONE SHALL RETURN.
In the background Naruto could hear the kyuubi screaming, but it didn't matter, fire burned him, light caressed him, each nerve turned slowly to ash, and his voice mingled with the beast as it's power was drawn through him. The light surrounded him, The kyuubi however wasn't so quiet.
No...NO! I Shall NOT perish! It is his bargain, let him pay the price! My Foolishness may have been my downfall, but I will not go so quietly!
There was a massive shudder, and naruto's screams became a howl, the agony of the kyuubi's power flowing through him became the torture of his own being ripped away.
Bound together, we return together! For the price of ten two shall return!
The light was the purest agony, and it erased him atom by atom
SO MOTE IT BE.
With a final cackle from the Kyuubi, the light consumed them both.
The premise of this story is a 'Naruto goes back to change the past' Fic. While he has above average Chakra, he doesn't have the capacity to throw around 'Kage Bunshin' like he's breathing any more. He was 19 when he went back, and at that time his own reserves were at just over Neko's level of power, Now he has 'only' Kage level power, and nothing he can do will ever increase that amount. Kyuubi still lost the most, he's now only a one tail, and like Naruto, even if he escaped nothing he could do would ever raise that amount. The Idea is a smart Naruto who actually does have decent and improving chakra control going back to fix the past, while he can still draw on the Kyuubi's power he can go one-tail maybe once a week and can actually get chakra exhaustion now if he pushes too hard.