To start off, would all of my regular readers kindly put away their pitchforks and torches? It kinda makes it hard to write if everyone's trying to roast you alive for not updating the things they want you to. While I am working on Phantom's next chapter as you read this, I needed to get this idea out of my head since it just would not leave me alone. Anyway this is the product of too much time on my hands and having drunk six Brisk Lemon Ice teas in a row. Okay here's a little bit more of what to expect from this story: Grey-Danzo, in this he will have some morals but he still is a patriot above all else; random gender-bending, there is an example of that in this chapter but this one makes sense since that character could go either way depending on the view point of the author; and a unique summoning contract, I have done Mobile Suits in the past as well as a few others but this one has yet to be used by any author. So if you want to know more about this idea, read on; if not, leave.
Project Kronus is unveiled:
Three years after the beginning of the Forth Shinobi War:
Three years had passed since the madman "Tobi" had declared war against the Elemental Nations. Even though he was an S-Rank Ninja and had an army of cloned Zetsus under his control, the Kage didn't take him seriously and only sent the barest minimum of their forces to oppose him. While the initial response was enough to stop the initial army of Zetsus, it also made them complacent; exactly as Tobi wished.
In the beginning of second year of the war he unleashed his true army, one that numbered in the millions. Much like the original one, this one was formed of vat grown Zetsus loyal only to Tobi. However unlike the original this army was composed of specialized groups of clones; weapon usage, demolition, jutsu, stealth and infiltration, hand to hand etc.
As such the Shinobi forces were easily being pushed back by the nearly limitless, by comparison to the villages, force. However by unleashing such a massive force he drew the full attention of the feudal lords and the other nations to the conflict he had started; and the previously unaffected factions quickly sided with the Shinobi alliance, if only to maintain the statis-quo.
However even with the non-shinobi forces joining the war it was useless, Tobi's army was endless because of the simple fact that more Zetsus were constantly being grown. As such even though there were only one million Zetsus at any point in time the number never fell below that mark for long.
Half-way through the second year of war the Kages secretly sent Naruto and Kirabee far from the frontlines to train. However the two were not the only ones sent on this trip, there was also a representative from each of the Shinobi Villages in the group as well as a samurai to balance it out.
The representatives were: Kurotsuchi from Iwa, Temari of Suna, Haku Momochi from Kiri (yes she's alive in this fic due to the convenience of blood clones being sent to the bridge instead), and the legendary Oda Nobunaga from Iron; Kumo and Konoha did not send representatives for the simple fact that their two Jinchuriki were the ones the training trip was for. Because of the intensive training the two went through by the time three months had passed the Alliance felt comfortable enough to bring the expedition back to the front and launch a counter attack.
However they launched the attack far too late, Tobi had found a way to improve upon the dreaded Edo-Tensei. Instead of just summoning a single "doll" version of a long dead person, he summoned entire legions of those shinobi by sacrificing tens of thousands of Zetsus; instead of just having an inexhaustible army of Zetsus he now had a corps made of legends like Madara Uchiha, Hashirama Senju, and Minato Namikaze.
With such legends flooding the battlefield the alliance was decimated, and forced into hiding. While Tobi didn't consider them much of a threat anymore he still sent his legions after them to ensure that no resistance remained to his rule. It took two months to annihilate all but Naruto Uzumaki Namikaze, who was critically wounded and left for dead in the ruins of Konoha.
With the deaths of every member of the alliance Tobi moved to solidify his rule; however he forgot one thing, never underestimate the indomitable will of Naruto. The young man clawed his way back from the grasp of the Shinigami, and for half a month rested and recuperated; and after he rested he searched Konoha for something to turn the tide against Tobi and his absolute rule.
He found the answer to his problem within Konoha's forbidden scroll, a storage seal that contained a project that predated the creation of Chakra. For the benefit of those who were not there, here is what the note that came with the vial said:
"To whoever has activated this seal, know now that you have in your hands power that should belong to God alone. In our pride and hubris we sought to do what no one in the history of the world has been able to do, create a method to control time itself. We succeeded. Within this vial you now hold is the culmination of hundreds of years of research into both Nanites and time-space theory, code named Project Kronus. When we realized that we had been successful we tried to destroy it so no one would go back in time to try and rule the world, however the Nanites were indestructible. When the Sage approached us with a way to seal away this terrible power we accepted. If you have need of the power to rewrite history, inject this vial into yourself; but be aware that the Nanites are programed to only serve those who truly need their aid; however if your need is not great then your life will be forfeit."
Seeing as it was his only chance of preventing Tobi from ruling the world, he injected himself with the entire vial; only to pass out from the searing pain that filled his body.
Naruto's Apartment, the day before Naruto's cannon academy entrance:
A pair of cobalt blue eyes cracked open and quickly judged the surrounding area, and quickly widened in shock. The figure then formed his hands into the "dispel" handsign, believing it to be nothing more than a Genjutsu; only for it to fail and reveal nothing. A young boy's voice came from the figure's throat in a mutter: "What the hell…Wait, why the hell do I sound like a child again?"
With that the figure sprinted to the bathroom, only to find the face of a much younger Naruto Uzumaki staring back at him. This in turn prompted the young boy to faint dead away; which caused the ANBU agent, one wearing a weasel mask, watching the kid to sweatdrop: "This is going to be a long day."
Harem: Haku, Temari, Koyuki, Anko, and three slots that I will pick as I further develop this fic.