The moment he appeared in the training field, he shed his Hokage robes, laid his hat in the pile, and conducted a deep chakra scan to ensure that he was not followed out of his office by his personal ANBU.
Naruto Namikaze turned to him; shock evident on his face that the Sixth Hokage would suddenly appear in the training ground he was going to use. He wore the standard Jonin fatigues, his wild blonde hair, and sparkling blue eyes tinged with the slowly spreading yellow of the Senjutsu that was slowly mixing into his chakra system. He looked almost identical to his father, aside from his three whisker marks, higher cheekbones, and tan skin.
No… he was not surprised. Itachi could tell that he sensed him before he even appeared. Was that a power that came from being a full sage? Or was that a side-effect of being the Jinchuriki of the Nine-Tail fox? Naruto was prepared, his pupils set in the strange design that occurred when natural chakra rushed through your system.
The Hokage wore the same fatigues he wore during his ANBU Captain days, with the addition of the Totsuka no Tsurugi that he took from Orichimaru. After all, he would not need it since he killed him for attempting to take his body.
Naruto stared into the activated Sharingan of the Hokage, seemingly deflated but still prideful, like a dog that had been disciplined but ready to remind you that it would defend itself.
Naruto's normal chakra reserves likely quadrupled Itachis and adding the natural chakra of the World to his reserves made it difficult to even understand how much chakra Naruto had at his disposal.
'It would be nearly impossible to try to trap him in any Genjutsu…' Itachi thought.
"I trust you with S-Rank missions. Your record is above critique. You are a splendid shinobi that will likely take this very hat from me." Itachi said while vaguely motioning towards the discarded Hokage regalia.
"You are a hero, a hero from the moment you were born, and your father sealed the Nine-Tail into you. The village's last Uzumaki. The village's last living sage. The village's last Toad summoner." Itachi continued.
"Are you ready?" Itachi asked.
Itachi did not wait for an answer. A perfect sealless shushin had him in Naruto's guard, a kunai ready to pierce Naruto's neck. The blade sparked as if hitting dense metal, breaking at the point as it impacted his neck. Itachi was able to use the flat side of the Kunai to shield the fist that Naruto retaliated with. Itachi slid several feet, feeling the impact of the sage's ground-shattering strength.
'His skin is also strengthened to unimaginable levels.' Itachi thought.
"Hokage-sama, this is unnecessary. I am only asking permission to court…" Naruto was unable to finish his sentence as he slid into the next Toad kata to avoid the chakra-enhanced kick that Itachi sent his way.
Itachi was not gifted to the point of perfection as Tsunade with the strength-enhanced technique, but his near-perfect chakra control let him get close enough. As they continued to throw blows at each other, it was clear that while Naruto had more strength and speed, Itachi was not far behind. Itachi's Sharingan and additional experience made him the clear winner in this exchange.
But Naruto could continue doing this nearly indefinitely, and from the sheer jarring impacts of even blocked hits from the sage, Itachi knew he would not win this way.
As Itachi gained some separation from Naruto, the Mangekyo formed instantaneously, releasing the flames of Amaterasu at Naruto. Naruto quickly reacted, creating a stone wall that barely slowed down the eternal black flames. However, the stone wall gave Naruto enough time to cast a Doton: Moguragakure no Jutsu. The hiding-like a mole technique allowed Naruto to hide anywhere under the ground.
His chakra was so intertwined with nature that Itachi could not sense him. But why use a scalpel when a hammer would work? Itachi summoned the partial ribcage and right arm of his Susanoo, applying the black flames on the fist and slamming it on the ground. Naruto darted out, a Rasenchurinken heading towards Itachi. Itachi, dismissing his partial Susanoo, jumped over the technique. However, at the last second, the Rasenshuriken turned back around to hit him squarely in the back.
Naruto landed in the middle of the destroyed clearing in between the peak of an overturned slab of rock. Naruto's Jonin jacket was roughed up, a few tears appeared on his trousers, and a cut above his left eye was dripping with blood, his accelerated healing already closing the small cut. As he watched his jutsu eat away at the Crow clone, Naruto conducted a chakra scan.
'Something is not right…" Naruto never had an issue with finding anyone he needed to with his nature sensing. His eyes widened in shock and fear as the world turned upside down. The ground became the sky, the sky became the ground, he could not move, and the world turned red-tinted. He found himself staked to a wooden cross, the pain of the stakes driven into his palms and feet unbearable.
"This is Tsukuyumi, my domain, and here I am God. Did you think you were immune to Genjutsu just because nature favors you?" Itachi said.
Naruto said nothing. He continued to struggle against his bonds, but the more he moved, the greater the pain.
"Stop fighting it, you will not be able to escape" Itachi said as he unsheathed the Totsuka from his shoulder sheath.
"Here, seconds will stretch to hours, hours to days, and days to weeks. Are you ready?" Itachi asked as he slowly let his blade bite into Naruto's midsection.
Naruto screamed. His scream slowly turned to laughter. His laughter gave way to a nasty smile that set Itachi on edge.
"Do you know what happens to those who are not prepared for natural chakra?" Naruto smiled.
Itachi quickly dropped the Tsukuyomi. Naruto dropped to a knee outside of the Tsukuyomi, the clearing once again appearing without any evidence of the destruction he believed they wrought on it. Across the clearing, Itachi curiously inspected his fingertips, which even from here Naruto could see were slowly reverting back to skin from stone.
"There are two ways to use Genjutsu. First, you could overpower your target's chakra by filling their chakra system through a medium with your own chakra. Like holding someone underneath the water, drowning them in your chakra. Second, when your target has sophisticated control over their chakra or likely has more chakra than you, you inject your own chakra into your target, to manipulate their chakra system and subsequently their senses to fool them into seeing what is not there. Like venom entering the bloodstream and having the body's antibodies react against itself." Itachi deduced.
"Yeah, but when you do the second option, it flows both ways. Your target's chakra mixes with your own. Natural chakra is unique in that only a few can even feel it, let alone even use it. Your body rejected it and you were turning into stone." Naruto finished.
"What an interesting technique" Itachi admitted.
"The Nine-Tails, alongside every other beast, is primarily natural chakra infused with some elements unique to them. Like the One-Tail and its control over the sand and wind of its domain. I am guessing you must be able to take this Sage technique further and infuse it with the Nine-Tails chakra?" Itachi questioned. Naruto tried not to look vulnerable. This was Itachi, someone whose genius was described as only second to his father, Minato - the Fourth Hokage.
"I am working on something like that…" Naruto supplied.
Itachi's Susanoo sprouted around him, the chakra moving as if it had sentience and was quickly forming a second skin over Itachi. It was compact, less like the giant Naruto was used to seeing, and seemed more like the armor that the samurai of Iron Country wore, slowly the sentient-like chakra settled on Itachi's form.
"Best learn to use it now. You will likely need it to survive this." Itachi smiled, savagely.
Naruto reacted with legitimate fear. If it didn't involve his sibling, Itachi rarely showed emotions. Naruto reacted instantaneously, siphoning chakra from the Nine-tails and as his Bijuu Sage Mode set upon his skin.
Author notes: As you can see, Itachi had some kind of disagreement with Naruto. They seem to be arguing over something that Naruto did. Itachi was not pulling any punches in this scenario.
Yes, Itachi is the Sixth Hokage here. Kakashi is alive, but in this story, Itachi does not slaughter the clan. Rather, Obito (masquerading as Madara) and Zetsu orchestrated the culling of the Uchihas. Several of the Uchihas survive, but I will get into that next.