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Kakashi Hatake was an interesting character. He was one of the most powerful ninja in the Leaf. He was one of the most renowned and well known ninja in the world. He was also one of the weirdest. Walking around with a lazy, boneless posture was one of the reasons. So were the books he would read as he did it.
There was a time when Kakashi had been fully immersed in said works of art. After Minato sacrificed himself, he felt like he had nothing. The scandalous looks and scoldings he got made him feel a little more alive. A little more cared for. After a while, they stopped. People either got used to it or were too scared by his reputation to comment. The Sandaime looked at him with sadness instead of reprimanding him.
That had all changed though. The Uchiha Clan had been murdered by the boy he'd once been in charge of. He'd taken it upon himself, at least somewhat, to watch after the last remaining one. That responsibility had ignited a spark in him. The third hokage had fanned it into a flame when Naruto and Sasuke graduated.
Assigning him to be in charge of all the graduating genin had been a stroke of genius by Sarutobi. He hated him for it. The responsibility made him spend more time around not only Naruto and Sasuke, but the other future pillars of the village. That made him care, more than he ever wanted to again. It was nearly unavoidable for him to care, not when he was in such close proximity to these kinds of people. He'd have to avoid direct, meaningful orders. That was a line he hadn't and wouldn't cross. It was a double edged blade though. Certainly it set him up for a lot of pain. The other side was beneficial though. Kakashi Hatake was a dangerous man when he cared.
When he had a motivation and a reason, there were few in the world that could stop him. The Sandaime ordered him to train and to watch over the genin. So Kakashi Hatake did that to the best of his ability. He sharpened his own skills. He returned to his old Anbu training regimen. He practiced jutsu he'd long since forgotten he knew. His stamina training was extended farther than he'd ever taken it, allowing his use of the sharingan to expand, both in skill and time limit.
No, Kakashi Hatake was no longer the lazy boneless man that people thought he'd become. He'd always been dangerous, but now, he was truly something to be scared of. When he walked around with Icha Icha, it was no longer for his pleasure. As much as he enjoyed the book, he used it for cover when he was in public. A consequence of rehoming his senses and skills to the highest of levels was that they were very hard to turn off. That's why he noticed the intruders when walking by a tea shop, instead of missing them because his head was buried in his book.
He looped twice, once in a disguise to throw them off just in case they were on edge. When they exited, he trailed them, a single henge'd shadow clone helping keep the trail clean. It didn't take him long to see that Asuma and Kurenai had noticed them too, and were also following. They were jonin, and very skilled ones at that. Kakashi was better, and thus noticed them. From the way they were being led around, it seemed that the intruders might have noticed too.
They ended up by the river on the outskirts of town. Strangely far from any possible patrols of ninja that were above chunin level. Thankfully that meant they were also far from any civilians.
Kakashi stayed back, letting Asuma and Kurenai take the lead. They could handle themselves, and he could do more with the element of surprise than by revealing himself early.
He wasn't afraid to admit that the red glowing sharingan threw him off. His shadow clone immediately took off for training ground nine, a strategic decision. The Hokage would likely send Gai anyway, better to just shortcut his way there and have one of the genin warn the Hokage.
He revealed his own sharingan, and got a good look at the attackers. Itachi looked so much older than the 17 years that Kakashi knew he was. The lines in his face were etched deep. His skin was paler than he remembered. The air of cold precision about him that screamed warning had only gotten sharper.
His companion was a massive man. He had blue skin and a face like a fish, carrying a massive bandaged sword. Kisame Hoshigaki then.
Two S-rank ninja, wearing black cloaks with red clouds. This must be the Akatsuki. He heard rumblings of them the times he'd filled in for Jiraiya. The Toad sage had filled him in on the rest of what he knew about them. A mercenary group, but what did they want with Konoha?
The decision was made then. Protect village and comrades, gain intel, take out missing nin. In that order.
As he watched, Kurenai tried one of her more resilient genjutsu. He sighed. A foolish maneuver. One that likely wouldn't have worked on 13 year old Itachi, let alone one who'd had almost five years of development. Itachi quickly flipped the genjutsu on her, drawing a kunai to stab her. Kakashi couldn't wait any longer. He let his tight hold on his chakra loose enough to let it flow through his body. His enhanced muscles left cracks in the concrete of his hiding place as he rushed forward.
He hadn't left himself enough time to perform any spectacular jutsu to save his comrade. Instead, he had to settle for a quieter version of Gai's dynamic entry. His foot made contact with Itachi, and the rogue nin's body dissolved into crows. His momentum not meeting any sort of force, he flew past Kurenai and onto the river, easily standing atop the water. Itachi's ploy was unsurprising, but he achieved his goal. Kurenai was released from her own genjutsu.
"Kakashi Hatake. What a surprise." Itachi reappeared next to Kisame, his tone showing no sign that he was surprised. In fact, he seemed slightly amused, if he was even capable of feeling that way. That only served to irritate Kakashi, but he decided to play along. Every delay increased the chance that they would all survive the fight.
"Itachi. Can't say I'm happy to see my former subordinate. Come to torture Sasuke some more?" Kakashi said. There was a sneer on his face, Obito's eye spinning wildly.
"My little brother is of no interest to me at the moment." Itachi said emotionlessly. "We're here for the 4th Hokage's legacy."
Kakashi considered that for a moment. "So you're after the Nine tails huh?" He said. It may not be wise to voice his deductions, but it would stall for time even more.
"You always were too smart for your own good, Kakashi." Itachi said into Kakashi's ear. The sudden appearance of him so close caused Kakashi's eyes to widen, but not before Itachi plunged a kunai gently into his kidney.
The Kakashi that Itachi stabbed dissolved into a puddle of water. There was a splash behind Itachi as the real Kakashi emerged from the river, dashing at him with a kunai. Itachi brought his own to bear, the metal clashing in a stalemate as the former comrades came face to face.
"For somebody using a stolen eye," Itachi said. "Your mastery of the sharingan is truly impressive."
Kakashi ignored his comment, avoiding eye contact. There was only a slight warning as to the impending jutsu. He substituted as quickly as he possibly could. The clone of Itachi exploded, sending water and steam flying everywhere. Kakashi appeared next to Asuma, holding his shoulder. He'd been clipped by the explosion.
"Kisame," Itachi said, once again standing next to his partner. "Take care of these two."
The monster of the hidden mist grinned a sharp toothed smile, hefting his massive sword off his shoulder.
"Gladly." He swung down. The legendary sword smashed into the concrete as Asuma dodged back, leaving a crater in the ground. Kisame hadn't moved anymore than just his arm to do so. The monster moniker appeared to be well earned. Then the former swordsmen of the mist loosened the hold on his chakra, and it became apparent that monster might be an understatement.
While Kisame dealt with Asuma and Kurenai, Kakashi held his focus on Itachi, watching his hands to avoid the sharingan. He would have to trust that the other jonin could fight well enough together to stay alive. Itachi brought his hand up slowly, making no move to run through seals. Instead, he pointed at Kakashi.
"Your sharingan may be well trained, but is it enough to deal with a true genjutsu master?" Itachi asked. Chakra swelled at the tip of his finger, but nothing happened. Itachi lowered his hand.
"Just what kind of game are you playing?" Kakashi said. He turned to his left, checking in on Kurenai and Asuma. They were both lying on the ground. That couldn't be right. Less than a second had passed, and as monstrous as Kisame's chakra was, he hadn't performed any jutsu in that time. Slowly, they started to stand up. As they did, their images morphed into that of Itachi. He was surrounded by him. Genjutsu.
Kakashi formed a hand seal, building chakra to break it. A quick flash wouldn't be enough against Itachi, he would need a large amount. As he did so, he felt the skin on his face peel away.
"Ka-ka-shi." That voice. It couldn't be. "Kakashi." The skin finished peeling away, and somehow, he knew what he looked like. The right side of his face had become Obito. It was wrinkled, as if he'd been crushed. Aside from that, and the lack of goggles, he looked just as he had when Kakashi left him under that rock all those years ago.
"It should've been you. You stole my eye, Kakashi." Obito said. Kakashi knew he hadn't, but it still crushed him to hear it all the same. "And now I'm going to take it back." His right arm lost control, and lifted up to his left eye. He caught it with his remaining arm, wrestling for control as Obito tried to take back his sharingan. There was a bulge in his stomach, and a head of brown hair popped out through his vest. It was a girl, no older than 14. She had purple markings under her eyes. Blood dribbled out of her mouth, as if she'd suffered an internal injury.
"Kakashi." Rin said. "How could you do this to me?"
"You killed her." Obito said angrily. "You were supposed to protect her! You're worse than scum!"
"You killed both of us." They said in unison. Their voices resonated deep in Kakashi's soul. "You let Sensei and Kushina die."
Kakashi fluctuated his chakra wildly, panicking as he tried to break the genjutsu and fend off his own arm at the same time. Tears streamed out of his sharingan. He was suffocating in his own mind.
Just when he felt as if he might lose the battle and fall unconscious, a hand rested on his shoulder. He felt a wave of chakra shatter the make-believe world. Kurenai stood at his back, an anchor against the turbulent feelings. Itachi hadn't moved. Kakashi exhaled shakily, trying to gain control over his emotions. Feelings long since buried were brought to the surface.
A shout of pain brought him out of his shock. A splatter of blood in his peripheral vision caught his attention. Kisame's blade had shed its bandages, spikes sticking out in all directions like weaponized scales. Asuma held his shoulder as blood gushed from it. It looked to be only a glancing blow, but the flesh that had been hit was shredded into ribbons.
Bad news got worse, as a memory of a shadow clone invaded his mind. Gai hadn't been at the normal training ground. He'd been nearly all the way across the village, running laps. Unless he unleashed several gates, it would at least be a few minutes before he could arrive. In their current state, Kakashi didn't think they would last even that long.
"Hm," Itachi hummed. "Even I didn't believe that jutsu would be so effective on you. I wonder which comrade you saw?"
Kakashi stayed silent. There was nothing left to say. He was rattled in a way he hadn't been in a long time. All there was left to do was fight. Of all the fighting machines the shinobi world had produced, Kakashi Hatake was one of the best.
Kisame made a move to go after Asuma again. Kakashi was there, a wall of earth protecting the injured jonin. The massive sword destroyed the wall, possibly sucking the chakra out of the jutsu if the rumors were true.
Itachi fired his clans signature jutsu at Kurenai. Kakashi countered it with a water bullet. Kisame chose that moment to run through hand seals of his own. Kakashi's sharingan spun like mad, copying the jutsu. His fingers were a blur, and he channeled his chakra into the existing water of the river, using it to match Kisame's power. The water shark bullets collided, exploding into thousands of droplets.
Itachi molded the water into drills, attempting to run Kakashi through with them. The copy nin formed a water wall in the nick of time, just barely blocking the jutsu. When the wall fell, Itachi was in his face, engaging in taijutsu. Kakashi looked him dead in the sharingan as their forearms connected. Itachi attempted to put him under a genjutsu, but failed. Kakashi's body morphed into lightning, electrocuting Itachi.
The Uchiha leapt back, irritatingly seeming to be fine. His right arm was hanging limp, but the rest of his body seemed unharmed. Undoubtedly, he had used wind chakra to insulate his chakra system and body, minimizing the lightning clone's damage.
Kakashi reappeared near land, sliding out of the water nearly silently. His intention to use another jutsu was cut short when his instincts screamed at him. He leapt up, narrowly avoiding the sword being swung at his waist. He launched high into the air, putting him in a bad position. Kisame grinned as he fired another water shark bullet at him. Kakashi formed a shadow clone, using it to swing himself out of the way. The moment he landed, he was slamming his hands into the ground, forming another mud wall. Itachi's phoenix flower jutsu slammed into it, shaking the wall. It held. Not that it really mattered.
Facing two powerful S-rank ninja was too much for him. He couldn't keep shifting between one and the other. Asuma wasn't much use. Kurenai was casting genjutsu even as she tried to bandage the Sarutobi. None of her jutsu seemed to stick though, as both ninja seemed to be a bad matchup for her.
As the fire and hidden shuriken contacted the wall, Kisame appeared behind Kakashi. His sword was already cocked back, ready to swing. Kakashi tried to rotate out of the way. He wouldn't make it in time though, and he knew it. He brought his forearm up, the best he could hope for was a ruined limb, and shifted to take the hit with his momentum. The pain never came.
There was a loud clash as Samehada connected with something metal, and another as it was deflected into the ground. The blow crushed the concrete and caused something of an explosion.
Standing in front of Kakashi was Naruto. He could feel the Kyuubi's chakra, though from behind he couldn't see its tell-tale presence. Everything after that happened quickly.
Naruto, even enhanced, hadn't been able to withstand the strength of the blow. Instead, he had used Zabuza's executioner blade to deflect it into the ground. The blond let go of the blade, and channeled a massive amount of chakra into his hands. He summoned as much wind as he could, pushing it out forcefully, to try and throw Kisame back. Despite the force of the technique, the missing nin only slid back several feet, never letting go of his sword.
"So you're the brat that disposed of Zabuza, huh?" Kisame asked, genuinely curious how a genin had ended up with one of the legendary swords. He'd heard of Zabuza's death, but details on it were hard to come by. He didn't receive an answer though. Naruto was already gone though, leaving the blade in front of Kakashi. The message was received. Kakashi picked up the sword, using both hands to heft it. He was hesitant to leave Naruto while Itachi was around, but he didn't have much of a choice. It had already been proven that he wasn't capable of fighting both enemies at the same time. He would just have to dispose of Kisame as quickly as possible.
—-
Itachi stared at his younger brother. He had grown since he'd last seen him. It was almost nostalgic seeing him. If only the younger Uchiha wasn't staring daggers into him.
"What are you doing here, Sasuke? Shouldn't you be off pretending to be a ninja?" Itachi said.
"I'm here to kill you, Itachi. I will avenge our clan." Sasuke's voice was cold.
Itachi chuckled at him. "Foolish little brother. You lack the power. Run along. You'll only get yourself killed."
Sasuke's nostrils flared in anger. His three tomoe spun in his eye with rage. Those words had been repeated in his mind over and over in the last month. The enraging part was that he knew they were true.
Naruto appeared next to him, apparently having done his job helping Kakashi. When he laid his eyes on Itachi, he instantly channeled more of the Kyuubi's chakra. It only took seconds for two tails to appear behind him, Naruto's features turning even more fox-like. He wasn't under his normal control though, his anger at Itachi and what he did to Sasuke clouding his mind. He looked Itachi in the eyes, intent on challenging him. He wouldn't back down. That was a mistake.
The sharingan whirled hypnotically, and he found himself face to face with Itachi. They weren't standing near the river any more though. He felt the presence behind him and knew he was in his seal.
"So this is the cage that houses the nine tailed fox." Itachi glanced around, sharingan taking in all the details. "It's truly a work of art." A loud growl was the response, chakra bubbling out of the cage, and forming the visage of the Kyuubi.
"I will wipe that repugnant sharingan from existence, Uchiha." The fox said.
Itachi walked up, right in front of the Kyuubi's nose. Naruto made no move to stop him, knowing instinctively that he would pass right through him. It was only his mindscape, after all. Just an image created to represent the seal.
"You may try, Nine-Tails," Itachi said. "But for now, I can't have you interfering with my plans. We will come for you another time." He smoothly placed his hand on the foxes nose, and squeezed. The chakra visage popped, and suddenly they were back in the real world.
Naruto flinched back at the reaction. The chakra cloak he'd been using was gone. His greatest advantage neutralized by the sharingan. He dropped to a knee, disoriented and shocked.
Sasuke looked at his friend, hurt by only a glance. The same eyes that had traumatized him. The rage in him built.
'You aren't strong enough.' The ever present voice from the mark said. 'Let me show you true power, let me help you avenge your clan.' It said, it was as loud as it had ever been. This time, he didn't try to fight it. Just like in the fight with Gaara, he gave in to the voice. He felt as the mark on his neck unfolded, drawing across his skin, covering his body in black flames. When the small transformation was complete, he felt the power. Power that he couldn't have achieved on his own, as much as he hated to admit it. Power that would help him kill Itachi.
He ran through the hand seals again. This time his intention wasn't to challenge Naruto. He would use the chidori to kill. He would run his hand through his brother's heart. More lightning than he'd ever wielded formed in the palm of his hand. He felt the pull on his chakra pool, his previous spar with Naruto wearing him down enough that he wouldn't be able to fight long. It didn't matter. This jutsu would slay Itachi. He would finally avenge his clan. He was sure of it.
The chidori screamed to life, and Sasuke wasted no time in rushing his brother. The elder Uchiha stood by stoically, as his brother tore after him. His sharingan slowly turned, taking in the chidori. It was powerful, more powerful than he would have thought his brother capable. Those black lines were troublesome. They looked like a curse seal. Perhaps Orochimaru had done that to him during his attack on the village. It was hard for Itachi to get concrete details out of Konoha these days. He would have to see about strengthening his information gathering skills. Perhaps he would do a favor for Sasori in exchange for more information.
The lightning technique ripped apart the water as Sasuke stepped onto it, vaporizing it instantly. His speed was greatly increased, though he was still slow to Itachi's perception. He saw Sasuke's next move before he made it. The sharingan was clearly needed to make such a jutsu possible. He would have deduced that even if he hadn't been on Kakashi's Anbu team. His brother was foolish to think another sharingan wouldn't cancel that advantage out.
The chidori was reared back, and brought forth to slam into him. He would have to give Sasuke credit, he aimed straight for his heart. That ruthlessness was admirable. The chidori blurred as it flashed through the air.
The jutsu detonated, blowing water sky high, drowning out the sound of a bone snapping. When the water cleared, Itachi had Sasuke by the wrist. The bone was broken cleanly.
"I admit, foolish little brother, you are far stronger than I imagined you would be." He looked his brother in the eyes, seeing the rage in them. His sharingan looked him over, focusing on the cut to his ribs. "You are still nowhere near my level, however. You lack hatred. You've clearly forgotten what I'm capable of. Allow me to remind you." Itachi looked up to where Kakashi was locked in a stalemate with the executioner's blade. He grabbed Sasuke by the throat, lifting him into the air.
"Kakashi," he called out. "Let me show you the power of a true heir to the sharingan." Kakashi watched, his borrowed sharingan picking up the channeling of chakra to Itachi's own set. He saw the shift in the pattern, and nearly lost his leverage on Kisame in his shock.
Itachi looked back into Sasuke's eyes, his own spinning into a three pronged shuriken, spiraling out from the center.
"The true power of the sharingan. Its most powerful form." Itachi seemed to announce to nobody in particular. "Mangekyo Sharingan: Tsukuyomi." He looked into Sasuke's eyes, and triggered the genjutsu. Everything went wrong in that moment.
Naruto Uzumaki was as unpredictable as ever. He recovered from Itachi silencing the Nine-tails, in time to look up and see Sasuke being held by the neck. He heard him boasting to Kakashi about his sharingan. His body just reacted. Later, he would realize that he had used the substitution technique. That in itself was an accomplishment.
Switching places with a conscious human was difficult to do. You had to overwhelm their chakra by such a degree that they were hopeless in fighting the jutsu. Naruto had channeled enough chakra to summon Gamabunta, using it to enhance his body, and grip Sasuke's system. He pulled the Uchiha out of his brother's grip, his own body being slid into place nearly instantaneously. He found himself staring straight into the shifting sharingan of Itachi Uchiha.
It was too late for Itachi to cancel the technique. The tsukuyomi was cast on the jinchuuriki. For the second time in seconds, he found himself in a falsified world with Naruto Uzumaki.
"That was foolish, Naruto." Itachi said, sighing. His back was turned to the blond
"Like hell I was going to let you hurt Sasuke!" Naruto yelled, his anger bleeding into his voice.
Itachi considered the boy and his emotional state. "You seem to care a great deal for my brother," He said. It was a statement, not a question.
Naruto growled, more beast than human in that instant, despite the lack of bijuu chakra. "I'm more of a brother to him than you've ever been!" He shouted, straining to attack Itachi. He couldn't move though. His body was frozen, only able to speak.
With his back turned to Naruto, the small, sad smile on his face went unnoticed to the brash jinchuuriki. Itachi let the indifferent mask fall back over his face, before turning around to face him. "That may very well be the truth. How much suffering are you willing to undertake for him though? An hour? A day? More?" Itachi mulled over the question.
"More than you can dish out." Naruto said resolutely. The determination in his paralyzed body was admirable. Itachi was internally pleased that somebody was willing to go to such lengths for his brother. It was a shame he'd have to suffer for it.
"We will see about that." The world shifted, colors inverting. The sky turned red, the clouds black. "This is one of the ultimate genjutsu of the sharingan. It is unbreakable without a mangekyo to counter it." Suddenly Naruto was stretched out and stuck to a crucifix. "I am in complete control over this world." Naruto blinked, and there were clones of Itachi as far as the eye could see. Each one held a sword. "It's space, it's time, it's substance." He stepped forward, plunging the sword into Naruto's gut, twisting it, and withdrawing it. Naruto refused to make a sound.
The blond looked up, and saw himself on another crucifix, surrounded by Itachi's. Then he was suddenly there, his mind struggling to keep up with the warp. "It's space, it's time, it's substance." Itachi said again. This time, two clones stepped forward and stabbed him. This repeated several times, until Naruto finally let out a scream, more in mental exhaustion than pain.
"Time is a fickle thing. In this world, only a second has passed. It felt much longer though, didn't it? I wonder how you will fare after a full week of this."
The stabbing repeated several times, but Naruto hardened his resolve. When the loop reset, he drew shaky breaths.
"Two seconds." Itachi said. "How are you holding up?" He was somewhat impressed that somebody so young had this much mental fortitude. He had broken more experienced shinobi much easier.
Naruto took a few more shaky breaths, and looked Itachi right in the eyes. "I… can take it… if it means… others don't… have to." The glare Itachi received had more venom in it than any gesture or word could convey.
"You are a curious character, Naruto Uzumaki." Itachi thought for a second. "You have lived a hard life. You seem to be able to take pain better than most, especially in defense of your comrades."
"I wonder how you would handle watching them go through the same pain."
Naruto tried to spit on him, but the saliva disappeared in the air. The world shifted again. He was no longer on a crucifix. Instead, his loved ones took his place. His team, his sensei, Jiraiya, the old man. Everybody he loved was strung up, surrounded by Itachi. The rage in his body turned to desperation.
"No. Please no." Naruto pleaded.
"I am sorry, Naruto-kun." Itachi said, slightly confusing Naruto. "The Tsukuyomi is a heavy technique, not without consequence or backlash. Since you are caught in it, I must remove you from the battle." Anything else he might have said was completely drowned out, as one by one, his loved ones called out to Naruto. Pleading with him to help. Then they were stabbed, and the blood curdling screams were enough to shake his own body.
After one round, he was in pain. Tears streamed down his eyes. After five rounds, he'd screamed his voice hoarse. Around the tenth time Hinata was stabbed by multiple blades, crying out for him to save her, he curled up into a ball. No matter how hard he shut his eyes or covered his ears. He could still see them being tortured. He could still hear their desperate screams. It didn't take long for him to go completely numb. He was certain that it was an automatic response by his brain. If he didn't, he would probably die from the stress. The numbess didn't stop the pain though, only dulled it enough for him to survive. He laid on the floor of this dream world, sobbing.
He wasn't sure if it was a full week he spent there. It felt simultaneously like minutes and years. His mind was completely numb by the time the world shattered. He was completely disoriented. His psyche was shattered. The bright light hit his eyes as his senses returned properly. All he could manage was a broken scream and an inelegant grunt, before he fell unconscious. Itachi dropped him, and he sank below the surface of the water.
—-
Kakashi watched as his sensei's son went from fully conscious one second, to screaming traumatically and passing out the next. His sharingan had seen the technique. It was tremendously powerful, that much he could tell. Itachi's chakra had shifted to something entirely different when his eyes had changed. There was a tightening in his chest as Itachi dropped Naruto. The only sign that he was still alive was his chakra system still working, and the lack of a rampaging tailed beast.
His more immediate problem though, was Sasuke. He completely lost it when Itachi dropped Naruto. Even with a broken wrist, and no chidori, he rushed after his brother again. A blur of green likely saved him.
"SEVERE LEAF HURRICANE." Gai shouted, swinging a powerful kick at Itachi before Sasuke could get there. The older Uchiha was forced to leap back, or risk serious injury trying to block. Kakashi had never been so happy to see the tights wearing jonin before in his life.
Gai landed on the water, spraying it up everywhere from his force. He wasn't shouting of youth or eternal flames. There was a serious look on his face that was saved for only the most difficult missions. He stood imposingly, already looking at Itachi's feet, knowing better than to look into the sharingan.
"Kisame," Itachi said. "We're retreating." The swordsmen grunted, but didn't question his partner. He disengaged from Kakashi, leaping back to join Itachi. The two turned and ran without another word.
Kakashi turned to his fellow ninja, issuing orders. "Kurenai, get Naruto and Asuma to the hospital." There was no questioning his commanding tone. She nodded, diving under the water briefly, coming back up with Naruto. "Gai, I'm going after them. Make sure Sasuke doesn't follow, and report to the Anbu squad and Hokage." Gai tried to argue, but Kakashi was already gone. He turned to Sasuke, who looked torn between going with Naruto, and chasing down his brother. Gai used the confusion to knock Sasuke unconscious with a quick chop to the neck, and hoist him over his shoulder. He took off in the direction of the Hokage tower.
This chapter was way easier and way more fun to write. Itachi caught Kakashi in the same ephemeral jutsu that he used on Naruto in shippuden. Naruto had 4 characters grow from his body (Sasuke, Sakura, Kakashi, and Gaara) Kakashi only has two because his genjutsu defense is better, and I felt like if Minato popped up on his shoulder, even Kakashi's subconscious couldn't picture Minato or Kushina blaming him.
I hope my explanation for the substitution was satisfactory. It's hard to make up stuff that's already in the series but not really delved into that greatly. Kakashi uses it on a Naruto clone in the bell test, but we don't really see any other characters using it on another person that I can recall, so it seems plausible that you would need to override the other person's chakra either through strength of will or sheer amount of chakra. Typically if a character can do that there wouldn't be a reason to do so in a fight because they should just be able to win the fight easily. Naruto has so much chakra and is so familiar with Sasuke that it seemed like it could happen to me if Sasuke didn't try and fight it, which he wouldn't if he was paralyzed in fear.
Naruto receives more time in the Tsukuyomi because the Akatsuki and their spy network would have some information on Naruto from his missions and what not, and his liberal use of shadow clones would be one of the first things they would find out. Itachi, I think, would understand that Naruto could handle the overload of information a little better than most, but doesn't want to kill him, so he gets more time than Kakashi, but not 80 years or so like Izumi does in the novel. Itachi also hadn't used his mangekyo yet unlike in canon.
Only a couple chapters left till the time skip! Poor Naruto keeps getting the shit kicked out of him, but what doesn't kill you makes you stronger. Iron Man taught us that.