What probably should have happened. Set in the same AU as A New Naruto, can be considered a side-story or completely separate. Take it how you will.
Naruto was quietly humming happily to himself while he slipped past the guards and into the personal vault of the Hokage, wanting to look through some files. He wasn't really looking for anything in particular, but... he supposed he was just feeling nosy today. It wasn't like the Hokage would do anything to him over it, anyway. He could probably even swing it so that he got paid for testing the security on the place!
He was flicking through files, not really finding anything interesting, when he came across one that got him very curious.
"Hmm?" His jaw dropped. "What the..."
The Hokage stared at Naruto, once again at a loss for words because of something the blond said to him. He could feel the ANBU's shock at what they'd just heard, as well as Inu's exasperation (he was on guard duty today while both his ANBU and Genin teams had the day off training and missions to rest... he wasn't quite sure how it was managed that both teams had the day off at the same time).
"Naruto... do I even want to know what you were doing there to begin with?" Hiruzen asked, tiredly. He actually took his hat off to rub a hand down his face. If possible, the ANBU were even more shocked that he didn't even try to deny any of what Naruto just said.
"Eh... probably not." Naruto chuckled sheepishly, not even bothering to act the least bit nervous.
Hiruzen sighed. "You know I could have you branded a spy and have you hauled into T&I for being in there?" He asked dryly.
"Yeah..." Naruto shrugged. "But you won't." He grinned cheekily.
"And if those busybodies I call advisors find out you were in there?" He asked, and waited for Naruto's answer, it would be what he told them, he wasn't in the mood for coming up with something himself at the moment.
"Simple! You asked me to test the Secret Archives security system. How can you improve it if you don't know where the holes are?" He asked rhetorically. The Hokage and attending ANBU took the statement for what it was, a warning that they really needed to secure that room better, and that there were huge holes currently in the security protocols surrounding that room. Who knows who else had been in there if that was the case? Even if Naruto was known for being able to get in and out of places he shouldn't have been able to get into in the first place. But, if even he found it easier than it should have been...
None of them had known he'd been anywhere near that room until five minutes ago, and they knew that if he hadn't said anything, they never would have.
Hiruzen sighed. "I suppose you want paid for your 'services'?" He asked in the most long-suffering, put-upon tone that he could manage.
Naruto's grin widened. "It would help sell the story to those old bats." He nodded wisely.
"Oh, very well..." He sighed, looking put out. "The amount for an... A-rank assignment will be in your account by the end of the day." Hiruzen promised, then got back to why Naruto was here. "Why do you want us to inform Sasuke Uchiha of the truth behind his Clans massacre and his brother's involvement?" He asked.
Naruto's grin disappeared. "Because he is no longer a civilian student to be protected or threatened. He is now a Shinobi of the Village and protected by that status, as well as his status of being the Heir of the Uchiha Clan so long as Itachi is on his mission. Also, would it not be better for the news to come from you, instead of a twisted version of events fed to him by an enemy who also knows the truth?" He asked. Kakashi had been helping him with grammar, apparently being the son of a Hokage meant potentially attending official events when the news broke, so he had to be able to talk 'correctly' to not embarrass himself.
"You've been reading Itachi's reports." Hiruzen frowned in disapproval. Itachi had reported seeing a man wearing an orange spiral mask speaking with the Uchiha Elders on several occasions, and Minato had also briefly mentioned fighting against a man by the same description the night the Kyuubi was freed, before he left to seal the Fox Demon away again.
Naruto looked unrepentant.
Hiruzen looked down, deep in thought. "You do have a point, though." He admitted. "However, the choice is not only mine, but young Itachi's as well. If he agrees, Sasuke will be told... and I think it would be best for Itachi himself to be there... as well as Kakashi and perhaps Inoichi as Sasuke's therapist." He muttered to himself.
Naruto's bright smile came back. "You can test out a new invention of mine, then!" He held out a scroll, which the aged Hokage took curiously.
He could tell that this must have been Naruto's project before Kakashi let him move onto the higher level work. If he remembered right from his and Kakashi's conversation the other day, he was going to need to send for Jiraiya soon if Naruto wanted his work evaluated properly.
The borders of the scroll were lined with small Fuinjutsu symbols, barely visible to the eye, even one as trained as Hiruzen's. Naruto handed over a sheet of paper, where an enlarged version of those same seals was drawn out, that way he could actually study it. After a few minutes of studying the symbols, he looked up at Naruto in amazement. "This works?" He asked.
Naruto shifted and rubbed the back of his neck awkwardly. "So far. I haven't tested them at any kind of distance yet, though. Well... I had some clones go to the village limits one way while I went to the other end of the Village, and it worked there, so... that's the farthest I've been able to test them, though. But there's no reason to think they won't work at greater distances."
"This would make undercover or infiltration assignments so much better. Safer, too. Most of our operatives only get caught out because their messages are intercepted or they're followed to a meet/drop point." Hiruzen murmured, running through all the uses he could put something like this to.
"It would make communicating with them faster, too. That way urgent messages will be guaranteed to get here in time, or back-up can be sent out faster if needed." Naruto said, more eager to discuss his work now that the Hokage obviously approved "Also..." He said this more hesitantly. "It would give them a chance to communicate for a short time with loved ones, to remind them what they have waiting for them." He knew it was always a risk when infiltrating a place long term for the Shinobi in question to 'forget' why they were there, and to 'go native', forgetting what they were leaving behind.
Hiruzen glanced up at him sharply, before he nodded thoughtfully. Yes, that would also be a pleasant factor for their agents. Inu was oozing nothing but pride, his Chakra practically danced with it. "I will hand a few out to teams going on simple C-ranks for further testing." He announced after a moment. That way, there would be less risk of losing one to the enemy, or of critical information being lost because it wasn't working at that distance. Naruto cheered, excited that his creation was being approved, and did an odd dance around the office.
Before he left, he gave the Hokage three other scrolls, explaining that they came in pairs, of course, and then showed how to set them up to make a secure 'connection'. Then he left.
"Inu." The Hokage said once the blonde Genin was gone.
The ANBU in question jumped out of his spot in the shadows and tilted his head almost smugly, unable to tamp down his pride enough to act more professional or respectful. "You're in charge of overseeing security upgrades on the Archive room." His Hokage said flatly. "Take Naruto with you, have him run you through how he got in, find and patch up the holes." He waved Inu away, then pulled writing materials towards himself to write Itachi a message requesting his presence in Konoha as soon as he could get away.
Hiruzen chose to have the same guards in the room that were there when Naruto spilled everything he'd found out about Itachi, that way he could limit the amount of people who knew about it.
As it was, he was glad when Itachi arrived, three weeks after he sent out the request for a meeting. It had been a few years since they were last able to meet up, and he was looking forward to seeing how the young Clan Head was doing.
He was out of his chair and rounding the desk before he himself really registered what he was doing, pleased to see him. "Itachi, good to see you again. You look well." He greeted the seventeen year old. Not that he could really tell if Itachi wasn't looking well, not with Itachi's skill with Genjutsu.
(Was he really only seventeen? So young... too young for the burden he carried.)
If Itachi was startled or shocked by his enthusiastic welcome he didn't show it. "Lord Hokage. I am well, thank you." He inclined his head respectfully, but didn't salute or take a knee. His years and status as a Missing-nin negated the need, he didn't think he could get back up easily enough for it not to be noticed even if he did. He didn't say anything about his illness, though, and he didn't plan on it any time soon. As it turned out, he didn't need to, because his old captain was suddenly in front of him, looking for all the world like a lazy Jonin without a care in the world, except for his sharp, piercing gaze.
"You don't smell well. You smell sick." Kakashi's visible eye narrowed.
Itachi sighed. Trust his Senpai's nose to call him out on a lie. "Alright... I am sick, but there is nothing to be done. I've seen numerous doctors already." He informed the two before the Hokage could order him to the hospital in disguise.
"Hm... have you seen Tsunade?" Hiruzen asked, concerned.
"No. I doubt she would agree to see me, anyway." Itachi shook his head.
"She will see you." Hiruzen declared, quickly writing and passing Itachi a letter. He assumed it was orders for Tsunade, so he took it and tucked it away with a grateful nod. He chose not to mention his currently failing eyesight, there was truly nothing that could be done about that until Sasuke's own Sharingan matured, and even then Sasuke would have to agree to it. He wasn't sure he wanted Sasuke to mature that much, though, not with the cost it would demand of him.
"Sir? Naruto Uzumaki and Sasuke Uchiha are here." The Hokage's secretary poked her head in after knocking once. The moment the knock sounded, Itachi was on the ceiling, out of sight.
"Ah, excellent timing. Send them in." He ordered, right as Inoichi made his own way in through the window.
"You asked to-" Sasuke's query halted midway, and his eyes widened when Itachi dropped down in front of him. He cursed and immediately went for his Kunai, but Kakashi stopped him with a hand on his arm before he could get it out. "What are you-?!"
"Enough!" The Hokage barked, and sat down with a sigh. "Sasuke, put it away. Itachi is here at my invitation."
"What?" Sasuke demanded, incredulous. Yes, he'd been planning on getting the truth out of Itachi before deciding whether or not he still needed to die, but he was not expecting this.
"Sasuke, let them explain." Naruto spoke up, lounging on the couch near Itachi, seemingly without a care in the world.
"You know what's going on? How do you know what's going on?" Sasuke narrowed his eyes at his teammate. How did Naruto know something about his clan that he didn't? Why didn't he know about it?
The Hokage coughed. "Naruto found out three weeks ago during a... security check of my personal archives." Sasuke missed the amused or annoyed glances sent the blondes way from all the older Shinobi in the room. "And brought it to my attention that now you are graduated from the Academy, and are going outside the village now, that you should know this." Itachi went to say something, to protest, but the Hokage glanced at him in regret. "Better you learn the truth from us, instead of a twisted version from others."
"And before you do something you will regret later." Naruto piped up, referring to Sasuke's stated desire of killing his brother, of taking revenge.
Itachi glanced at his little brother, longing in his eyes, before looking away again. "Sasuke's safety is dependent..." He started to remind the Hokage, startling Sasuke.
"Sasuke is not a Civilian child anymore. The moment he put that Headband on, he became protected from those elements." He said. "Besides, I'm sure you can pay him a visit after this, remind him you are watching." Itachi was silent for a few moments before he nodded slowly, agreeing.
"Protect me from what?" Sasuke demanded, eyes darting between everybody in the room.
"There are certain... figures in the village who do not want you knowing of any of this. It was only your ignorance of events going on at the time that have kept you safe from them. As a civilian, there wasn't much I could do to protect you from them, as they were Shinobi matters. However, as I have been recently reminded, you are not a civilian any longer." Hiruzen started to explain.
"Who? Who in the village didn't want me to know why my clan is dead?" Sasuke demanded. He'd figured that was what this was about. Was it the Council? Who on the Council?
"That is not important right at this moment. Just know, not even the Council is aware of this. It was only myself, Itachi, the ANBU commander, and three others." Sasuke assumed those three others were the ones threatening him.
Sasuke glanced at Inoichi. "He is here as your therapist, not as a member of T&I." Kakashi said quietly from behind him. Inoichi nodded in agreement. He'd only been told this the night before so he could be ready to help Sasuke deal with it. He'd been making good progress since Kakashi forced the boy to come see him, he would hate for all that to be undone.
Itachi moved in front of Sasuke and lifted his hand, hesitating, before he finally laid it gently on his baby brother's shoulder. "The last thing I ever wanted to do was hurt you, little brother. Let us explain?" He asked quietly.
Sasuke finally nodded. "What happened?" He asked, not taking his eyes off the hand on his shoulder, but not removing said hand, either.
"Shortly after the Kyuubi attack, whispers began. They were saying that it was an Uchiha who released the Kyubi on the village, or that they knew the attack was coming and hadn't warned anybody. Matters were not helped when somebody realized the Uchiha had almost zero casualties from the attack. This was, of course, because Fugaku ordered his clansmen to get the villagers to the evacuation zones. He saw everybody rushing to fight the threat, but nobody bothered to consider the civilians trapped in the village behind them." The Hokage started to explain.
"It was an Uchiha, but he wasn't from our clan." Itachi clarified.
"What?" Sasuke asked, confused. A rogue Uchiha?
Itachi glanced at Hiruzen. "He calls himself Madara, I haven't been able to figure out his real name."
"Anyway... distrust grew for the Uchiha clan. Teammates stopped having clansmen's backs, started leaving them out of planning missions and giving them the most dangerous jobs without backup. Within the village, they were being blocked from doing their jobs as police by a distrustful population, and then blamed when crime went unpunished. The old resentment Madara Uchiha held for the Senju being in power came back, and the Uchiha started planning."
"I saw him there. The rogue. He was at every planning session, hiding in the shadows. I'd see him before or after meetings, talking to father and the elders."
"Planning what?" Sasuke asked.
"A coup. They were going to take over the village, by any means necessary. Itachi didn't like what he was hearing, so he came to me and told me everything he knew." Hiruzen nodded at Itachi. "I asked him to keep an eye on the situation and keep me informed, a week later I was approached by Shisui with the same concerns. In the meantime, I started trying to speak with your father, started trying to negotiate a peaceful outcome." Sasuke stared at the Hokage in horror.
"A week before the coup was scheduled to take place, Shisui was approached by Danzo Shimura. Danzo said that the only way to end this without further bloodshed, was by ending the Uchiha clan. Shisui refused and tried to get to the Hokage to warn him. By the time I found him, he was barely alive. One of his eyes was missing, he said Danzo had taken it. He told me what happened, gave me his other eye, and killed himself." Itachi looked down, still grieving for his best friend.
"The next day, they found him in the river and accused you of killing him." Sasuke said slowly, starting to put the pieces together.
"Yes. I came straight to the Hokage, and received my final orders. Negotiations for peace failed, so a kill order was given for those involved in planning the coup and most of the adults. Those who were uninvolved and the children were to be spared. I don't know who wrote that suicide note for Shisui, but it wasn't me." He added as an afterthought.
"If they were to be spared, then..."
"Danzo had other ideas. He didn't want anybody spared, not even you. I spared you, and everybody else I was supposed to spare. Danzo has his own elite force, he thinks he has it hidden under the Hokage's nose. They went through the compound behind me and killed everybody else. It was only my threats and that Danzo knew he wouldn't stand a chance against me that spared you. I must have killed half of Danzo's men as they tried to kill you on your way home from the Academy that night." Not to mention his efforts to stop them from killing the innocents. In the end, there had just been too many of them, and he had to protect his brother.
The room was silent for a few moments as Sasuke tried to process this. "But... Lord Hokage, if it was ordered and you know who else was involved, then why..."
"The plan was always for Itachi to leave the village after dealing with the traitors. He is currently on an assignment for us, infiltrating the group of missing nin that the rogue Uchiha belongs to." The Hokage revealed. He was only revealing this much so that Sasuke didn't get the wrong idea that Itachi was run out of the village anyway, despite everything being done under orders. "As for Danzo and his group... just because I know about them, doesn't mean I know where to find them, despite efforts to rectify that. And Danzo has much political power, and is good at covering his tracks. Not even I can simply drag him into T&I or order him executed for his crimes without proof." And oh was that frustrating. But it would also set a dangerous precedent that he refused to be the one to set.
Sasuke was silent for a few minutes.
"Sasuke?" Inoichi asked, concerned. Sasuke was his patient, and they had been making good progress. He was worried that this might cause a set-back. On the other hand, it could also be a breakthrough. He honestly didn't know which it would be at this point.
"I need time." Sasuke finally said, not looking at anybody. He turned, but hesitated before leaving. After a moment, he turned and gave Itachi a quick hug before bolting from the room, Inoichi following after him, worried. He was going to give Sasuke space, but he didn't think the boy should be alone right now.
Hiruzen sighed. "That went better then I thought it would." He sat back in his chair heavily.
"Tell me about it." Naruto muttered. Sure, it had been his idea, but he'd been expecting a lot more yelling.
"Are you able to stick around for a few days?" Kakashi asked Itachi, tilting his head.
"Hn." Itachi grunted absently, still watching the door Sasuke had just left out of as if he might come charging back at any moment. The sudden hug made him hopeful that he hadn't destroyed his brother, or any chance they might have.
Kakashi snorted. "You can take my bed, then, I'll take the couch." He rolled his eye at the Uchiha. He knew that the Uchiha Head had a bed in the Uchiha compound, to his knowledge his old room hadn't been touched, but he didn't think that either brother really needed to be there, not with all the memories of both before and during the massacre. Personally he thought they would be better off emptying the place out of anything related to their clan and just selling the entire place. With just the two of them left, it would take a while before the Uchiha clan would be numerous enough for the compound to be filled again, in the meantime the place was just an empty husk of reminders.
There was a reason Sasuke lived in an apartment off the compound, after all.
Naruto made a noise, but didn't protest Itachi coming to stay with them for a few days. It wasn't like he could go back to the compound, not after everything that happened there.
"Before you leave again, come see me." Hiruzen cut in. Those scrolls Naruto had created had been tested by ten different teams on C-ranks, and even a few B's. So far there were no range-limits or other issues, it worked perfectly well even for the team's that had to travel to Suna and Kumo. Another was currently with the teams in Kiri for the Chunin exams, it was interesting to be getting updates as it happened instead of waiting for the newspapers to arrive or for a runner, or even a hawk. So far he was pleased with how the Chunin hopefuls were performing so far. He felt safe giving one to Itachi and knowing it would work just fine.
If he wanted, Sasuke could of course have access to the Hokage's half of the scroll pair to speak with his brother occasionally.
"I will." Itachi promised. "Same apartment?" He asked Kakashi.
"Of course." He'd had no reason to move, after all. Even the few times that potential enemies tried to follow him home to watch him weren't enough since he was good at losing them, or turning the hunt around on them.
"Hn." He grunted, and left. He already knew where Sasuke lived after a past conversation with the Hokage (and the fact that his pay for this mission was what was paying for it, not the Uchiha fortune like most thought). He would check on the security of the place before going to visit Danzo to... leave a message.
"Ah, Sasuke. Come in." The Hokage said, surprised when he saw Sasuke standing outside his office the next morning. "Is everything alright?" He asked, concerned when the boy came in, sat down, and said nothing.
"I don't know. I wanted to kill him. Then Naruto said something, and then I just wanted to know the truth. Inoichi's been working with me, too... His mission isn't going to end, is it?" He asked. "It's long-term. He's never going to be able to come back to the village." He looked at the Hokage, hoping he would say otherwise.
"We don't know yet." Hiruzen admitted. "The group he's infiltrating is working on something big, and he says that they're almost ready to begin their plans. What they are, he doesn't know yet, the leader has kept things quiet so far. Once we do know, we'll see where we go from there."
"And after? With the way people think of him now, could he ever come back? After everything that happened and was said about him?" He'd read about what happened to the White Fang, one of the most powerful Shinobi in history. He was on the verge of getting Flee on Sight orders in the Bingo book when that mission happened. The way the village was reported to have turned on him completely destroyed him to the point where he killed himself. He didn't want that to happen to Itachi.
The Hokage looked at the young Genin and sighed heavily. "... I don't know. Sasuke." He paused to collect his thoughts. "I have been working on dealing with the rogue elements in the village since your brother left, trying to get them taken care of so that Itachi coming home after this is an option. The evidence in your brothers favor is hidden and only one knows of it's location so that if something happens to me before Itachi can come home, the next Hokage will know the truth. I've done what I can to leave that door open." He assured the boy. "It would have to be done carefully, of course." And then, of course, there was the matter of this illness Itachi had. They would have to wait for Tsunade to have a look to see if it was even treatable.
Sasuke nodded absently.
"He's here for a few more days. For now I believe he's staying in Kakashi's apartment if you wish to speak with him some more." He revealed to the younger Uchiha.
Sasuke looked uncertain. "Could I? I mean, after everything I said and wanted to do..."
Hiruzen sighed. "Sasuke. He wants to see you. While I don't agree with everything he did or said that night, in his own way he was trying to make you stronger. Strong enough to survive the loss and everything that is to come."
Sasuke was quiet. "Thank you for your time, sir." He finally muttered, bowed, and left. Nothing was said about Sasuke not saying anything about this to anybody, he'd grown up in a Shinobi household, he knew the value of keeping secrets.
"Anytime." Hiruzen muttered, frowning after the young Genin, worried. So far all of Inoichi's reports were good, perhaps he should say something, suggest extra sessions in the coming days or something. He decided not to, Inoichi was good at his job, after all, and would know that Sasuke might need to see him more often in the coming weeks.
For now he could only watch. All he knew, though, was that this wasn't a mistake.
When Naruto had left his office three weeks ago, he'd worried, until he realized just how likely Naruto's fears of somebody else spinning a twisted version of events was. That would very easily turn Sasuke against the Village, which would weaken them considerably.
Not only was Sasuke a talented Genin with plenty of potential to become one of the strongest, he was also one of only two surviving Uchiha. The Sharingan had it's downsides, but it was also a strength when used correctly. The Uchiha had brought many new jutsu to the village, when they were in a sharing mood, and the Sharingan had enabled many teams to avoid falling into traps they would have otherwise never seen. The Hyuga were now overworked trying to fill the gaps left behind that fateful night. And the perfect memory recall that came with the Sharingan was as much a boon as it was a curse.
So yes, it would be bad if Sasuke were turned against them.
Now he just had to trust that Inoichi and Kakashi could straighten him out, and keep him tied to the village.