She nods.

"And more importantly as far as some people are concerned, weaponized by someone who isn't on our side. In the meantime, if someone like that does show up, my advice is to cover and close your eyes while making as much noise as possible. It's not foolproof, but even the most capable ninjas would take seconds to force them open without risking injury to your ability to see, and seconds are a long time in a fight between Jonin. It seems unlikely that they would be bold enough to try it in the village, but it's better to have a plan."

Personally she thinks it's more than merely unlikely that they would make the attempt, what with how they haven't in the intervening years and their one attempt involved striking at a helpless opponent well away from any possible reinforcements, but Naruto is nervous about it and she'd never forgive herself for dismissing that fear if it was wrong besides.

She nods, and without really shifting in stance somehow nonetheless really looks like she wants another hug.

"It does seem unlikely, but the whole thing seems unlikely, so...  Who knows.  ...Thank you."

Mikoto has two kids of her own - she's more than capable of interpreting that without any help. She'll just quietly hug Naruto for a few minutes in silence.

"Now, is there anything else you want to get off your chest, or can I tell Sasuke he can come back inside if he wants?"

"...Think I could maybe go out to him.  It'd be kinder.  ...There's a lot I maybe want to tell you, but a lot of it is..."

"Speculative and secondhand.  So I don't want to...  Make any accusations of people in good standing.  But...

"When I asked the Kyūbi who he thought would be running an eugenics program that Konoha wasn't supposed to have, since, uh, Uchiha eyes, and the flesh of Senju Hashirama, don't normally end up in the same people...

"He didn't say Orochimaru.  And yet, the Hokage found him, instead of some other guy.  ...I don't think Hokage-sama would be able to fake being surprised by what I asked him, when this started.  I don't think he lied when he said we really aren't supposed to have any sort of eugenics program.  But...  I would be very careful around some of the other people who wield power in Konoha.  I don't know what they might want, but...It already smacks of attempted bloodline theft, and possibly collaborating with whoever it was who attempted to wreck our village.  ...That's the other thing that has me worried about being kidnapped.  Just, so you know.  ...Oh, Sage's breath, I probably really am in some kind of danger from them already by existing if they've already stooped to doing whatever backwards nonsense this was...  I'd convinced myself for a minute there that with no opportunity for an outsider to get near, the threat of - worse than the social situation I've been in since I could start thinking - was really actually unlikely, but no, it's really not, and it's gotta be near and subtle...  Please, Mikoto-sama, be careful, yourself.  There's gotta be a reason you weren't allowed to do any of this, despite clearly wanting to, until I kinda forced your hand, and...

"I bet whoever it is isn't gonna be happy that I have found an ally and hopefully a - a friend."  ...She doesn't say the word she really means, but she expects that Uchiha Mikoto already knows.

"I will be. There's some rumors we've been suspicious of ourselves, but someone doing experiments involving grafting flesh onto a Uchiha are the kind of thing that merit a much more thorough look."

She then ruffles Naruto's hair. Lord third will complain, but as long as she mostly sticks to violating the spirit instead of the letter she doesn't think he'll be able to do much if she presents it as a fait accompli. He owes them after a screwup of this magnitude on his watch anyway.

"I'd be delighted if Sasuke had a friend with him at the academy. Please, feel free to come over any time."

"I'd be delighted to visit on a more regular basis.  I couldn't possibly disappoint Sasuke-kun, after all.  He'd be so sad.  I just can't.  The idea of a sad Sasuke makes me want to give the real him a hug."

"...If there's anything you'd like Hokage-sama to know, by the way, I could probably tell him for you.  About the - rumors that you don't like.  He's promised me he'll listen if I tell him things, and maybe that was because of Kyuubi-sama, but I'm not above using that for the good of the Leaf - once I can actually get in touch with him again, I don't know why we didn't arrange for something if I'm going to walk around while holding S-class secrets but next time we meet I'm gonna fix that... -", and her voice dips out of the frustrated grumble it was in as she gets to her reasons.  "...I just...  An injury to any of us is an injury to all of us.  And I want to return the favor you've done in tending to my own emotional wounds."

"I can talk to the third if I have to. I don't want to imply you aren't capable, or that the problems you're dealing with aren't serious, but as an adult it's my job to solve problems for kids, not your job to solve problems to make me happy.  You've got a lot on your shoulders already, and while I might not look it, I'm still a Jonin."

"...I know.  It's not like trying to appease people has helped much anyway.  I'm offering to help because I want to.  Not - I - you've done so much.  And maybe it's basic decency, but that basic decency...

"So many just haven't learned it.

"So I do, I suppose, feel like I ought to.  But it's because of...

"The sort of person I want to be.  ...A lot like you, or what I've seen so far at least, really."

Mikoto smiles at her.

"From what I've seen, you're on track to grow up to be a good person already. But if you really want to help... you could talk to him about the inclusion of Lord First's DNA. Since we'd just be repeating to him what you told us, he might take it more seriously from the source."

She nods.  "I'm pretty sure I already mentioned that, but I'll be sure to tell him, in case I actually haven't."

A few moments pass.

"...Is there anything else you'd like to say, or shall I go play - er, I mean, practice - with Sasuke now?"

"I think as long as you know you're welcome to come back later, that's everything i wanted to say right now. As for what you end up doing with him... well, you're not wrong that the Academy is prepared to teach people who don't know what they're doing. I think he'd be perfectly delighted to practice with you, but if you'd rather distract him with a game I won't say anything if you don't."

She nods in agreement, giggling, 'steals' another hug for the road, and makes her way outside.

The training-playing-bonding passes, uneventfully; she shows off her acrobatics and her sneaking skills.  She's actually pretty decent at target practice, despite herself; she has very good hand-eye coordination.

...Several days later, the Hokage's office door is no longer buried under a pile of classified paperwork, and she's still looking for Hatake Kakashi's gloomcloud.

Upon his return to public life, the Hokage made another speech, this time with the goal of putting to rest the ever intensifying rumors. Yes, there was human experimentation performed, yes by one of the sannin, and yes, some of the victims were citizens of Konoha. Thanks to the warning passed on by one of her loyal citizens, however, they had been caught in the act, and the labs were thoroughly dismantled with the research burnt. He swears before the crowds that this tragedy will not be permitted to happen again, and that even now Konoha's anbu are tirelessly pursuing Orochimaru. Things don't completely calm afterwards, but they are certainly calmer; for many people, that there is an official story at all is sufficient if the Hokage is still alive. And if the Sandiame seems slightly less spry and active than he used to, well, the fact that he had emerged victorious from a fight with another S rank ninja was enough to prove he was still as dangerous as ever.

It would, admittedly, be something of a lie to say he was free now, but the most urgent of the paperwork and meetings that piled up in his absence has been dealt with by now, and he needed an excuse to put off the rest of it anyway. A discreet hand signal has his secretary send Naruto on in. 

"Hokage-sama."

...They don't normally meet in his office.

"Is...  Everything alright?"

Because, well.  He doesn't look it.

"...Or, well.  Nevermind if everything's alright, nothing about what's been going on lately is alright - but go talk to a Yamanaka about that, rather than me, maybe.  I think that's their job?  ...Maybe I should be talking to a Yamanaka, it's not like we're not both going through some stuff, lately..."

"...Anyway.  There are a couple things I want to talk to the hat about.  And one thing I want to talk to Hatake Kakashi about, if where he's gotten off to isn't a secret, so I figured I'd ask you if he was busy and if not I guess I can write him a note since I can't find him for whatever reason.  But most of those things aren't really...  time-sensitive.  Only, like, 'before the Academy starts up' sorts of time limits.  So we're gonna go get ramen, because you need to be anywhere but in this office.  C'mon, old man."

"I'm fine, just... feeling my years more than I used to, is all. Getting something to eat is a great idea, though, I've been spending too much time in this chair."

On the way there he steers the conversation mostly to polite nothings, but when they're seated with food he finally lets things wrap back towards more serious matters.

"What did you want to see young Hatake for? It's no surprise he's busy, most of our Jonin are right now."

"I want to see if his Sharingan, from Uchiha Obito, matches the pattern of the Sharingan that the Kyuubi told me got him.  Once it's in the right mode, which, I don't know if he knows how to do that, but I wasn't told to not tell him what I know.  To - maybe, hopefully - either rule out a potential source of that Sharingan, or.  Well.  If it does match, that's...

"That would be, bad, but also good, but probably mostly bad.  Definitely something, at least...

"Oh, and, while we're on the subject of other people I'd like to speak with, I have something I want to ask Jiraiya-sama for help with.  I don't think the Yondaime expected some of the things that are frustrating me with his seal-work."

"You think Kakashi-"

There's a look of pure confusion on the hokage's face for a moment, her words having overcome his poker face.

"Naruto, I'm not sure what ideas the fox has been putting in your head or why you think you can identify a sharingan, but I can assure you that I am absolutely certain that Hatake Kakashi was not responsible for the attack six years ago. Besides which, if I had the slightest suspicion he was I wouldn't let you anywhere near him!"

"...Yes, obviously he couldn't have been responsible for this.  The perpetrator had two functional Sharingan eyes.  But as far as I know, Konoha hasn't recovered Uchiha Obito's body, which is therefore one of the few places a Sharingan might have been recovered from, even in poor condition, and who knows what someone could have done with -

"...I did mention the bit where apparently the person who did it smelled like Senju Hashirama's corpse?  Or something, I forget if there was a specific analogy...  Still, evidently Made With Hashirama Bits.

"I'm almost certain I did, but Uchiha Mikoto-sama wasn't sure you knew; we spoke a few days ago, since I figured that the Kyuubi might be more likely to divulge information if it looked like that information would actually, well, not be pointless to tell me about.

"Anyway.  The thought is, if Hatake-san's Sharingan manifests the same evolved pattern as the unidentified one, we might have a lead on where the Sharingan involved could have come from.  It doesn't match records of Uchiha Madara's, for example."

"I'll confess, I don't really follow the logic. If you know the attacker had two sharingan, then even if Obito's eye had been recoverable they would have had to get another eye from somewhere. Why wouldn't they have just gotten both eyes from there without bothering with Obito's? Eye surgery is also an extremely delicate process even with an intact eye to transfer, and Rin Nohara was a skilled medic. if she felt it was irreparably destroyed, it's rather unlikely someone else had done better."

Trying to drive a wedge between Naruto and Kakashi is not what he had expected of the fox. The closest he could imagine to a motive would be if the creature wanted to prevent the man from being assigned as Naruto's Jonin teacher, and as explanations for behavior went it was far from satisfying. That implied it was the Uchiha's doing, and their motive was all too obvious. He'd have to have a talk with them about not trying to overreach just because other matters were occupying him.

"...Hokage-sama.  Whoever it was that did this, had medics on par with Orochimaru.  As is evident from how your looking for those medics turned up literally Orochimaru, and who knows what else.  Are you sure he couldn't have done it, especially with the resources he had?

"If the answer is no, then I think that proves my point."

She finally stops fixing Hiruzen with her patent-pending 'I Am Disappointed In Your Critical Thinking Skills' Look(tm), as she begins expositing.

"The activation conditions for the Mangekyo Sharingan are definitely highly specific, though I'm not certain they're as specific as the clan or the Kyuubi have, apparently independently, concluded.  And they'd be horribly hard to produce in a lab, no matter whose thoughts you believe on what they are, so that rules out cloning.  So the search is narrow, and it's better to attempt to disprove the few possibilities of natural Mangekyo Sharingan than send ourselves on a wild goose chase for ones that don't exist.  Which is why I want to find out if Kakashi's Sharingan manifests the same pattern, if it even can, or if it manifests a different one.  Because if it is a different one, we know it wasn't Uchiha Obito's.  Or are at least pretty sure.  ...Come to think of it, I don't actually know what meaning, if any, that the patterns have, just that the assailant's...pinwheel thing...did not match Madara's...

"...Let me put it this way.  I want to - run this experiment - to hopefully rule out that it was Uchiha Obito's Sharingan that was used.  If it does turn up the same pattern, that's...

"Probably its own whole can of worms, actually!  But if we don't rule it out, we can't be sure that we're not passing up a potential major lead on the person who tried to use the Kyuubi as a deadly weapon."

"...who succeeded in using the Kyūbi-no-Kitsune as a deadly weapon," she murmurs, after a pause.

The hokage sighs, showing the weight of his years.

"Naruto. If there is one thing I have learned, in all my years as a ninja, it is that simple explanations are almost always correct. There are, on rare occasions, masterminds who will evade this maxim for a time, but even then their efforts are heavily reliant on luck. Complicated explanations involving someone having someone having a way to reconstruct damaged eyeballs, one of the most difficult of all the body's organs to repair, from a corpse in a warzone that they had no way to predict in advance would be there or easy way to know where is, and also have an entirely separate way of obtaining other sharingan eyes that they used to get a second eye... it simply doesn't happen, especially not when whatever their other method of obtaining eyes is would be sufficient. By far the most likely explanation in my mind as to how the assailant obtained the sharingan is that they got it the same way everyone else does, by being born to a Uchiha parent. Bloodline clans are usually more careful about that than the average person, but more careful is very much a relative term, and there are no shortage of young men lead around by their hormones who would then not admit to it afterwards."

"...Yeah, sure, if it's just a regular Sharingan - but I'd put money on that not being easier to arrange for the... especially tragic, Mangekyo.  The eye with the power of the kaleidoscope, the Kyuubi called it.  The eye of a kinslayer, he said - and Uchiha Mikoto said something very similar, even if significantly different in the details.  If there was a way to artificially induce that particular evolution, the Uchiha would not have nearly had such a thing become all but history to them - but it has, so that's significantly more - weight on the scale - towards the theory that there isn't one and if you want a Mangekyo Sharingan you must find one that already exists, or arrange for one in - well, a mastermind plot!  That's what you'd need, to pull that off!

"And we still have no conclusive proof that Obito is dead.  Just guessing, even if it's particularly smart guesses.  So even if it has to be an Uchiha by blood - which the experiment I want to try could disprove - we still haven't ruled that source of a Sharingan out.  Especially with the unknown potential of Senju Hashirama's unique weirdness involved!  It may normally be the simple answer, but in this case, the simple answer leaves too many questions open!"

"...I don't want it to be Obito's Sharingan.  Obito's Sharingan is just the one that's the easiest to hopefully rule out."