SPOILER ALERT: This one shot has some spoilers to Mitsuki's own arc in the anime, which was around episode 80, I think. Nothing major, though.
Who We Are
Mitsuki is Orochimaru's son.
It was still hard for Konohamaru to believe, but he knew it to be true; Naruto wouldn't lie about something like that.
"But to think that he'd keep it a secret from me" he thought with a sigh. Why had he been the one assigned to look after the boy when Naruto knew of his family's history with Mistuki's? Literally anyone else could've done it!
"You seem troubled" Naruto says casually as he suddenly sits down next to him. Konohamaru hadn't even heard him coming "Something on your mind?"
As much as Konohamaru would've liked to snap at him, Naruto was his Hokage, so he controls himself, simply giving the man a look that clearly said "Are you kidding me?"
Naruto lets out a laugh before smiling sadly, which catches the younger man off guard.
"You think that I should've told you earlier, don't you?" he asks.
"Yes" the answer comes immediately "Preferably as soon as you admitted him in to the academy."
"Is that so?" Naruto asks "Had I done that, what would you have done differently?"
Konohomaru stays silent at that, wondering what to answer. What would he have done differently? He would've been warier around the boy, that's a given, but other than that? It's not like Mitsuki ever did anything to harm anyone, Boruto dragging him in some of his pranks not counting, so there was no reason for him to be hard on the boy. Orochimaru's son or not, Konohamaru didn't want to treat him unfairly.
"Nothing, really" he admits "But it would've been good for me to know, just in case something had gone wrong."
"Shino knew. Iruka too, of course" Naruto says, quickly adding: "I told them not to tell anyone."
Logically, it made sense; Iruka was the principal, and Shino had been the class's instructor. However, if those were the reasons, shouldn't he had been told when he became Mitsuki's team captain?
"Hang on" he thinks "Anko-san doesn't know?"
Naruto just shrugs.
"I never told her, but she's not stupid. As a snake user and Orochimaru's former student, she probably figured it out at some point" to Konohamaru, that made it sound like he was stupid for not figuring it out. Or maybe Naruto didn't mean it that way; unlike Anko, he didn't know Orochimaru personally, even though he had met the man a time or two when delivering messages to the ones watching him. He preferred it that way, too, though since he was Mitsuki's teacher now, he supposed it was only a matter of time before he had to deal with the man. And with that in mind-
"Did Mitsuki run away? Or did Orochimaru sent him here?"
"Neither, apparently" Naruto says, much to his surprise "He said that Mitsuki wanted to come to Konoha and that he simply allowed it, wanting his kid to make his own choices or something."
"…And how do we know that it's the truth?" Konohamaru couldn't help but ask "How do we know that he isn't here to spy for Orochimaru?"
"We don't" Naruto says with a shrug, his face growing serious "But he's a child, and one of our own genin no less. Unless there's a good reason to suspect otherwise, we will consider him innocent."
Konohamaru almost, almost says that there is a good reason, with the boy leaving the village on his own under suspicious circumstances and all, but holds his tongue. That was nothing Naruto didn't know already.
"While I do worry, the fact stands that Mitsuki is a Konoha genin" the Hokage says "Until we have actual proof, he's innocent."
Naruto stands up, stretching.
"Honestly, you know him better than I do. He's your student after all" the blond says "What would make him, the Mitsuki you know, act out on his own?"
Honestly, Konohamaru didn't know. His impression of Mitsuki before this mess was that he was a good kid, if not one that took things a bit too lightly sometimes, and that he was talented. But what did he really know of Mitsuki as a person? Not much, he now realized.
"I don't know" he admitted "Should we contact Yamato-san and the others? Tell them to keep an eye on Orochimaru, just in case Mitsuki tries to get in to contact."
Naruto frowns, and there is a look on his face that Konohamaru can't quite read, but it's not a pleased one.
"…Perhaps I'll do that" he says, turning to leave "I'll see you later, grandson of the third Hokage."
"Yeah" Konohamaru says, only realizing what Naruto had said after the man was gone. How long had it been again that anyone had addressed him as that? As much as he had loved and respected his grandfather, he still hated when someone did that. He was his own person and-
It hit him like a lightning, and Konohamaru lets out a disbelieving bark of laughter. Of course, Naruto had called him that on purpose, just to make a point. Despite being the grandson of the third, Konohamaru was his own person.
And Mitsuki was his own person as well.
Of course, with him being Orochimaru's son, it was a fact that some caution should be practiced, but he was still Mitsuki, a person of his own and Konohamaru's student. As his teacher, it was his responsibility to have faith in the boy and see what he was up to, not to mention guide him back on the right track if he got lost. And that's what he was going to do.
He had to go to Iwagakure.
A.N: I'm still a little salty that they didn't really focus much on Konohamaru's feelings about the situation, not to mention how unnatural his meetings with Orochimaru seemed. One would've thought that there'd be at least a little tension, considering their history.