CW: Misgendering (but the guy who does it gets punched out, if that helps)
It had been a close-run thing. Though Zabuza had died in his banzai attack against Gato's men, Haku had been found almost dead but barely clinging to life. With some well-performed medical jutsu and a truly impressive will to live, she had been back on her feet by the time Team 7 was almost ready to head home. Naruto had not been in the room when any of this was happening, but he was glad to have a new friend nonetheless. It had been determined that Haku would be brought back to Konoha as a prisoner - contingent on her good behaviour, she might be permitted to join Konoha's ranks as a kunoichi. Naruto sure hoped that was what would happen, it'd suck to have to go to visit her in a dungeon.
That day marked the first time she'd been up and about, and the first time she'd come into contact with Team 7 since the fight on the bridge. Sakura seemed willing enough to make peace, for which Naruto was grateful, but their other comrade was another story. Sasuke eyed Haku strangely for first a moment, and then for too long. It was almost as if he was trying to tell where he'd seen her before until he said "Oh, it's him. I see your fashion sense hasn't improved."
"I don't have to take that kind of talk from you", replied Haku hotly.
"Where do you get off calling Haku a boy?" interjected Naruto, "She's the prettiest girl on this whole island!"
Haku blushed and smiled, which Naruto thought made her even prettier.
"That's a guy, you moron. I've got the Sharingan now, remember? I can see things in more detail than you and I've noticed a few particular...things about your crush here." Sasuke glanced at Haku's throat, and then at her waist - or rather, below it.
Naruto saw red and went to take a swing at his teammate, but was quite literally beaten to the punch when Haku slipped under him and cracked Sasuke square in the jaw. Naruto was impressed, especially considering the girl had been confined to a sickbed just the previous day. He resolved to ask her for a friendly spar sometime.
Sasuke flew a noteworthy distance, and when he came to a stop Kakashi was suddenly there, perched over him like a guardian spirit. "I think we've all had enough excitement for one day, don't you?" he asked. "Sasuke, no using your clan's greatest legacy to leer at girls. Haku, I'll remind you that you're on parole. You get this one for free, especially considering you were provoked, but don't push me."
She stayed in her fighting stance for a long moment before bowing briefly, "I understand."
"Great", replied Naruto, "Because I sure don't. Why does Sasuke keep calling you a guy?"
"I do not wish to speak of it here", she said softly, "I will explain tonight, if we can be alone together." She glanced at Kakashi, who nodded idly, before looking back to Naruto and asking, plaintively, "Only... promise you will not hate me?"
"I really don't hate a lot of people, Haku. Whatever you've done, I promise to at least hear you out."
The rest of the day passed in an uneasy truce. Kakashi managed to keep Sasuke and Haku busy on opposite ends of town, and neither could contrive a good way to get back to the other for another round. Naruto was more distractable than normal until Haku came to him later that night and invited him out into the forest.
"I'm glad Kakashi wasn't mad", said Naruto as they sat atop a tree. The night was beautiful, and the moonlight perfectly highlighted Haku's face. Naruto privately wished he was a poet, because he was sure he could write a doozy given her as a muse.
"Yes, he has been very accommodating", she said softly.
Naruto could tell that she wanted to tell him whatever was so important, so he forced himself to wait patiently until she could talk. When she looked his way, he shot her an encouraging smile and a thumbs-up.
She blushed at the gesture and hid her face in her hands. Just as Naruto was about to ask what was wrong, she looked up again and said, "Naruto...I am a woman. Or, at least I am a girl."
"Well duh. I said you were the prettiest girl on this island, and I meant it. Heck, you're probably the prettiest girl I ever saw."
"It is not as simple as that. Though I do thank you for flattering me."
"Flattering nothing, I meant what I said."
"I have... I was born in the wrong body. This form you see is of a boy."
"What do you mean?"
"My body is a boy's."
He tried as hard as he could to add up what he was hearing with what he was seeing. "Were you turned into a boy, by some weird Jutsu?"
"No. My body has always been a boy's, but my heart is that of a girl. I do not know how I can explain it."
Naruto nodded. "Well, they say it's what's on the inside that counts, right?"
Haku made a disbelieving noise. "How can this be so simple for you?"
"Haku, as far as I'm concerned, I've only ever known you as a girl. First you were a pretty girl in the forest, then a pretty kunoichi who really socked Sasuke one when he tried to perv on you. What else do I need?"
She started crying.
"No! Aw Haku no I'm so sorry, I didn't mean to make you cry." He hugged her fiercely and brought her head to his shoulder, "I don't know what I said wrong but I'm sorry. Please, I'll make it up to you somehow."
"No, Naruto, you said nothing wrong", she managed to choke out between her tears, "I'm crying because I'm happy. Because I've yearned for so long to hear someone to speak as you do."
"Of course!" he replied, "I'm only being honest." His smile faltered, and he gathered up the courage to continue, "Haku...I kinda know more than you might think. I..."
"Yes, Naruto?"
He shook his head. "Sorry. Not sure I know how to explain it." The Kyuubi was not a subject he could just casually drop on someone, after all.
"That's alright. I'll be happy to listen, whenever you want to talk."
"Thanks, Haku."
"Not at all. You did the same for me, and that's more than most people ever do."
Naruto huffed a sigh and looked back out over the moonlit night. "Yeah, but the difference between you and me is my secret is actually a bad one."
"Most people would say mine is pretty bad."
"Well yeah, jerks. But there's nothing bad about being a girl one way or another, I don't get why some people are weird about it. Sakura's a girl, and she can kick my ass in sparring."
The next morning they were making their long way back to Konoha. Sasuke, to his credit, hadn't tried to rile up Haku again. For her part, the hostage girl seemed content to chat with Sakura rather than figuratively or literally needle Sasuke about the events of the previous day. They were making good time leaping between the trees, and it was probably about an hour until lunchtime.
Naruto hung back just a little, and eventually found a good opportunity to ask "Hey, Sensei? Have you ever heard of someone having one kind of body but another kind of heart?"
Kakashi made a wordless thinking noise and eventually answered, "During the last war, I fought a man who had a woman's body."
"Huh. Like the opposite of Haku."
"I suppose. Like I say, he had the body of a woman, though obviously I couldn't tell at first. He walked and spoke and acted like a man, and he sure as heck fought me like a man." Kakashi rubbed his jaw idly, "I could usually dodge him, but when he got a good hit in he broke two of my ribs."
"Did you take it like a man?" asked Naruto impishly.
"I did! And so did he, when I could hit him. So to answer your question, it's not exactly common, but it's happened before and it'll probably happen again."
"Huh. Is there a jutsu to give people the right body?"
"Not that I've ever heard of. You'd need a supremely skilled medic-nin, and even then it would probably be risky. There would be a danger of death if things went wrong." He gestured vaguely with one hand, "Remaking an entire human body from the ground up...it's a complicated thing. All sorts of organs and systems and so on."
"Well if I ever meet one, I'll have to let Haku know."
"You would want to take that chance?"
He shrugged, "I'd want her to have the option, I guess. Be nice to choose whether or not to risk it."
"Heh", agreed Kakashi, "I guess choosing whether or not to risk your neck is better than most ninja get, huh?"
"Do you think we could swing her mission pay? It's a B-Rank risk, right?"
Kakashi laughed, "I think that depends on the medic-nin. If we slum it a little, we might be able to get her paid for an A-Rank."
Naruto grinned. He might not have been able to share his own secret, and he might not fully understand what was going on in the depths of Haku's heart, but now he had a goal. Get back to Konoha, get Haku inducted into the Hokage's forces, and then find the best medic-nin in the world to give her the body she deserved. Being Naruto, he naturally cared not a jot just how difficult that last part might be. What sort of future Hokage would he be if he couldn't do a favour for a friend in need?