Kind of word-vomit all over the page about a wild headcanon that I thought about and then decided to run away with (and boy, did it run), and then actual plot? of some kind? Honestly this is more a drabbl-y excuse to write down the headcanon than anything with real plot. Oops.
Also, guess what 'neutralized' means, even more considering this is ninja we're talking about :D (I really don't envy that OC a single thing...)
It was a common misconception that Jinchuurikis' bodies were healed from every wound or illness by their Bijuu.
It was an easy mistake to make by both civilians or shinobi, be it because they thought the container was the monster itself or be it because the powers of a Bijuu were Great Unfathomable Things–and well, the injuries did heal faster than average, didn't they?
From there, it was an easy mental leap to make that Jinchuuriki couldn't hold any kind of lasting damage.
(Naruto, if asked, would've squinted at the person, and wondered if he'd lost his hearing someway along the way as well.)
It was a common misconception that Jinchuuriki's accelerated healing translated into some kind of immunity to the possibility of the incomplete or deficient healing of a wound: cellular damage, infection, tissues growing where they shouldn't... It was an easy mistake to make by both shinobi and expert medic-nins, by confusing the contained creature and the container.
It was not a confusion made out of ill-will, in any way: after all, Bijuu were creatures made of chakra, able to reform their bodies no matter what way it was destroyed, and within the considerably short span of ten years. Any non-lethal wound could be healed quickly, and that without considering their already sturdy and difficult-to-damage skins. Shinobi knew that much of Bijuu, at least.
And it was that knowledge that gave way to the misconception that, if given its time, any wound carried by a Jinchuuriki would heal itself as flawless as it would have under the care of medic-nin.
It was both a blessing and highly unfortunate that so few Jinchuuriki existed to prove these myths wrong.
Because if Jinchuuriki had really been so immune to any kind of lasting damage, Bijuus wouldn't be so hell-bent in making sure their containers (that is, if they were in any kind of cooperative relationship) weren't extensively hurt, and they wouldn't bitch so thoroughly to their Jinchuurikis when they were. Surely, Bijuus wouldn't tackle with so much dread the task of fixing any kind of delicate damage, even more harassed by the fact that most times they had to put themselves to such a task while their containers where still fighting. (And if possible, the ones with a less positive or respectful relationship with their containers would take over and try to end the fight as quickly as inhumanly possible, if just to take care of the wound before it became too irreversible.)
But alas, such complains couldn't be heard by anyone outside their containers, and none of them was usually interested enough in the healing arts to ask about the specifics of the healing or the reason of the Bijuus' anger. None was either a medic-nin or in training to be one, quite logically.
But, if someone would've asked? Many Jinchuuriki would've shrugged, making a face as they absently rubbed some part of their body, or frowning as they caressed marks never questioned by anyone.
And honestly, if the Ichibi's, the weakest of the Bijuus, favorite method of protecting its container was by means of an impenetrable sand barrier (and a secondary sand armor covering his entire body), was it so difficult to reason that maybe a Bijuus raw power of regeneration didn't translate perfectly to very human, very inherently solid flesh?
Apparently, it was.
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Naruto Uzumaki started to squint at the age of seven.
One month before, the Uchiha Massacre had left everyone but a single clan child to join the Uchiha catacombs.
One week before, his eyes had been gouged out by the kunai of a chuunin whose teammate had been one of the victims, in between screams of pain and accusations of being the cause of Uchiha Itachi's madness.
The chuunin had been neutralized by the ANBU squad before he could finish the boy's life, and the wounds had taken a scant five days to heal completely.
The child remembered nothing, and the Sandaime made sure to personally accompany him in public for the next week or so, and later always have some blatantly-conspicuous shinobi dogging the boy's steps and sending a very clear message to any would-be attacker.
Overall, it was considered a victory against another assassination attempt on the Jinchuuriki, even if this one had come a little too close for comfort.
Naruto himself, while annoyed about not remembering falling from a tree and hurting his eyes with some stones lying around, had been overjoyed when he'd been finally relieved from the itchy bandages, and more so when he'd been discharged from the hospital (which, thanks to an almost successful escape attempt the moment the bandages were off, had come pretty quickly). That, added to the fact that his Jiji was less busy than usual and could thus go out with him or let him stay at the Hokage Tower for hours, made the following week one of the best in Naruto's life.
So he didn't pay much attention to the fact that he began to squint a little to see things better, because some shapes were too blurry to recognize without squinting. It was just a little detail in the full picture of his day-to-day during the Awesome Week with Jiji.
After that, he never really paid much attention to it, or to the fact that there were times when he could see perfectly without needing to squint, and times where everything would be so blurry he'd need to squint really hard to see anything. On those times, he learned to trust his nose, ears and sense of touch when he couldn't quite pinpoint what was what by simply looking at it. And since the episodes never lasted long, well.
Out of sight, out of mind.
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(When eighteen years old Sakura Haruno made a thorough diagnosis jutsu on his teammate's head after Naruto received a fireball to the face that left him looking like a half-dissolved surrealist picture, she was startled to find an internal, and by the looks of it long-term, injury in the blond's eyes, one that by any means should've rendered him completely blind long ago. When she later interrogated the man about it, Naruto would only give her a wide eyed stare that more than any screamed words manifested his utter bewilderment. When Kakashi fell under her mercy in her quest for answers, and specifically the answer to how in Kami's sake had no one know about this before, she only received veiled explanations about it being a S-class secret and to ask the Hokage for further information.
That said, when Senju Tsunade was informed of this, she furiously searched through the archives until she found the document detailing the attack and the medical procedures that followed it, and by then it was really lucky that both the Sandaime and the Head Medic-nin of that time were long dead.
It was very, very lucky for them indeed.)