When the Fourth Hokage summoned the Shinigami to seal the Kyuubi, he had no idea that someone had managed to slip something into the seal work at the last minute. That someone being a dimension-hopping vampire who wanted to cause a little chaos for Konoha and a headache for a certain white-haired Archer.
In short, when Minato summoned the god of death, he also summoned Archer EMIYA and accidentally tied the Servant's existence to his son.
It took Shirou four years before he found his "Master", and once he did, he knew he couldn't sit back and let things stand. He had already established himself as a blacksmith in the village. Thanks to the Kyuubi attack, no one was going to look too closely at a civilian blacksmith who was serving food he had killed in the Forest of Death for free to those who had lost everything. And by the time things had settled enough that people would question his presence, they had become accustomed to the kind blacksmith who bought and lived in a house most wouldn't want because it took too long to bring it back to livable standards.
He bought it, he fixed it up and as far as the shinobi cared, he was a civilian and therefor not worthy of notice.
So when he found a small blond child trying to avoid a drunk with a broken bottle intent on doing harm, Shirou intervened. The second he went to check the boy for injuries, he felt the familiar presence of command seals. Indeed, he could see from the torn shirt the boy had a massive set of Command Seals in the form of nine tails.
So he had nine of them, as opposed to the usual three.
Shirou didn't hesitate. He made sure the boy was safe before discreetly stalking him. Shinobi turned a blind eye to civilians, as if they were assured of their superiority. Because he barely had any 'chakra' he was obviously not a threat. And no shinobi would trust a civilian to spy on a village. Certainly not one as noticeable as Shirou Emiya was.
What he saw had him frowning.
The boy was more than just a pariah...he was the village's personal scapegoat for when things went wrong. And if the boy died, then he would go back to his own personal hell again.
And that was entirely unacceptable.
The first time Naruto meet the strange man, the only thought in his mind was that he was different.
He didn't have the same aura of misplaced hatred or disdain. In fact if he had to put a word to the white-haired man's personality, the first thing that came to mind was apathy.
This man didn't care about whatever percieved injustice he had done to the village. He didn't care about shinobi or the Hokage. He didn't give a damn about any of the things people thought important.
And that fascinated him.
He noticed the man observing him from a distance, wondering if he fascinated the odd man as well.
Then came the day his life changed for the better.
Every other year, his birthday was a day he dreaded. He was kicked out of the orphanage, and with the number of drunken idiots in the streets the risk factor shot up to terrifying levels for a recently turned five-year-old.
A drunk tried to swing a full sake bottle at him, and right as he was about to duck, a now-familiar figure stopped it. The ANBU were busy at work dealing with other idiots, and the ones in charge of 'guarding' him were those who had hidden their disdain of the boy well enough that the Hokage hadn't seen it.
They would stop him from being killed, but shielding him from a nasty beating was another story.
They didn't even bother to report the odd civilian picking up Naruto and absconding with him.
The next morning...
Naruto woke up to the most heavenly of smells. Food. Actual, hot food that was being cooked.
He had never had a properly cooked meal, save for the ramen he got from the Ichiraku stand when they could spare it. Which sadly wasn't often. Other than that, the best he could hope for was just-expired meals.
Naruto carefully walked out into the kitchen, where the man was cooking breakfast. It looked like he was cooking for more than one person, but he knew better than to assume kindness from anyone.
Last time he had thought that, he was almost sold to some particularly unpleasant people before the Hokage found him. He had been very angry about that.
"I know you're up kid. Take a seat. I should be done with cooking in a minute or two," said the man.
Naruto could hear the apathy and disinterest in his voice. However it was infinitely preferable to the tone of those who would like nothing more than to see him drop dead for something he had done nothing to deserve.
The man placed a plate in front of him. It smelled delicious.
Naruto looked at him in shock. But seeing that the man was already eating his own plate, Naruto dug in.
It was the best thing he had ever eaten. Bar none.
They ate their breakfast in silence, and though some might be put off by the stranger's lack of questions, Naruto didn't really care. He was the first person in the village who didn't pretend around him.
Even the old man Hokage seemed like he was holding back a lot from him. He refused to even mention vague hints about his parents, despite Naruto asking repeatedly.
Once he had finished (and borrowed the bath long enough to get cleaned up with freshly laundered clothes), the odd man showed him how to bypass the traps around his house long enough to get him back to the village.
He should have known he was doomed to be stalked by the five-year-old the moment he showed him kindness.
Though honestly the man ("My name is Shirou, kid.") didn't seem to actually care that he had set himself up for a frequent intruder/stalker.
A few weeks later...
Shirou seemed resigned to Naruto's presence in his home. To be honest, he had suspected this would happen after feeding the kid and letting him get cleaned up.
It made protecting his Master easier, even if Naruto had no idea of what the "odd birthmark on his back" really meant. The morons in the village took the tails, whisker marks and the fact the kid had the WORST luck to be born during the attack to mean that the boy was the fox reborn or some such nonsense.
Though the moment Shirou saw the piss poor stances they were teaching him at the Academy, he knew he had to intervene. Well, that and the semi-frequent attempts to break into his home or interrogate him discreetly spoke volumes that something was up.
The Hokage couldn't legally drag him into interrogation because the only thing he had done was let Naruto crash in his house and generally take care of him. After all, Shirou was a "civilian". There were laws about harassing them and he was respected and well known enough that if people found out, the merchants would raise one hell of a stink.
He was the best person to go to for weapon repair and he paid the best for old kunai too damaged or rusted to be of any use. He was the only blacksmith who could take the weapons no one wanted or used anymore and turn them into acceptable swords to practice with for genin or the odd chunin. They weren't of decent quality, and they broke when faced with a superior sword, but they were good for training and light combat. That and they were cheap for exactly that reason.
Hence why he had one of the most profitable smithies in the village, next to Higurashi Weapons. They had a friendly rivalry.
No shinobi under jonin was going to snub his shop because he was being nice to the village pariah. The younger chunin and most genin needed his place to make quick cash for things like groceries or rent, and scouring old training fields was easier than chasing Tora the demon cat again.
When the orphanage kicked the boy out permanently, with only a few paltry possessions to call his own (mostly small gifts from the Hokage, like a frog wallet or his sleeping outfit) it was no surprise Naruto declined the offer of a pathetically small apartment.
Shirou had a resigned, but bored look when the kid showed up on his doorstep almost a full day after he collected his things.
To be fair, he had expected this to happen and had already made a room for him.
And he even had a fair deal for the kid to pay "rent".
"Here's the deal. You can have the small garden near the dojo to grow food and whatever plants you want in, and you have to help with the chores and keep up with the place whenever I leave the village for a few days."
Naruto nodded his head, and the Hokage looked surprised at the fact Shirou was letting Naruto live with him. He wasn't adopting him, but letting the boy act as a renter was more than most would consider.
Naruto dashed into his new room, and Shirou looked at the Hokage.
"I only need help with the food bill until he gets a proper garden growing. After that the only thing I need is permission to hunt in the training grounds for meat."
Sarutobi Hiruzen looked at him shrewdly.
"What's in it for you?"
Shirou's laugh was hollow and full of bitterness. He found no humor in the situation.
"You let your own people beat and treat a child like a pariah and scapegoat for their own problems because of a few birthmarks. He's regularly starved, fed expired food, and the only other people who even treat him like a human being are the father and daughter who run the ramen stand! And you're really questioning whether or not I care about the rumor the kid is some kind of demon. Really?" said Shirou flatly.
The Hokage winced. When he put it like that, it did sound callous and manipulative.
Shirou was a civilian who had the bare minimum of contact with the shinobi, and he never brought anything suspicious in or out of the village.
In short, he was labeled a "curiosity, but not a threat" to village security. Even Danzo, the old war hawk, didn't think he was worth investigating.
The fact he was taking in Naruto upgraded his potential threat level, but Shirou Emiya still gave them nothing to bring him in. And without that, the Hokage's hands were tied.
A shinobi's paranoia was a strange and terrifying thing.
Shirou saw Naruto practicing outside with the training dummy, and the first words out of his mouth upon seeing the abominable stances was...
"What in the name of all things good and holy is that supposed to be?"
"Taijutsu!" said Naruto cheerfully.
"That is not a real stance. That is what happens when a brawler is given a fake style and told it was real," said Shirou, pinching his nose.
Naruto looked downcast.
"How would you like to learn a real style?"
Naruto's smile light up the entire area.
"Using that crap is almost guaranteed to get you killed. And from what I've seen of your healing factor, you might be able to use my fighting style almost as well as I can," said Shirou.
The first thing he did was toss Naruto a bow and arrow.
"I thought we were learning taijutsu?"
"Lesson one. Until you learn how to fight your enemies off up close, you need to know how to keep them at bay from a distance. This also teaches you patience and how to aim, as well as meditation."
Naruto perked up at that.
"Now since you're no where near ready to fight a skilled opponent close up, you're going to deal with them from a distance. And to do that, you're going to learn archery."
Archery wasn't as easy as it looked. In fact Shirou had to replace the bow three times before Naruto learned how to draw it without accidentally breaking it. To be fair, it was the "child-friendly" version Shirou sold to civilians for their children. It came with blunted arrows and cheaply made bows.
Perfect for children pretending to be shinobi and as a starter set for aspiring archers. Back when he was alive, such things had been made of plastic and cheap string.
Naruto had a single-minded focus when it came to training. He took every lesson and actually listened to what Shirou was teaching him. Like Shirou, he had naturally sharp eye-sight and a knack for aim. What he didn't have was experience.
Teaching him archery was giving him something his teachers were neglecting because of who he was.
The ability to hit things with sharp and pointy objects, even if he had to use a modified crossbow.
And the moment Shirou got even a brief look at the trash they were calling 'text books', he went to the bookstore and got real books on the subject. Multiple sources and all of it backed up by hard evidence and fact. The stuff on chakra was regulated, but only in the shinobi run villages.
He was not going to let the crazy little kid he thought of as his little brother be held back by idiots.