Disclaimer : This is a fan-made work. Fate/Stay Night and Harry Potter are owned by Type-Moon and J.K. Rowling respectively. Please support the official release.
I'm rewriting the story up to so far. This includes retcons, and combining some chapters.
Harry Potter did not like his current living circumstances. He was living in a cupboard, and he was barely getting enough food to live. He was still extremely malnourished. His cramped cupboard also did not help his growth,
He had just woken up, and he had hit his head on the top of the cupboard. "Ouch!" he yelped. Then from the outside. Petunia Dursley yelled "If you're awake, go down, and prepare breakfast!"
Knowing it would be unwise to take too long. He rushed down, and got started on the cooking. He, being 6 years old, burned his hands on the stove. He made a small noise in pain, but then Petunia heard it. She immediately shrieked ""Be quiet, freak!"
He then focused back to the food. He took the bacon, and the eggs off of the stove. He plated it, placed the food on the table, and started his other chores. He started tending to the garden; however, Petunia called him back.
Then Vernon who already finished his breakfast made an announcement. "Today it's Dudley's birthday. So, we are taking him to the arcade. Freak, we are dropping you off at Mrs. Figg" I was slightly sad, but it would be better than being with Dudley and his friends the whole day.
So, they all got ready to get into their car. The car started, and it fell. It drove forward as a portal suddenly opened up underneath it. "AHHHHHH!" screamed everyone in unison as the car fell through into the Nasuverse.
A man was holding up his hand showing his command seals. This man was Kiritsugu Emiya, and he said "Saber, by the power of my first command seal. I order you, destroy the grail." He then repeated that command two times over.
Saber, who was in tears, held her sword up. Unwillingly, she brought it down while shouting its name.
Excalibur!
Light burst from the blade. It engulfed the grail, but when the vessel was destroyed. The grail started spilling its contents. It destroyed the building, and almost everything else around it. Which included the car that fell through the portal.
Kiritsugu Emiya, could only watch, horrified at what he had just unwillingly caused. Kirei Kotomine, was feeling joy. He thought that this was the grail's answer to his question. Why did someone like him, who could only find joy in other's misery, exist. He thought this was the grail's way of telling him that causing misery was his purpose.
Zelretch, however, didn't know what to think. He made an honest mistake. He was about to travel to a certain dimension to pickup his apprentice, but his calculations were a bit off. He felt bad for the people caught in the explosion. Surprisingly, out of the wreckage emerged a lone boy with black hair, green eyes, and a scar. He recognized him. He was a Harry Potter. There were many Harry Potters with many different paths, and destinies. This one, however, seemed to be one of the more "normal" versions of him.
The boy then walked, on and on. He did not turn back. He did not stop to help the others who were also dying. He knew that if he stopped. He would surely die. So, he walked with his only thoughts being "I want to live." His body, however, gave up. He collapsed. The devastation around him not improving. The fire burned. All he could hear above the sound of the flames. Were cries of agony.
Rubble then fell on top of him the pain stopped, and he felt numb. "S-so, this is the e-end, huh?" he said to himself.
Fate had different plans. Kiritsugu Emiya, desperate to find one survivor, dug and dug through the rubble. He finally started digging the rubble on top of the boy. The boy saw light, and then saw a figure. He saw a man smiling. Joyously, the man shouted in Japanese "You're alive, you're alive, you're alive!"
The boy did not understand those words; however, he could hear the joy from every word. His only thought before his mind went blank was-
"I wish I could smile like that."
With that the boy formerly known as Harry Potter, fell unconscious.
Skip
The boy awoke. The room, had several medical tools. It had white walls, a white floor, a white ceiling, but it wasn't completely white. It had the color of the heart monitors, IV bags, and so on. He could see a doctor. The doctor realized that the boy was awake. He said a few things in Japanese, which the boy couldn't understand.
Then moments later, Kiritsugu came into the room. The boy could tell he was the man who saved him. He stated in Japanese "So, you're awake." The boy not understanding it, asked in English "I-I don't understand what you're saying." Kiritsugu was slightly surprised, but then quickly changed to English.
"So, you're awake." he repeated. The boy then nodded. Kiritsugu then asked the boy "There are no records of you. Who are you?" The boy then thought hard, but everything before the fire was gone. He then shook his head and replied "I don't know, I can't remember anything before the fire."
Kiritsugu then sighed. He then gave the boy a choice, "You can go to an orphanage, or you can be adopted by a man you just met." The boy thought, and then he pointed at Kiritsugu. Kiritsugu smiled. He then told the boy "Alright, since your recovered. I'll get the adoption papers ready."
The boy then asked for his name. "My name is Kiritsugu Emiya." He stated. Then he continued Speaking of names, we need one for you. Any preferences?" The boy couldn't think of anything, so Kiritsugu gave a suggestion.
"How about Shirou?" he suggested. The boy then asked "What does that mean?" Kiritsugu replied "It means white. I thought it fit because you are like a blank slate." The boy thought for bit, and then he nodded. "Huh, I like it actually."
So, Harry Potter became a nameless boy without memories, and the nameless boy became Shirou Emiya.
Part 2
Albus Dumbledore did not like the current situation. He saw all the charms checking the blood wards on the Dursley's house, fail. He rushed out to check on the home, scaring McGonagall in the process. He saw the home was empty. No sign of damage or attack. Just an empty house, like they just disappeared without a trace.
He then apparated back to Hogwarts with a pale face. McGonagall, still surprised, asked him what was going on. Dumbledore replied "Harry Potter is gone." McGonagall's face also grew pale, and she said "What do you mean he's gone!" Dumbledore replied "I mean he has disappeared."
Quickly, he sent letters to gather the Order of the Phoenix. After they all gathered. Remus Lupin spoke up first "Why did you call us here Albus?" Dumbledore with a grim expression, told them the horrible news.
A moment of silence was there. Then Remus was the first to reply "How could this happen! You said he was safe!" Remus then almost felt sadness. He lost all of his closest friends, and now he had lost his friend's only child. Dumbledore said "I do not know. The house of the Dursleys was empty. No sign of any attack. Which means that either a massive case of accidental magic occured, transporting them somewhere, or that someone who was is skilled in hiding evidence attacked the home."
Next, Moody spoke "This is bad. If news gets out. Then the light side will lose morale." Everyone agreed with that statement. Snape was silent; however, his thoughts were not. "How could this happen. Lily's only son, missing or dead." Snape although not liking James Potter knew that his son was still Lily's son. His former best friend's son.
Then Dumbledore with a serious face stated "We must do all we can to find him, or at least what happened to him. We will require everyone's cooperation." With that, everyone got to work.
However, Harry Potter was not reachable to them. For he was in another dimension.
Firstly, they made sure that no one knew Harry Potter was gone. After all, the chaos would be disastrous. Then each person used all the methods they could think of to find him.
So, Dumbledore first decided to call up all of his contacts, and he used all of the favors owed to him. Still, he had no leads to the location of Harry Potter. He tried every spell he could to track him, but none worked. He even tried a forbidden forced summoning, and still nothing happened.
The Weasleys did not have as many resources, but they still tried. Snape used his connections to the dark side of the wizarding community to try to get any lead. Moody also looked for Harry.
They kept trying and trying, for he had to find Harry Potter. If not, then the prophecy could never be fulfilled, and Wizarding Britain was doomed. So, with this in mind the Order of the Phoenix, fruitlessly, searched for Harry Potter.
Meanwhile, Zelretch thought of a way to try to make it up to the boy he brought into the Fuyuki Fire. The world he sent him to did not originally have a Shirou Emiya, but then due to the boy's appearance in this dimension. The world tried to correct itself. It used an alternate universe as a base. So, when Harry Potter was found by Kiritsugu. The world integrated him into the world as Shirou Emiya.
Zelretch decided to accelerate his growth in power as an apology. He secretly placed a modified Archer class card into him. It did not have the include or install function, but it linked the boy to his alternative, future self. This would lead to Shirou Emiya developing his reality marble in a much faster pace. Maybe he could closer to his impossible goal.
"It's the least I could do after bringing him into the hell that is the Fuyuki Fire." thought Zelretch. He then starting thinking about some other things he could do.
He watched as Shirou Emiya was living his new life, completely oblivious of his past.
Chapter End