AN: I have been told this is hard to understand in some parts,
To stop confusion:
Harry Potter is who Harry thinks he is and the rest of the world knows him to be.
Harry Snape is his real name found on all magical documents.
A Snape Is the Father of Harry's Fic.
This story is a: 'Snape-is-the-father-of-Harry-Story'. In this 'Snape is the father of Harry story' nobody knows that Snape is the father of Harry. Lily knows that Snape is the father of Harry. However she took that knowledge to her grave. Snape didn't know that he was the father of Harry, hell, even Harry didn't know.
Harry Potter was neglected, that much is certain among the Harry Potter community. Indeed some fanfic writers take it one step further, they think a lot more than neglected happened to our young hero.
No matter what happened, when this author found Harry Potter he was very unhappy. Our hero was dreaming of someone, anyone, to take him from the Dursley's. Somewhere safe.
In Hogwarts School, it was that time of year where the Hogwarts letters were to be sent out to all the future first years. This Process is done automatically, a simple spell transforms the list of students into Hogwarts letters, and another spell sorts the muggleborns out from the rest.
Due to the fact Harry Snape has two magical parents Lily and Snape, his Hogwarts letter recognized him as a pureblood and a letter was automatically sent. The process had holes in it, yes, Harry didn't know he was a pureblood, hell he didn't even know he was magic, he didn't even know his real name.
Everyone at Hogwarts assumed Harry Potters letter was sent that day.
Harry Potter was walking home from school, blood running down his white shirt; he had just recovered from a round of Harry beating from Dudley and his friends. An owl flew gracefully down, Harry saw it and stopped for a moment to watch it, it landed on the path close to Harry. Harry saw there was an envelope and looked down to it.
"Shame, my name is Harry Potter, not Harry Snape" Harry thought to himself.
The owl hooted and Harry could tell the owl was annoyed.
"Do you want me to take the envelope?" He asked the owl.
The owl held out a leg gracefully in response. As soon as Harry took the envelope it flew off.
Harry sat down on the grass between the pavement and the road, he opened the envelope, yes he was covered in blood but he wouldn't get any sympathy by going home. He read the letter, the Harry Snape person had got admitted to a place called Hogwarts.
The next morning Harry Potter was made to get the post by his uncle.
Harry laughed at the BT envelope, Uncle Vernon wouldn't be happy with that bill. There was another envelope but it had no stamp, it was addressed to "Harry Potter" and looked exactly the same as the one addressed to Harry Potter."
"Daaaaadd" Dudley whined, "Harryys got some pooossst." In the blink of an eye, Vernon had snatched the post out of Harry's hand.
Vernon cried "Out, Out."
Harry smirked. "I know what it says anyway. I got one yesterday for Harry Snape." Harry's uncle and aunt turned at him at the same time.
"Say that again Harry." Petunia ordered.
"I know what it says."
"No the name. What was the name?"
"Harry Snape." Harry replied. "I don't know anyone around here with the name Snape."
Petunia sat down, visibly faint. "Show me the letter." she asked.
"You're still in love with him?" Vernon half asked half shouted.
When Harry returned with the envelope Petunia and Vernon were arguing. Needless to say this frightened little diddyduddlykins.
"He is going to Hogwarts." Petunia said. "We will go to the alley today.
"Harry, dear, go outside and see if there is an owl there."
Vernon was mad, under no circumstances was that brat going to Hogwarts.
"HE is my sister's son, and if I say he goes, he will go." Petunia then turned to her son. "Dudley do you wanna come?"
"I refuse to let my son anywhere near that place."
"In that case, Dudley spend today cleaning out your second bedroom. Harry is moving in there."
"WHAT?" Vernon shouted, purple in the face.
"Look at the envelope; they know he sleeps in the cupboard."
Harry came back a few minutes later with an owl following him.
"Come here" Petunia said to the owl. "I will write a reply." And she did. It read:
Harry will be going to Hogwarts, I shall take him today to get his Hogwarts list.
After the owl flew of Petunia Dursley went into the attic nobody knew why she was there but there was an unbreakable silence in the Dursley household about the men.
"Come on" Petunia said once she had come down.
(Harry and Petunia drove to Diagon Alley. Well not to Diagon Alley itself but they found a car parking space nearby. Both were thankful that Vernon had not come, he had terrible road rage and London traffic would have sent him crazy.)
"Why was the first letter addressed to Harry Snape?" Harry asked in the car.
Petunia didn't know. "When you were left to us, that head teacher said your name was Harry Potter."
'Lily married a Potter' Petunia thought to herself.
"If you are Severus' son it would have been an out of marriage affair." Petunia said bluntly before seemingly talking to herself. "Potter couldn't have known - They never divorced - You do look exceptionally like James though - Lily had green eyes - you have your mother's eyes - But then there is no telling what those freaks can do"
Harry noticed that Petunia kept looking straight ahead as she said this.
"But why would they send two letters addressed to two people?" Harry asked.
" - I don't know - don't ask questions-" Petunia Snapped. "Gringrotts will tell you - They can do things like that- "
(And so they went to Gringrotts, they did a random magical ritual where Harry was found to be Harry Snape. Conseieved through an out of marriage funness. Harry was also allowed the money left to him by James simply because it was in his will.) They went shopping and Harry got to ask Petunia questions about his fathers and mother. Petunia always got annoyed and told Harry to go to his room but he was always allowed to ask questions the next day.
Nobody at Hogwarts School of witchcraft and wizardry realized Harry Potter had a father by a different name, when it came to Hogwarts replies the names were automatically ticked off by the magical signature each person held, therefore Harry Snape was on the Hogwarts list but Harry Potter was not.
McGonagall was the only person who had access to the list of firsties. She didn't look at it, she spent the night before betting with the other teachers on which house Harry Potter was going to be in. Every head of house put two Galleons in their house except Snape, the scrooge, who didn't bet. Snape simply came for the elf made mead.
"Have a good term at Hogwarts Harry", Petunia said at Kings Cross. "I will have a nice perch or something for Hedwig in the back garden by the time you get back."
Harry for once was wearing some nice clothes, Petunia had brought them for him soon after he got his Hogwarts letter.
"Don't get up to too much mischief " said Remus, Petunia had finally answered Remus' post and allowed him to visit, Remus took Harry out to all the places Harry wanted to go, the zoo, the cinema, Chessington world of adventures. Remus also told Harry all about Lily and James. These stories including the horrible tales of the Marauders and Severus Snape. Harry was sure this Harry Snape was a half brother or something.
McGonagall's head was aching slightly from the night before, not even the potion Severus gave her stopped her head aching, at least she wasn't seeing double anymore. The deputy head read down the list of names for the sorting hat, when she got to the place where Potter should have been she pause for a moment looked up, spotted Potter in the crowed, shrugged and carried on.
Finally she got to "Snape Harry". The Boy who looked like Harry Potter had stepped up and went to the stall.
Ron Weasley could be heard over all the noise, "That boy told me he was Harry Potter, but he's that evil git's son; wait till I get to him."
Meanwhile Dumbledore could be seen by the students give a glace to McGonagall, they then both looked at Snape who had not moved an inch since that name had been called out, a clear sign he was trying to control his emotions.
Harry put the hat on his head, "Slytherin" It shouted at once.
There was silence in the great hall, Harry missed the shocked look the teachers gave, he missed Severus hiding his head in his hand, he missed McGonagall's smirk at Snape's reaction he did however notice the silence in the great hall as he went to take his seat.
Needless to say it took a few minutes to resume the sorting while everyone got out of their shock.
As soon as the sorting was finished Snape stood up and walked out the great hall, this brought about much muttering amongst those students second year and above.
Don't expect updates take it as a one-shot, if anyone wants to continue the story please do.
BT stands for British Telecom; it is essentially a phone line company but also does broadband ECT.
I think the reason Harry got two letters, the first was magically done, and the second was Dumbledore's manipulations/Hagrid's doing.