Before you read this please keep in mind this is my version of what could have happened. This is a work of fiction and my version of Snape, so he will be different.
I own nothing
The Order of the Phoenix sat around the old table in Headquarters after "burying" their dead leader. Harry, Hermione, Ron and Ginny have been removed from the school and brought to Grimmauld Place where the elder order members felt they would be safer. A very worried Albus Dumbledore sat waiting for his potions master to arrive. You see Severus Snape refused to kill Albus and enlisted the help of Remus Lupin to convince the headmaster to fake his death in order to buy Severus time to find a potion to cure Dumbledore. When an angry and distraught Harry Potter made his way back to the castle after trying to hex Severus Snape he nearly fainted when his head of house led him to the headmasters office where none other than Albus Dumbledore sat flanked by Remus Lupin and Kingsley Shacklebolt. He was then told about the plan along with Hermione Granger and Ron Weasley.
The Order decided to go ahead with the burial and service. The only people aware of Dumbledore's amazing recovery were the people present; that would be the Golden Trio, Minerva McGonnagal, Madeye Moody, Filius Flitwick, Shacklebolt, the Lupins and the rest of the Weasleys. Albus was going to stay at Headquarters, leaving only in disguise. The golden trio was going to spend their summer there as well and continue their studies, sitting for their Newts in September. This night they were officially brought into the Order.
Hermione's parents had been whisked away the night before Dumbledore's "death" and brought to a secure location known only by Dumbledore, Lupin and Snape. Their practice was closed while they were on sabbatical. They sent Hermione a letter telling her they were fine but asked her to consider joining them. She wrote back telling them that though she desperately wanted to see them she felt honor bound to stay and fight with Harry. Her parents knew about the problems in the wizarding world and had implored Hermione to leave the school but she refused stating that she had to fight for what was right. This frightened her parents but also gave them an overwhelming sense of pride in their daughter.
Harry's aunt and uncle were much more difficult. Actually it was Vernon who proved to be a problem and he didn't relent until Dudley made his parents see reason. Dudley had stopped growing physically and matured mentally. Ever since Harry saved him from the Dementors he had been visiting Mrs. Fig and asking her all sorts of questions. That was how he had found out the truth about Lily and James' death. Dudley explained to his parents that choosing to not believe in magic would not make it go away and he was choosing to leave with Severus and Remus. This of course prompted Petunia to follow and Vernon grudgingly agreed. They were brought to the same location as Hermione's parents and were safe.
Three days after the faked murder and the evening of the staged burial they all were waiting anxiously for Snapes arrival. Only Albus and Minerva knew what he was doing and why it was taking him so long to join them.
"Albus do you think Severus is ok, you don't think You Know Who found out about the plan and Severus's true allegiance."
Dumbledore was about to answer when a silky voice said from the doorway, "No Minerva he is presently celebrating the death of the one man he feared above anyone else. It took me a while to get away and then to gather Amelia and her things." Everyone looked up to see Severus Snape enter the kitchen holding a small child in his arms. The little girl looked at Minerva and smiled sleepily reaching her small arms for the older woman to hold her.
"There, there little one, Aunt Minnie is here. Hermione dear will you help me get her settled in the room next to Severus's. I'll explain it all to you. I'm sure Severus has a lot to tell the rest of the order."
Wide eyed Hermione followed Professor McGonagall to the stairs. She looked at the little girl in the older woman's arms and instantly fell in love. The little girl smiled sleepily at Hermione and yawned. Whoever the little girl was Hermione was sure she was related to Snape, the dark eyes and hair was a giveaway. A niece perhaps or a cousin or his daughter. Daughter? Well Snape wasn't married as far as she knew but he was a man and men have affairs. But Severus Snape with a daughter? Hermione allowed herself a small smile thinking about the girls first date and the poor unknown boy who would ask her out.
"Hermione I'm sure you are curious. I'll get right to it then, this little angel is Severus's daughter. It's a very long story and one I am sure he is telling everyone else at this moment. You see when Albus asked Severus to join the Dark lord after his resurrection there was a revel. I will not go into detail about what goes on at these revels but suffice it to say Muggle woman become the entertainment. Severus is a brilliant potions master and was able to feign impotence with the help of a potion. He did however go to a Muggle bar after witnessing the horrors and got pissed as you young people say. The potion wore off. He woke the next morning next to a brunette who had been just as drunk as he was. It was of course awkward but they did continue to see each other a few times after that. Three months later she contacted Severus and told him she was pregnant and the baby was his. He of course checked with a simple spell and immediately proposed. Kate refused telling him that she would only marry for love and that she would raise the child alone. Severus vowed to support her and the baby and he was there when she was born. Six months ago Kate was diagnosed with stage four cancer and given only a few months to live. Four months ago she died. She did not have a family and Severus is now a single father. Amelia has been at the castle this whole time living in Severus's chambers and being cared for by Winky and other house elves. She will be living here with Albus now because anytime now the school will be taken over by You Know Who and there will be Death Eaters in the school."
Hermione was shocked, not that her potions professor had an affair but that he got so drunk he ended up in bed with a stranger. She always thought of him as someone who was always in control. She looked down at the little girl who was now fast asleep and wondered what kind of father Severus Snape was.
Minerva and Hermione walked into the kitchen just as Snape finished his story. Harry and Ron looked shocked and Ginny was looking at him with new respect. Molly was the only one who seemed upset.
"Severus Snape that little girl cannot stay here being taken care of by a house elf!"
"Molly Albus will be here, I cannot very well bring her to Hogwarts, the Dark Lord has already told me that once the ministry falls he will make sure I am headmaster and install the Carrow twins as teachers. I will not have Amelia near them."
"Molly, Amelia will be fine here. Remus and I have agreed to stay here as well to instruct Harry, Hermione and Ron. She will be safe and well taken care of." Tonks said.
Snape rolled his eyes, "My daughter will be surrounded by a bunch of Gryffindors and a Hufflepuff, wonderful."
Hermione took a seat in the only available space, right next to Snape. He nodded to her and she said, "Your daughter is sleeping peacefully sir."
"Thank you Miss Granger." Hermione was stunned, that was the most civil thing Snape ever said to her.
"Now since we are all here I will share the plan with you. Harry, Hermione and Ronald will study for their Newts under Remus, Nymphadora, Kingsley, me and Minerva. Ginerva will attend the defense lessons with Remus. Severus will continue to instruct them in potions but Hermione you will be working with Severus more than the others to create a few special potions. He will explain it to you another time. We need to research and find the other horcruxes. Harry destroyed the diary, I took care of the ring, and we just found the locket Regulus stole in Kreachers hideaway. I believe I asked you to bring Godrics sword Severus so without further delay let's destroy another part of Tom Riddle." After seeing the initials RAB on the note in the fake locket Dumbledore knew it had to be Regulus. Upon entering Grimmauld Place he spoke to Kreacher who admitted to having Regulus's things and told them Mundungus Fletcher stole the locket. Kingsley found Fletcher and deduced that Dolores Umbridge bought the locket. Kingsley spotted the piece of jewelry around her neck and without the woman suspecting managed to relieve her of the horcrux. It was something he learned in his younger days. This was all accomplished the day before. Shacklebolt wasn't just called the best in the business, he was the best there was.
When Severus handed Albus the sword Albus then handed it to Remus who struck the locket. The kitchen was filled with howling cries but in the end the locket was no more and they only needed to find four more which Albus was sure two of were at Hogwarts and two more were breathing.
Later that night Madeye, Filius Flitwick and Remus followed the Weasleys home where Flitwick cast charms and spells to put the Burrow under the fidelius with Madeye as the secret keeper. Bill and Fleurs wedding was going to take place privately at the Burrow with only her parents and sister as the only non order members present.
As the house quieted for the night the four youngest members sat together in the kitchen talking about all that had transpired in a few days.
"Who would have thought Snape a father eh? That woman must really have been drunk to sleep with the git." Ron said to Harry.
"Ronald Weasley that poor woman is dead, and Professor Snape is not a git. It is obvious he loves his daughter." Ginny reprimanded her brother.
"Gin I was only saying that, well you know Snape isn't all that attractive with that big nose and greasy hair."
Ginny and Hermione just stared at him, "Ronald, Professor Snape is very attractive. Besides the fact that he is brilliant, that voice of his is sexy, he is tall, fit, he has striking eyes and though his nose is large it fits his face. He reminds me of Trent Reznor." Hermione added.
"Who?" Both Ron and Ginny looked at her.
Harry laughed, "A Muggle musician, now that you mention it Hermione he does sort of look like him."
"You can't mean you find him attractive Hermione. You turned me down twice!"
"Ron not only do I find him attractive but many of the girls at Hogwarts do to. There's something special about a mysterious man. Remus had a few admirers too when he taught there."
"Remus had a few admirers where?" They all turned to see their favorite werewolf standing in the doorway smirking. Tonks was right behind him.
"Hermione thinks Snape is attractive and said girls at Hogwarts think so too, then she said there were many who admired you when you taught there." Harry informed Remus grinning.
Remus blushed and Tonks laughed. "Yes well those girls at Hogwarts need to keep their hands off of my werewolf. And I have to agree with Hermione, girls were attracted to Severus when I was at Hogwarts too. Now I believe you four need to get to bed, lessons start right after breakfast."
"Already?" Ron whined.
"Yes Ron already, your Newts are only three months away. Now off to bed with you, you too Ginny." Remus said to the redhead when she was laughing at her brother.
Ginny made a face but dutifully followed the others up the stairs. She wasn't studying for her Newts since she was a year behind them; she was going back to school in September and she was given a role to play by Professor Dumbledore. She was to start up Dumbledore's army again and get the sixth and seventh years ready for the battle, because Dumbledore knew that was where it would take place. She was going to learn as much as possible from Lupin and Tonks in defense; she wanted to help as much as she could to defeat Tom Riddle.