This is another explanation fic. This kind of explains Snape's feelings toward Harry and Harmony in chapters 10 and 12. I believe there will be two chapters to this, but if there ends up being more I'll let you know.
Seeing
Severus Snape was sitting at the staff table at the beginning of the feast as he did every year. In a few moments the first years would walk through the doors and be sorted into their houses. He would of course mark in his mind every new Slytherin's name so he could find out more about them. So he was not the most liked person in Hogwarts, but he was, in fact, an amazing Head of House.
The doors at the end of the hall opened and all the first years filed in. Snape watched as their little nervous faces approached the High Table, then they stopped and lined up in a neat line facing the students.
Immediately Severus picked out the white blonde hair of his godson, Draco Malfoy. He scanned the row of first years in front of him and there in the middle was the black hair he had been warned he'd see, James Potter's son, Harry. 'Of course Lily's genes were overrun by that pompous, foul . . . well in any case . . . no doubt he'll be just as arrogant and awful as his father.' Snape thought. 'But wait, where is his sister?'
Snape scanned the line of first years harder now for the same jet-black hair. He didn't find it. He shrugged it off as if he didn't really care, but his eyes kept wandering over the first years. 'Stop it, Severus!' he chastised himself. 'You'll see her eventually anyway. She has to be Sorted and Dumbledore told you she would be here. So quit acting like a nervous school boy!'
The names started getting called. A new Hufflepuff, a new Gryffindor, a new Ravenclaw, then as expected Draco was sorted into Slytherin. No Potter, not yet anyway. As the Sorting went on Snape began to feel more anxious, every name called seemed to push him forward in his seat. 'What if something went wrong? What if she's not here . . . Why are you so worried about this Severus?' He already knew that answer, though he thought that Potter's genes had dominated Lily's he still hoped that maybe by chance that was the case only with one child.
"Potter, Harry!" Snape looked down and saw the black haired boy be Sorted into Gryffindor. 'Figures—just like his father.' Severus failed to mention to himself that Gryffindor had also been where Lily was put, but he disregarded that fact due to the way Harry looked.
"Potter, Harmony!" Severus sat stunned. Instead of a black haired girl there was a girl with reddish-golden hair. She was an almost exact replica of Lily from the back. Severus felt his heart leap involuntarily, which House would she be put into? He hoped against hope that she would turn out to be a Slytherin.
"Sly—" He heard the Sorting hat say and he sat up a little straighter, ready to receive Lily's child to Slytherin, but then . . . "Gryffindor!" 'What?' Severus thought alarmed. 'It said Slytherin—I heard it say Slytherin, or start to anyway.' Then he realized the obvious, something must have happened to change the Sorting hat's mind.
He watched in a little disgust as the little girl went running over to the Gryffindor table and sat right next to her brother. Then he saw it, her eyes were all wrong. They were hazel, not green. Severus felt something harden in him, the way it did whenever Potter's memory crossed his mind. Suddenly Severus hated the girl, it was a sin to have that arrogant toe rag's eyes on Lily's perfect face.
He watched the girl for a while and saw that almost every gesture she made was somewhat what Lily used to do. 'Maybe I can forget the eyes. She does seem a lot like Lily.' He thought, but as soon as he looked back and saw her eyes he knew he couldn't, at least not very easily. Then Quirrell engaged him in a conversation and he forgot the Potters for the moment.
Snape felt eyes on him and he looked past Quirrell to check on the Potter girl and saw her looking at him as well. He saw a slight look of pain cross her face then she bit her lip. 'What was that?' Snape asked himself. She still had her eyes locked on him then saw a questioning look in her eyes and then she turned to talk to the prefect Weasley boy.
Snape knew what she saw. He had let his emotions come through for one split second and the girl had read them. She must have seen his hostility toward Potter and his hope that she might be like Lily. He could feel her eyes stay on him as he turned back to Quirrell.
He looked at her one time that luckily she didn't see. He saw her run her hand though her hair, and that did it. It was something Potter had done often. Now he felt the hardening sensation. He was liking Lily's child less and less because of how much Potter leaked from her. He turned back to Quirrell once more.
'What color of eyes did the boy have?' Severus thought to himself, then he realized he didn't know and he was curious. He looked toward the Gryffindor table once again. He saw green eyes staring back at him from his enemy's face. 'No he does not have Lily's eyes! He cannot!'
He watched the boy clap his hand to head when their eyes met. He watched the twins begin to converse. Then he turned back to Quirrell and promised himself that he would not look back.