Hey, sorry for the wait. I didn't really think anyone was reading this but turns out they are. So yeah.
My original intention was to rewrite certain scenes in the HP books to include Lyra and Dracos story. That is still the case, but I expected each book to only take up 1 chapter. After writing this, I can see that isn't going to happen, therefore you will be getting a story 2x longer than expected.
I hope this pleases you :)
Also, if you would like to know what chapters the scenes are from, just ask me.

The meeting.

Draco had not had an opportunity to welcome Lyra during or after the feast.
His fellow Slytherins had tried, in vain, to get his attention and include him in their conversations, but Draco had ignored them, too busy trying to catch a glimpse of the girl.
From what he could see, she was sat alone and only spoke if spoken to. Draco didn't understand this, surely the best thing for this girl to do would be to make friends.
It wouldn't be much of a hardship either. Most of the boys Draco had noticed, much to his despair, saw exactly what he did; a beautiful girl who would need people to help her around the castle and be her friends.
But, by the end of the feast, she was still sat alone. Then the prefects were calling for the first years and she was gone from his sight.

It was still dark when Draco awoke.
He checked his watch (a present from his mother and father last Christmas), it was only six o'clock but he got dressed and headed to the Great Hall anyway.
After slipping through the doors, he surveyed the room. No one was there, all trying to get as much sleep as possible before the first day of term, he supposed.
But out of the corner of his eye he saw a flicker of movement.
He turned and, to his most pleasant surprise, there sat Lyra.
Draco took a moment to, again, ponder the existence of god.
Then he shook himself mentally and walked over to her.
She was dressed in her school robes, sat staring at the table. At the sound of his approach she looked up.
"I hadn't expected anyone to be up at this time," she remarked, easily heard over the silence.
Draco, mesmerised by her voice, merely nodded. This seemed to amuse the girl, for she giggled and smiled at him.
It was the loveliest thing he had ever heard.
Her laughter was like music, ringing loud and harmonious through the hall. It was short, but echoed in so many different tones and textures.
Lyra stood from her seat and made her way towards him, seemingly impatient for him to come closer, as he had stopped at the sound of her laugh.
When she stood before him, he could truly appreciate how small she was, barely coming above his chest.
She took in his appearance, "Slytherin," she looked at the crest on his cloak. She smiled a little at this fact and held out her hand, "I'm Lyra and you are Draco Malfoy."
Draco took her offered hand and smiled, "how did you know?" His voice was raspy after sleeping.
"I asked someone who was sat next to me last night; you seemed to be staring at me."
Draco's cheeks warmed at this, "I was simply interested in my new housemates, I was looking at the others as well."
Draco was an accomplished liar, but something about her knowing look made him suspect that she did not believe him.
She turned and walked back to the table.
Draco followed behind but, as a group of people had just entered the hall, he chose not to sit with her.

The Weasley boy pulled his wand out of his robes, rather angry at Malfoy's comment about the howler his mother had sent him.
Hermione, the girl she had met on the train, closed her book and spoke. "Look out," she whispered, pointing towards the school building.
Gilderoy Lockhart was waltzing towards them.
When he reached the group of students he spoke, then proceeded to throw his arm around the boy with messy back hair and glasses.
Lyra assumed he was the Harry Potter boy Dumbledore had mentioned during their brief meeting before she came to Hogwarts.

Flashback:

Lyra was sat in her little, one roomed house, when she heard a crack outside.
She stood from her kitchen table, just as a knock came from her front door.
There, framed by the trees of the forest she lived in, stood the most wizardly looking person she had ever known.
She had met the tall man once before, when he had told her about witches and wizards and magic. Then he had had offered her a place at his school, Hogwarts, because she was a witch.
She had accepted gladly, wishing to leave the life of a forgotten, lonely, little orphan behind her.

This time, he had come to give her a little background history of Hogwarts and magic.
She had listened with rapt attention as he described how Hogwarts had come into being, of the four founders; Hufflepuff, Ravenclaw, Slytherin and Gryffindor.
Then he had told her about more recent events; the war with Lord Voldemort, which was sure to continue in the near future and about the 'boy who lived', Harry Potter and why he was famous.
This tale held no interest for Lyra, even if he was only a year older than she.
Dumbledore then told her about muggle borns' and squibs; this did interest her as she guessed that she was what they called a muggle born. Not that she could know for sure, never having met any of her family.
She had questioned him about it, but Dumbledore assured her that it would not be a hindrance to her ability.

End flashback.

Lockhart dismissed the group of students, and she watched as Draco turned away from him. She saw Draco's features shift from amusement to a frown as he looked towards her.
The frown turned to surprise as he realised that she had been watching the whole time.
He smiled at her, then he was being pushed towards the castle as the Slytherin fifth years crowded around him.

It was late on Friday evening and most had left the Slytherin common room to go to bed.
Draco was sat in one of the better armchairs by the fire, a group of Slytherins were sat around him, apparently ignoring the lateness of the hour.
Joining his usual cronies were the Slytherin quidditch team, who were all thanking Draco for the new brooms his father had bought for the team.
"We'll have the cup this year, no doubt, with these brooms," Flint, the Slytherin captain was saying.
"It was the least my father could do after you made me the seeker. He would like to see Slytherin win the cup as well," Draco acknowledged Flint's comment.
Pansy yawned, "Are we boring you?" Draco glanced towards her.
Her cheeks heated at his comment, "no, sorry. It's just late. I think I'm going to have to call it a day." She stood from the floor where she had been sitting at Draco's feet. "Goodnight."
They watched her leave, then the others decided that she was right.
"See you in the morning," they each went to their separate dormitories, leaving Draco on his own.
He then got up from the armchair and made his way to the stairs leading to the boy's dormitory.
Before he reached the first step, a voice spoke from behind him, "congratulations, Draco."
He spun round to see Lyra sitting in the armchair he had been occupying.
She smiled at him, and he smiled back, "thanks."
He carried on up the stairs.

... "You could raffle off those Cleansweep fives, I expect a museum would bid for them," Draco sneered.
Behind him, the Slytherin team howled with laughter.
Draco, seeing the faces of the Gryffindor quidditch team, was pleased to see that he had touched a nerve.
Then Granger stepped forward, "at least no one on the Gryffindor had to buy their way in, they got in on pure talent."
Draco flushed with anger, "no one asked for your opinion, you filthy little mudblood."
Outrage was shown clearly on the Gryffindor team's faces.
He stepped back when the Weasley twins jumped at him, only to be intercepted by Flint.
One of the Gryffindor chasers shrieked at Draco and the other Weasley pulled out his wand.
"You'll pay for that one Malfoy," he pointed his wand at Draco, under Flint's arm.
A loud bang was heard, then a jet of green light shot out of the wrong end of his wand.
Weasley flew backwards and the Gryffindor team ran to him, "are you all right?"
He opened his mouth, but instead of words, several slugs came from his mouth.
Draco fell to the floor, unable to stand because of his hysterical laughter.
He banged the floor with his fist, laughing so hard that no sound issued from his lips.
From the corner of his eye, he saw the Gryffindor team leaving the pitch. Potter and Granger supported Weasley.
When his laughter subsided a little, he stood up and wiped a tear from his eye. He drew deep breaths, watching the slugs crawling in the grass.
"Draco, what's a mudblood?"
All traces of amusement left Draco's features as he turned to see Lyra standing behind him.
He was surprised to see her there; he had not noticed her presence during their conversation.
He thought about her question, and was again surprised, this time at her naivety.
All Slytherins should know about mudbloods because all Slytherins should be pure or half-bloods.
He frowned at her, "why didn't your parents tell you?"
"My parents abandoned me when I was three years old," she said it with a detachment that shocked Draco.
Everything about her; her childlike looks and voice, her mannerisms, all made her seem incapable of such cold indifference to something that most people needed in their lives.
"Oh, I'm sorry."
"Mhm," she nodded, "that's ok, it's not like I care really."
This was even more unsettling to Draco and the rest of the Slytherin quidditch team, who had composed themselves and where listening to Draco and Lyra's conversation.
She was showing the same indifference as before, but this time as her usual, childish self. She was even smiling.
Draco nodded slowly, and then answered her question.
"Mudblood means dirty blood," he started, watching her reactions carefully, "usually people call them 'muggle-born', someone who has non-magical parents, like Granger. Muggles are inferior to wizards, that's what most purebloods think. A pure blood is someone who has only magical blood in them, not a single drop of muggle blood. Someone like me."
Draco paused to see that she was giving no reaction to his words.
Most people who heard this when they were older, and had not been taught from a very early age, disliked the whole concept of insulting people because of their heritage.
Lyra looked him the eye as she spoke, "Are mudbloods beneath purebloods?"
It was one of the Slytherin beaters who answered her, "yeah, it's wizards who were given the gift of magic, why should some lowly muggle be able to produce it as well?" The other Slytherins nodded and laughed at this.
Lyra hadn't taken her eyes of Draco as the other had spoken.
Now she lowered her eyes and bowed her head to him and the others, "then forgive me for speaking out of turn until now. Blame my naivety on this subject, for it is my belief that I am a mudblood."

"Enemies of the heir, beware! You'll be next, mudbloods."
Draco's voice echoed through her ears as everyone around her turned to go to their dormitories.
What did he mean, what would happen to her?
She saw Draco, looking rather smug, as he walked towards her. When he saw her, his face fell and he suddenly looked more pale than usual.
Lyra made her way over to him. "What did you mean Master Draco, when you said mudbloods would be next?"
Draco was stunned at hearing her address him so, "master? Why are you calling me master?"
"Well, you are not married, so you can't be 'Mr'."
"But why the formalities?"
"Because I know my place now."
"Your place?"
"My place is beneath you, as we concluded at the end of our last conversation. Not only are you pureblood, but yours is one of the oldest and most noble wizarding families. I have little right to be in Slytherin, let alone speak with you as an equal."
"Lyra, there isn't any need for this," Draco was almost pleading with the girl. What would people think if they heard her calling him 'master'?
But somewhere inside, he knew that that wasn't the real reason he was so uncomfortable with it.
"Yes there is, we are separated you and I. Why do you mind anyway? You would be happy if the Granger girl started calling you 'master' because you acknowledge the fact that she is inferior," Lyra's voice became a whisper, "I am no different."
Draco spluttered for a response.
Lyra lowered her eyes and asked again in a low voice, "what did you mean Master Draco?"
"Find out yourself," he spat and walked away.

There came a knock at Snape's office door.
"Enter," he called out. He heard the creak of the old wood and looked up.
The first year girl, Lyra, was stood there. "Yes, Miss-," he paused. Now that he thought about it, he had never heard her last name.
"Just Lyra sir," she bowed her head respectfully.
"Well, don't loiter in the doorway," he gestured to the empty seat in front of his desk. She nodded and closed the door.
The girl made no sound as she walked to the indicated chair and sat down. She kept her eyes lowered, again as a sign of respect. Snape liked this girl.
"How can I help you, Miss Lyra?"
She looked up, now that he had addressed her, and spoke, "I was wondering why I was put in Slytherin, professor."
Snape had heard this many times from different students, each one felt that they were too nice, too outward in their personalities to be a skulking snake.
"And why do you feel that you know better than the sorting hat, whose sole purpose is to sort you into the correct houses, Miss Lyra?"
Her eyes narrowed at this, "Slytherins should be of pure blood. Slytherins must be of pure blood, otherwise, Slytherin would have mo meaning. I am the opposite of pure."
Well, this was new. The girl was right, she shouldn't have been made Slytherin if she was muggle born.
But wait... "Why don't you have a family name?"
Lyra looked surprised at this question, but answered nonetheless, "I'm an orphan, sir. My parents left when I was little." The same cold detachment.
"How, then, do you know that you are muggle born?"
Lyra took a long time to ponder the question.
Finally she said, "I suppose there is no reason, I simply assumed," she paused again. "I guess we will know by the end of this year."
"What do you mean by that?"
"That's the other reason I came here, sir. When he saw Mrs Norris, and what had been written on the wall, Master Draco said 'You'll be next mudbloods'. I don't know what he meant, but it sounded rather ominous to mudbloods."
Snape was rather interested as to why she called Draco 'master' but he stayed his curiosity and focused on her question.

It took a while to explain what Draco had meant.
The story of the 'Chamber of secrets' was a long one, but he felt that this girl ought to know it.
He told her of the fight between the four founders, of Slytherins departure. How he supposedly built a secret chamber, which could only be opened by his heir and of the monster that would only do Slytherins heirs' bidding.
"And the purpose of this would be to rid the school of those that, in Salazar Slytherins mind, were unworthy to do magic. Muggle borns."
He finished and they sat in silence for a while.
Then Lyra stirred from her thoughts, "thank you, professor, for your time. It is late, I shall not bother you anymore."
"Not at all, Lyra. But please remember, most believe the chamber to be a myth. I do not think there is cause to worry. Not yet anyway."
Lyra bowed her head, "have a good night, sir."
She walked to the door and left.
Snape stared after her for a moment. Something about her made her seem like a Slytherin to him.
He rather liked that girl.