Author's Note: Alright, here's part two. Sorry for the long wait, I was putting it off for a while because I wasn't that sure it'd be good. I'm still feeling a little uncertain, but I think you all have waited long enough, so here you go!
When the Doctor comes through the door with Melody Pond in his arms, Amy feels her entire body light up with ecstasy. Every nerve, every synapse, every muscle, everything is so awake and so alive. For a brief moment there's a frisson of doubt, and her stomach sinks momentarily with the fear that somehow she's just imagining things, that they're not really there, and that at any second they'll disappear and she'll be alone once more. But as the Doctor gets closer the fear passes and soon she's completely forgotten why she was even scared.
"Doctor!" She cries out, eyes warm with tears of joy.
Amy throws her arms around him and pulls him into a crushing embrace, just barely able to feel his hearts thumping in his chest.
"I knew you'd find us." She whispers in a voice warbled by gleeful sobs.
It seems like they stand there forever, completely removed from the rest of the world. Completely safe, safe from anything and everything. Yet there's also a burgeoning knowledge inside her that their moment of peace is fleeting, as if they're safe inside a box of glass but the glass is paper thin and can be shattered at any moment.
"Here." The Doctor says after slowly pulling back from here.
He gently hands Melody to Amy, and she cradles her against her chest. She looks down at her, and with each passing second she realizes more and more how fragile she is. Even more she realizes how close she had come to losing Melody. If it weren't for the Doctor she might have never seen her daughter again. The thought makes her ache. Then she begins to feel guilt, because she knows that no matter what she does or says to show her thanks to him, it will never fully express her gratitude for all he's done for her.
Melody looks up at her with those brilliant green eyes, and suddenly she feels a sharp pain in her chest. How do I tell him? She asks herself, gently rocking her child in her arms.
"She's beautiful." The Doctor says, and Amy swears she sees tears in his eyes. "What's her name?"
"Melody." She replies, now feeling icy and stiff inside.
The Doctor grins, his green eyes sparkling. "Melody Pond. That's a lovely name."
Amy smiles, but the smile falters quickly. She wants to feel happy, she should feel happy, but she can't. Uncertainty tugs at her heartstrings and pain blooms in her chest like a wildfire. Maybe I just shouldn't tell him. She wonders. It would be the easiest thing to do. Just don't tell him. But when she looks at him, and she realizes all he must have done to find her and that if it weren't for him Melody would be in the hands of Madame Kovarian, it's painstakingly obvious that he has to know.
"Doctor, have you ever been a father?" She eases into the question casually and smoothly, but inside her body is wracked with fearful tremors and her heart is convulsing frenziedly.
His expression changes when she asks the question. His eyebrows creep together, his lips tighten, and he looks up at her. "Well, sort of once."
"What do you mean?" She says, narrowing her eyes.
"It's hard to explain." He replies, hands shoved in his pockets. "Why do you ask?"
Amy opens her mouth, but she stops to think carefully about what she says next. "Do you remember that night, in the TARDIS?"
That one night, that one night where recklessness, impulsiveness, and stupidity took control, and common sense was thrown out the window. That one night where one simple kiss led to so much more. That one night that had become a source of shame for the both of them, like a wretched scar marring perfect skin. That night that they both pretended to forget.
His expression hardens even more now. "Which night?"
His words are less like a question and more like a realization, and she nods slowly in reply.
"Amelia Pond, what are you getting at?"
Amy looks him in the eyes, which are steely with suspicion, and then the words come tumbling out of her mouth. "Melody is your daughter."