Completely AU and Timey-Wimey. Set S5 after the Weeping Angels before Rory.
A/N: As I stated above the story is AU. So to clarify, the Doctor never kisses nor marries River.
oOo
Stomping out of the console room after another fight with the Doctor, Amy Pond fumed. Muttering under her breath about stupid Time Lords, the Scot squealed in frustration down the corridors like a child throwing a tantrum as the TARDIS sighed.
The Doctor was treating her like a child, telling her she wouldn't understand any of the things he was talking to himself about. She wanted to try but even when he tried to tell her and she couldn't wrap her mind around what was being spoken, the Doctor told her there was no point in trying.
Obviously that had led them to the fight they had just had, with Amy trying to get the Doctor to explain just what it was he was trying to do but he kept telling her to go read a magazine or something.
Like she was too dumb to understand.
He didn't actually say that but it felt like he was implying it.
However, just as she had been about to storm out of the room, she had noticed him shoot her a wistful look underlined with sorrow. Not that she knew what that meant of course. He was just as annoying as ever.
Not watching where she was going, Amy smacked head first into something hard
"Ow" she grunted.
Stepping back, she rubbed at the sore spot on her forehead before she realized she had run straight into a door, one she knew hadn't been in her path before. Frowning but curious, she turned the door handle but surprisingly the door wouldn't budge. Rattling the handle several times proved to be futile and so the redhead gave up
"What are you hiding?" she asked staring up at the ceiling.
Amy had a feeling the TARDIS had put this door here in front of her for a reason but it was almost as if she was having second thoughts.
Sighing, the redhead turned around and headed back down the corridor, away from the door.
CREAK!
Stopping in her tracks, Amy slowly spun back around only to find the door slightly ajar
"Finally decided to show me huh?"
Walking towards the door, she pushed it open and stepped inside. The door shut behind her and the room was illuminated with a bright light.
Blinking several times adjusting her eyes to brightness, Amy suddenly found out where she was.
It was a nursery
"What in the world?" she wondered.
Driven by pure curiosity and wonder that the Doctor would have a nursery on board the TARDIS, Amy slowly began to walk through the nursery.
There was a baby's crib which looked handcrafted and beautifully designed painted white for innocence and she noticed symbols on the wood. She walked over and realized they weren't in English.
Moving away from the crib, she noticed a change table, a playpen, a chest of toys, a play mat with toys on it and a built-in wardrobe. There were shelves with books as well and a rocking chair.
The room was done in soft lavender colors with the wallpaper painted with animals she'd never seen and animals she recognized from earth even unicorns. Amy also noticed some of the frills back in the cot on the blanket.
It was obviously suited to a baby girl.
Walking over to admire the wallpaper of one of the walls, she ran her hand over it and jumped back when a panel slid back to reveal a screen. She didn't know what to expect and stared at the blank screen before it flickered to life.
There was a little static before it came into focus. The scene was of the nursery and there was a woman on the floor by the play mat with a baby. The woman had red hair and seemed very beautiful.
The camera moved closer and Amy realized someone was carrying it
"Donna is it on?" a voice asked that Amy didn't recognize but was clearly male
"Blinking red light means it's on, Spaceman" the woman on the floor named Donna replied with a laugh.
The man with the camera then lay on the floor of the nursery holding the camera, filming Donna and the baby
"Hello beautiful" the man said to Donna
"Hi yourself you sexy Spaceman" Donna replied with a saucy grin
"Donna, not in front of the baby."
The redheaded woman rolled her eyes before smiling at the baby, who Amy guessed was their daughter
"AJ" Spaceman called.
The baby raised herself up slightly and looked at the camera.
Amy stumbled back slightly in shock
"Hello baby girl, say hi to daddy."
AJ just smiled and the father laughed
"Who do you think she looks more like?" Donna asked him
"Both of us. She's probably going to look like me, possibly this regeneration or another. She'll have your hair but a mix of both of our eye colors maybe. But it doesn't matter, she'll be beautiful nonetheless" Spaceman replied.
Regeneration.
He had said regeneration.
It couldn't be.
The video continued on for sometime, both of the Spaceman and Donna switching over to play with AJ. Finally the screen went blank before it came into focus again and the camera had been set down because the man and woman were now currently standing together, arguing in hushed tones outside the nursery door
"I thought we would have had forever" Donna cried
"I know, love, and I am so sorry. I could only contain the metacrisis for so long. Donna, oh my love don't cry"
"How can I not? I barely got to spend any time with AJ"
"Darling I tried"
"Now I'm gonna die"
"No you're not. Just the Doctor Donna"
"What?"
"I am so sorry love. You know why"
"Because there has never been a Human-Time Lord Metacrisis before… At least I'll have AJ…what is that look for?"
"Donna I can't let you have her"
"What?! You are not taking away my baby"
"I'm sorry. We can't risk anyone finding out and with you without your memories, you'll freak out and your mum and grandfather won't be able to explain it to you"
"So not only are you sending me back to that life but without my only child"
"Donna Mari Noble, I am so sorry."
There was silence as the two adults just stood there, staring at one another the pain and unfairness in their eyes. They were barely starting their lives together. They had a baby and Amy knew how much they truly and deeply loved one another, it was apparent in the affection and glances they exchanged earlier
"You'll keep her?" Donna finally broke the silence
"I can't" Spaceman replied
"No"
"Donna"
"You are not putting her up for adoption"
"What choice do we have? Besides I've found the perfect couple. They go by the name of Pond and I will leave them AJ"
"Baby on the doorstep?"
"Baby on the doorstep."
Silence once again as the parents glanced into the nursery and stared at their daughter who was sleeping soundly, blissfully unaware of the pain her parents were going through.
Donna looked at her lover
"Doctor, I barely got any time with Amelia, barely"
"You carried her to term, nine months"
"It's not the same, you dunce"
"I know"
"Amelia Jessica Pond. Sounds like something out of a fairytale. A princess. Doesn't it, Doctor"
"Our fairytale princess, Donna Noble."
The screen went blank again and Amy's mind was racing at what she had just seen.
Her father was the Doctor.
The Doctor was her father.
And on top of that, her mother just so happened to be Donna Noble, the Doctor's former companion.
She'd heard a few stories of Donna from the Doctor and even one from the TARDIS herself but she had never actually put two and two together, even fathomed that the reason the Doctor was ignoring or rather freaking out at her advances was because he was her father.
'Oh. My. God.'
Amy just realized she had tried to kiss her father several times and succeeded at one point and suddenly, she felt sick.
But then she had a thought
'Wait, if I'm the Doctor's daughter how is that even possible? I should be like what, Two?'
"Timey Wimey" a voice replied behind her.
Spinning around, Amy saw the Doctor standing in the doorway to the nursery. At first she thought he would get mad but then she did a double take, she realized that he was looking at her with the love only a father could give a child.
And how could he be mad at her?
This was her nursery
"What?" she asked
"Wibbly-Wobbly-Timey-Wimey is how you're here as an adult and not a two year old"
"How?"
"After I wiped your mother's memories of our adventures and of me completely as well as you, I took her back to her mother's house and explained what had happened. When I explained why I couldn't keep you, your grandmother wasn't impressed but your great-grandfather understood. I took you back to 1989 to the Ponds, in Scotland, and left you on their doorstep with a note explaining who you were but not everything, though I told them to raise you well"
"Yeah look how that turned out"
"I'm sorry; I had no idea that would happen. I came back to my time and after a few last adventures, I was forced into one final battle against the Master. Unfortunately or fortunately, your mother remembered but luckily I saved the universe but at a cost. I was going to regenerate. I said my goodbyes, visiting old friends before I finally regenerated even though I didn't want to.
I don't know if it was Fate that I landed in your backyard when you were seven-"
"And now?"
"I know it was."
Silence filled the nursery as the two stood there, neither one saying a word. This was all so much to take in. Was it any wonder she had felt a connection to this man for so long? And even when she had just met him?
Walking over to him, she wrapped her arms around him and hugged him as his own arms wrapped around her, holding her tightly as tears stung both their eyes
"Hey" he said
"Hmm?" she wondered
"Gotcha."
She realized that no matter what, he was still her Doctor.
Only now
"Daddy's little girl" he whispered to her.
He was also…
"Always."
Her father.
The End