A/N: Sometimes, when I have the availability to fulfill prompts, I open up a window of time for people to submit an idea to my writing tumblr. This is the product of one of those times.
I'd also like to point out that I do not think the Doctor and Clara having kids would be a good idea. It doesn't matter whether it's Eleven or Twelve, the complications to the narrative would be too great and severely impact the story in a negative way. Even if Twelve does become a lumpy hobo of a space-dad, it won't be happy-fun times.
Getting the Hang of Things
"Daddy? We want to visit Mummy."
The Doctor cracked open one eye and peered at his children as he reclined on the couch in the library. Alison and James were all of four years old—old enough to plug into the TARDIS education docks but still young enough to miss their mother. Their eyes, wide and brown, inflated to the point of ridiculousness, which was something definitely not gained from his contribution to their gene pool.
"She's working, so we'll see her on Friday," he explained. Clara had made him promise to not skip ahead days while they were raising the kids, that she would spend time with them on the weekends, get dropped back off on Monday morning, and they would spend the five days between visits over five actual days.
Five long, nearly unending, twenty-four-hour Earth days.
"But Daddy, you can make us do the vworp thing and we can go see Mummy!" Alison insisted. She pouted, knowing full-well she was right. Maybe right wasn't the word… she was correct. Yes, she was correct.
"This is true, but rules are rules and you know that," he replied. "Besides, you have your Dad and Auntie Idris in the meantime."
"Auntie Idris is nice, but she's not Mummy," James said softly. Where his sister was brash, he was reserved. "If Mummy can't stay with us all the time, then why did she stay with us for so long as babies?"
"…because you were babies, and babies need their mothers." He wasn't about to admit that Clara had stayed on the TARDIS for nearly three straight years once she found out she was "pregnant with mutant half-alien babies". After allowing her to calm down and drink some chamomile tea, it had been decided that her having children would only make things more complicated with her life on Earth, one she felt incapable of fully abandoning, so she put in for the time at work for a sabbatical, told her family she was going to teach English in a place with shoddy wifi, and temporarily moved into the TARDIS. The time vortex was where her children were born and where they so far spent their lives. When they were old enough to fully grasp the severity of the situation, and only then they could live on Earth and attend Coal Hill and meet their grandfather under the pretense of being foster children.
Until then, the Doctor found himself a stay-at-TARDIS dad whose space-wife long-distance commuted.
"Well we're bored and Mummy always knows what to do when we're bored," Alison stated. She flopped down across her father's stomach and furrowed her eyebrows, ignoring the groan that came out of the Doctor. "What do you do when you're bored, Daddy?"
"I take standing catnaps and skip to my bits in the conversation," he deadpanned. "You know, and here I was thinking that the two of you were children, and that children were a wealth of not-bored-ness."
"…but we miss Mummy," James reminded him. "Can we please?"
"How about this, yeah?" the Doctor said as he plucked his daughter off his midsection and placed her back next to her brother. He gave them both a wide, enthusiastic grin, pumping up their spirits. "I am going to count to a hundred, and in the meantime you go hide. When I'm done, I'll come and find you. Ready?"
"Ready!" the twins cheered.
"Alright! Now, get ready… GO!" he shouted. Alison and James spun on their heels and rushed out of the library. "One… two… three… four… five…" The Doctor listened for their footsteps—not a one to be heard.
Perfect.
After another catnap, some tinkering with the TARDIS flight console, and planning on what to do over the weekend, the Time Lord decided that it was probably time to start making dinner. He found the kitchen and rummaged around, soon cooking some macaroni and cheese on the stovetop, some chicken nuggets in the oven, and a plate of leftover lasagna for himself in the microwave. Putting the plates down on the table, he looked around in confusion. Usually the kids came running at the faintest whiff of food being cooked, but now they were nowhere to be seen.
"Alison! James!" he called out into the hall. "Dinner!" The TARDIS whirred softly at him, chiding crossly. He glanced up at the ceiling and frowned. "Hey, they usually end up finding something else to do my the time I get to seventy-three, so don't look at me." A couple lights flashed accompanied by more whirring. "Oh, yes, go ahead and lecture me on my dad skills—all the children I raise end up top-notch and you know it."
The TARDIS chose to not dignify that with a response and the Doctor sulked off to go find his children. Not in the library, or their bedroom, or the console room, or the swimming pool, or the games room, or even the outdoor-indoor garden; with each passing room he checked, only to not find his son and daughter, he became increasingly worried.
"Kids? James? Alison? This isn't funny anymore!" he shouted, trying to remain calm. The Doctor began to run as he searched about, his arms flapping wildly and his torso unable to bend. It was only sheer luck that brought him by the kitchen again, where he heard a cherubic, reassuring, giggle.
"Daddy? Where have you been?" James asked as his father walked back into the kitchen and slumped in his chair. The TARDIS had the decency to keep the food warm for him, but the kids were already kicking their feet happily as they munched on their dinner.
"Getting what I deserved," he admitted, running a hand through his thick shock of silver hair. "Tuck in now; I don't want to see a speck on your plates once you leave the table, and no milk left behind this time either."
"Yes, Daddy," the twins replied in unison. The Doctor picked up his own fork and began to pick at his own food. One of these days he was going to get the hang of things.