This should have been in the series, though there really wasn't a place for it. So I'm writing it now!
Disclaimer: I don't own Doctor Who. I do, however, own way too much Doctor Who memorabilia.
Rory was wandering the TARDIS.
It had been a week since the planet with the flying fish and he was of the opinion that if he never saw a fish again, it would be too soon. He had managed to find the library, which was where he spent quite a bit of his time, reading up on future medical advances. The Doctor also kept a strange collection of children's books. And a swimming pool. He made a point to ignore them both.
He passed by the garden twice before giving up and deciding he was lost. He was trying to find something interesting, but most of the rooms he continued to pass were unused bedrooms or bathrooms. After giving up, he set his sights on the console room to find the Doctor, who would certainly be able to give him directions. It was another fifteen minutes before he managed to get there.
He stepped out onto the stairs to find the Doctor beginning to fiddle with a switch. It was the same switch that Amy had asked about the day before. It seemed as though the Time Lord had yet to answer her question of "What does it do?"
Rory cleared his throat. "Uh, Doctor?"
The Doctor turned his head quickly, hair flying about. "Oh, good morning Rory!" There was a loud thump and he peered down through the glass floor. Something had fallen, but it wasn't anything important. Probably.
"Morning," he replied. His stomach suddenly grumbled in mock anger; all that walking made him hungry for breakfast. "I can't find the kitchen. Has it moved again?"
"Probably!" the Doctor frowned at the switch, still unable to decide what it did. "I think it's down the hall, third hallway to the right, down the stairs, and two doors down to the left."
Rory nodded. "Thanks." He turned and left the Doctor to his machinations.
Precisely three minutes later, he ended up back in the console room. "Doctor?"
The Doctor looked up again. "That was a quick breakfast, do you inhale your food?"
"That's not where the kitchen was," Rory replied, descending the stairs. He'd just wait for Amy to wake up. She always seemed to know where everything was.
"Bollocks," the Doctor declared, frantically flipping the switch over and over again.
"I don't think that's going to make it do anything," Rory offered, which earned him an irritated glare from the Time Lord. He quickly put his hands up in defeat. "Sorry," he said, moving away to the other side of the console, still rather peckish.
The Doctor watched him walk away carefully, then put a hand to his face and ran it from forehead to chin. He let out a sigh, then followed Rory around the console. "Rory!"
Rory almost jumped out of his skin, turning to face him. "Y-yes?" He wasn't sure if he wasn't supposed to be there or what exactly was going on. An alien sneaking up on you was generally trouble.
The Doctor paused, then awkwardly lifted a hand to scratch his head. "I, uh, I owe you an apology." He dropped the hand, watching Rory's expression carefully.
"An apology?" Rory's eyebrows furrowed, honestly confused. "What do you have to be sorry for?"
"Amy forgot you," he said quietly. Rory's eyes darkened. "It was an accident, but she forgot and I never reminded her. She loved you, she still loves you, and I... I didn't make her remember. I didn't say anything because I didn't want her to be sad." He paused. "I didn't see that she was sad anyway. I should have told her. But I didn't, and I'm sorry."
Rory just nodded. "Ah, well, everything's alright now, isn't it?"
"That doesn't mean apologies should be forgotten," the Doctor said, eying the other man. "And I never did say..." He had to clear his throat a bit, swallowing his pride. "I'm glad to have you on board. And I'm sorry for treating you like you're anything less than magnificent, because you are. Magnificent, I mean."
Rory looked at him peculiarly. He wasn't exactly sure what the Doctor was talking about, but it might have had something to do with guarding a box for two thousand years. He nodded, slightly embarrassed. "It's alright, Doctor. Apology accepted and all that."
The Doctor smiled and clapped Rory on the shoulder. "There we are!" He started to walk back to the switch, then quickly turned on his heel as an afterthought. "Oh! Another thing, I'm sorry about ruining your stag night. And, uh, making fun of your big nose."
"That's al- Wait, you think my nose is big?"
At that precise second, Amy stomped from the hall and onto the stairs. She was dressed in her nightie and slippers, covered head to toe in over a dozen fluffy, white feathers. "Doctor!"
The Doctor turned to look, then paused in confusion. He furrowed his eyebrows for a moment, then realization hit and he looked quickly back and forth between Amy and the switch. He eventually paused at Amy and happily exclaimed, "I've found out what the switch does!"