Rory Williams was never an extraordinarily special person. Sure, he was a good nurse, and a good husband to his wonderful wife, Amelia Pond. But he never felt good enough to be married to her, and especially not good enough to be traveling around the universes with her and the Doctor. He always felt like a third wheel when he was with them. They'd be talking about things he didn't understand, and it'd feel like he'd walked in on a very personal moment in someone else's relationship. Which was ridiculous, really, because he knew that Amy loved him, and he loved her. And he might love the Doctor too. No, no, that's completely impossible. Rory wasn't gay. Of course not. I mean, his and Amy's honeymoon proved that. But there was just something about the Doctor that even the straightest of all men couldn't resist. Perhaps it was the way that he was such an old soul, yet so very young at heart. His adorable way of dressing, the tweed coat, the suspenders he just wanted to tug on, and of course, the little bowtie. Or maybe it was the way his hair flopped in front of his face and all Rory wanted to do was push it out of the way and kiss him.
"Stop it, Rory, stop it." he said, scolding himself out loud for thinking too much.
"Stop what?" The Doctor popped his head out from doing some work on the TARDIS.
Rory felt his face grow warm and turn ten different shades of red. "I... err... nothing. It was nothing."
Now, The Doctor, having been around humans (and many other species) for over 900 years, knew by the tone of Rory's voice that it was not nothing, and quite clearly something. He stepped out from under the TARDIS control centre and walked up the short steps to Rory.
"Are you missing Pond already? Her and River have only been out shopping for twenty minutes!"
Rory shrugged his shoulders and looked at the floor of the TARDIS, fidgeting slightly, shifting his weight from foot to foot.
"Ahh, not that at all, I see. What is it, Rory? Don't be shy, you can tell me, you know you can." The Doctor said, as charming as he always was, which was just a small part of the reason why Rory had fallen for him.
"No, Doctor, this is definitely not something I can tell you..." Rory continued to look at the ground as he said this.
The Doctor sighed, and put a strong hand under Rory's chin, bringing his head up to look him in his green eyes, which were clouded with worry. "Rory the Roman," he began, smiling. "I've travelled the universes for thousands of years... nothing you can say at this point will shock me, trust me on that." he said with a slight chuckle.
Rory closed his eyes for a moment and took a deep breath. "Well... it's just... travelling with you all this time... I think... I think I might just possibly be in love with you, Doctor..." he said, not being able to look him back in the eyes because he just knew that this would shock him and he'd bring him back home and continue travelling with Amy, and oh god, why did he just say that? But the Doctor seemed to sense how he was freaking out inside, and put his hand on his shoulder, giving it a slightly awkward cross between a rub and a pat.
Stuttering, he began "Well... that was... unexpected. But... but what about Amelia?" he asked.
"I know, that's part of the reason why I didn't want to admit it... I love her too.. I just... I feel so disconnected from her lately, and I think that's why these feelings for you have come up.." he said shyly.
The Doctor took a moment to ponder. Yes, Rory was a good looking man, nose and all. He could see himself taking him into his bedroom on the TARDIS for a shag, at the very least. But Amelia! It would break her poor heart... unless she never found out.
A cunning smirk appeared across his strong features, and he leaned down to whisper into Rory's ear.
"How about you follow me? And remember... Amy cannot know about this. Ever."
Rory's mouth gaped open for a moment, until he gave the Doctor a quick nod and took his hand as he led him through corridors in the TARDIS until they found their way into his bedroom.
"Wow..." Rory said, seeming to be at a loss for words. The Doctor's bedroom was utterly massive, the walls painted the same colour blue as the TARDIS, various knick-knacks across the room that he had picked up on his adventures, and in the middle, a gracious king sized bed.
"After you, Rory." the Doctor said, ushering him towards the bed.
Rory sat upon the bed, and the Doctor followed him, straddling his hips and leaning closer towards him for a kiss. Their lips entwined passionately, tongues swiping against tongues, teeth grazing lips. The Doctor reached a hand towards Rory's crotch, feeling him growing harder in his trousers. Rory grabbed the Doctor's firm arse, pulling him closer, a groan escaping his mouth as they continued to explore each other's bodies and mouths.
"I think these clothes need to come off, don't you, Rory?" said the Doctor as he gave him a sly wink, before pulling Rory's shirt above his head, revealing his small frame, his chest splattered with hairs here and there. He began to suck on his neck and collarbones, not so hard as to leave marks that Amy would no doubt question, but hard enough to draw quiet noises from the other man's throat. He pinched his nipples between his thumbs and index fingers, and ran his hands down his stomach, inching closer and closer to the button of his trousers.
"Please, Doctor..." Rory begged, his eyelids half closed, mouth opened slightly, awaiting what was coming, what he had waited for for so long.
The Doctor was happy to comply, and undid the button and the zipped, hauling off Rory's pants. He could see his hard-on clearly pronounced beneath his boxers, and he used his left hand to lightly stroke it. After a minute or so, both he and Rory really couldn't stand it anymore, so he pulled down his underwear, his cock springing to action. The Doctor grasped his thickness in his hand, stroking it up and down.
"Oh god, Doctor... suck me... god..." Rory began to buck his hips into the Doctor's hand, wanting more. The Doctor lowered his head onto his length, making sure to lap up the pre-cum that was on the tip of him, and began to bob his head on his cock, his hand playing with his balls. At this point, Rory was moaning uncontrollably. "Ugh, Doctor, yes!" he cried out. As soon as he knew that Rory was on the verge of cumming, he pulled back. "Before we go any further, I think it's my turn." the Doctor said, as he removed his clothing as well, so he was only in his briefs.
Rory eagerly pulled them down, his huge cock waiting for his hot mouth to envelop it. He took as much of him in his mouth as he could without gagging, and used the same motions that the Doctor had used on him, and the Doctor really seemed to enjoy them just as much as Rory did.
"Ah, good, Rory, yes... I think we can take this one step ahead now." he said before he was pushed over the edge. Rory knew what was coming, so he got on all fours. The Doctor reached in a drawer next to his bed and pulled out a bottle of lubricant, and stroked some on his cock, and also put a generous amount onto Rory's backside. "This may hurt a bit, but just relax." he said, knowing this from experience with Jack. He positioned himself at his entrance, and slowly pushed in. Rory winced slightly in pain, but he took the Doctor's advice and relaxed, and the pain eased and the more the Doctor penetrated him, the better it felt. He felt the Doctor's balls slap against his arse, and he knew he was all the way in. Slowly, he removed and re-inserted himself, and Rory was soon groaning and pushing back on him, wanting more. "Yes, Doctor, harder, oh god!" he moaned. The Doctor began to pick up the pace, slamming into him harder and faster, his hands around his hips as they fucked themselves into a state of bliss.
"Unghh.. Doctor, I'm gonna cum..." Rory groaned as he closed his eyes tight, and suddenly hot white cum spurted out of him and onto the bedsheets. The Doctor continued to pump into him, drawing out his orgasm and making it more intense. He then pulled himself out of him, and Rory turned around, knowing his orgasm was coming soon as well. He stroked his cock roughly, and opened his mouth. The Doctor bucked his hips and came into Rory's mouth with a cry. Rory was taken aback by the salty taste, but swallowed it all down and licked any remaining cum off of the Doctor's member. He collapsed by him, and they lay there for a moment, catching their breath.
"Now remember, Rory. Do. not. tell. Amy."