Author's note: This is set in the Alternate timeline that is mentioned where Rory and The Doctor get in the TARDIS and go away in the episode 'Girl who waited'. Hope you enjoy the Slash.
When older Amy told us to leave Rory was heart-broken. The Doctor thought that Rory needed a good-night's sleep and some time before they went to explain to Amy's parent's as well as they could what happened. Rory on the other hand had a different idea. He drank like a proverbial fish and then stumbled into the control room at what he would call late at night to ask the Doctor "Where to next?"
The Doctor shook his head and told him "Now Rory we go to bed"
Rory started giggling and told the Doctor "You should be that forward more often" he then started off on another giggling fit.
When the Doctor realized what Rory meant his face blanched so he added to what he said earlier "ALONE". Rory then drunkenly sauntered over to The Doctor. The Doctor told Rory "You just lost Amy and now you're delusional, please just go to bed"
Rory told The Doctor "I won't without someone else". The Doctor looked into Rory's eyes completely shocked and just stayed there until Rory's lips crashed down onto The Doctor's. In those few seconds The Doctor decided that Rory wouldn't remember in the morning and other than that Rory obviously wanted this. He then moved his lip against Rory's but slower than Rory was moving his own lips against the Doctor's. Rory's constant enthusiasm caught on and soon his lips were moving with the same speed. The Doctor had enough of the teasing and dragged Rory to what used to be Rory and Amy's room. He wouldn't have to drag Rory if Rory wasn't as drunk as he was. When they got there, hands and clothes were everywhere until they were both stark naked. They both went to the bed and wrestled for a very short time. As soon as The Doctor overpowered Rory he was lying underneath the Doctor with his knees clenched against the Doctor's sides. The Doctor paused and Rory reassured the Doctor "Just do it already, I'm not a virgin" To emphasize his point he wrapped his legs around The Doctor's lower back.
The Doctor slammed himself into Rory. They both moaned with pleasure then The Doctor asked "Was that good enough?" Rory bit his lip as he nodded. The Doctor then started to push his length in and out of Rory continuously. It was a steady rhythm of skin on skin and moaning until Rory started moaning even louder from the blinding pleasure. The Doctor's own orgasm was triggered by Rory's loud moaning. When it was finished The Doctor pulled out of Rory and soon Rory passed out. The Doctor took the opportunity to gather his clothes and say 'Good-night' to Rory and then he left.
When Rory woke up naked and hung-over he remembered what happened with Amy and started crying. Once he was done he got up and got dressed without a second thought. He started to eat breakfast without The Doctor which was odd but when The Doctor showed up he wouldn't look properly into Rory's eyes. The Doctor suggested they go talk to Amy's family and Rory started to get suspicious. Rory was going to say nothing but The Doctor was waiting for an answer so Rory said "Maybe tomorrow".
The Doctor said "Oh, I get it, you're hung-over! I'll get you something for that! I am The Doctor after all!" and then ran out of the little kitchen all without looking directly at Rory.
While The Doctor was gone Rory used the time to think and started remembering some things. So when the Doctor came back and quickly handed Rory two little pills Rory took them, swallowed them and asked "What all happened last night?"
The Doctor knew this was coming and prepared a lie "You got very drunk and I had to practically drag you to your room, I don't know what you did once you were there"
Rory remembered something different and told the Doctor "I think you do"
The Doctor realized the jig was up and asked Rory the question he had been pondering all night "What did you mean when you yelled at me 'Just do it already, I'm not a virgin'"
Rory's face suddenly went red while he explained "Well in nursing school I, uh, experimented" he then asked the Doctor "Would you like me to show you?"
The Doctor looked slightly confused until his face started to turn red and then he asked "What do you remember?"
Rory looked directly into The Doctor's eyes and leaned over the small table to brush his lips against The Doctor's. They both just stayed there for a bit until The Doctor moved his lips slowly. Rory caught on to the rhythm and moved his lips in time with The Doctor's. They slowly broke apart and Rory told The Doctor "If it's all the same to you, I'd like to let you pound my ass into a mattress sometime when I'm sober". The Doctor rolled his eyes at Rory's smirk and kissed it right off his face.
After the two of them told Amy's family what happened they went back into the TARDIS kissing and letting certain tweed coats fall to floor they heard a familiar voice say "Hello sweetie and Dad" They jumped apart and looked at River. She told them "Oh don't mind me, I'm glad for you, finally, just don't tell younger me I was terribly stubborn" she then realized neither of them were about to talk so she told them "I was going to ask you if you would join me at Torchwood for some coffee, but you two look busy"
The Doctor stopped her from strutting out of the TARDIS and told her "actually that sounds wonderful, Rory here hasn't had any of Ianto's coffee has he?" So they went to Torchwood and had coffee with Jack and Ianto.
Another Author's note: I hope you liked it and Do you think I should add another Chapter where they are all drinking coffee with Jack and Ianto, please tell me, even if the answer is 'no'. Thanks and such *insert smiley face here*