Silence.
The Doctor took that to mean that Amy was either asleep, in the library or in the swimming pool. Either way, he probably had, at minimum, a good hour to himself.
Sat on the stairs in the TARDIS, he thought of how he had changed since his latest regeneration. Since losing Rose, he'd never felt any desire to be with anyone else, yet now he had Amy…things were changing.
He allowed himself to slip into the fantasy he was having increasingly often; he and Amy, going further then even he and Rose had. He'd loved her but the sexual tension was never there, she had been happy to merely sit and talk, occasionally kissing him but never taking it further than that. His former self had been happy to do that as well, but he was a new man now, and he wanted more.
He absent-mindedly slipped a hand inside his trousers as he thought of Amy and everything he'd like to do with her. Drifting deeper into his mind, and further from reality, he closed his eyes and lay back.
"Doctor!"
He snapped back to reality, yanking his hand away from his crotch, hastily trying to arrange his jacket in a way that would hide the now obvious bulge between his legs.
"Oh! Pond! I was…must have…drifted off for a minute there, yes! Now, where were we?" Turning away from her he rushed to the TARDIS console, pressing buttons that had no real need to be pressed, but allowed him to act as though he was doing something important.
Behind him, Amy raised an eyebrow. She stopped at the bottom of the stairs.
"Of all the things I expected to see, you touching yourself in the middle of the TARDIS was down there at the bottom of the list!"
The Doctor couldn't tell from her voice if she was shocked, amused, angry or a mixture of the three.
"No no no…I was…it was…" he floundered. Amy stepped beside him.
"Don't deny it Doctor, you weren't exactly being quiet in it" The Doctor surprised her again by turning a bright shade of red. She'd never seen him blush before.
"And that", she nodded towards his still bulging trousers, "would need far more than a jacket hem to hide"
He knew there was no point in denying it anymore. He silently cursed the Timelord genes that made it so hard for him to hide an erection, any normal person would have lost theirs as soon as they'd been caught the way he had been. Still ashamed, he forced himself to meet Amy's stare. "I'm sorry Amy, I just…I had to…"
To his surprise she reached out, took both his hands in her own and turned him to face her. "How long have you been like this for?"
He couldn't lie, not when she was this close, and holding him so gently, not angry but caring, concerned.
"Since you started travelling with me"
Looking into her eyes once more, he thought he saw some of the lust he felt reflected in Amy's own face. Before he could consider this any further, Amy had moved her grip to his arms, sighed "and you never told me! This could have happened so much sooner!" and pulled him into a kiss unlike any he had shared with Rose. This was intense, filled with the frustration of the past few weeks. He stopped trying to understand it and focused only on the woman in front of him.
The Doctor pulled away from the kiss, grinning madly. He picked Amy up, felt her wrap her legs around his waist, and carried her to his room.
Lowered onto the bed, Amy again took hold of the Doctor's hands. For the first time she felt how warm they were, and the slight roughness that was the only hint that the Doctor was not as young as his face made him appear. She pulled him down on top of her, undoing his bowtie while he kicked off his shoes. He moved to pull her jumper over her head.
Soon they both lay naked, both looking at the body of the other. The Doctor reached out, running a hand down Amy's side, thumb brushing her breast. She gave a slight moan and rolled onto her back, parting her legs a little.
The Doctor moved over her before cautiously sliding 2 fingers inside of her. It had been a long time since he'd done anything like this. Taking her arching towards him as a positive sign, he began making a beckoning gesture, Amy's moans growing louder. She opened her eyes and again found herself looking at that boyish grin. With a final flick of his thumb the Doctor stopped.
"No" Amy whispered. "Please, more, don't stop"
Leaning down and pressing a kiss into her neck, the Doctor slid his hands underneath her, before flipping over so that he was now laying on the bed, Amy kneeling over him. He gripped her hips. "You lead now Pond"
Amy lowered herself onto him, gasping as his full length entered her. She slowly began to lift herself up before bringing herself back down onto him. Now he was the one moaning, arching. He couldn't stop himself from thrusting into her, both of them calling the other's name. Holding Amy once again, the Doctor pulled himself up so he was sitting. This change of position was all Amy needed and she climaxed screaming his name. He came seconds after her, years of tension released.
They lay side by side, the Doctor's arms wrapped around Amy's waist. "Sometimes" he whispered, "getting caught isn't all that bad"