He wasn’t sure how it happened. Maybe there had been signs and he’d missed them, but he was pretty good at reading people (Amy had taught him to be good at reading body language, it was sometimes the only way she could communicate with him) and he hadn’t read anything in the Doctor’s body language which said... that.
They had been standing underneath the main engine of the TARDIS, bathed in fluorescent green as
“What does that do?” Rory asked, pressing the button so the screwdriver emitted a soothing whir.
“It reverses the polarity of the neutron flow,” the Doctor said promptly, patting him on the shoulder. A tiny part of Rory’s mind noted that the Doctor was always touching him. Patting him on the shoulder, clasping his face, ruffling his hair, even the first time they’d met, the Doctor had grabbed him by the collar and then smoothed his hands down the front of Rory’s jacket.
“What does that mean?” he asked, watching red and blue lights go up and down the instrument.
“Absolutely nothing, but most people never bother to ask, if a sentence has long words in it then they assume it’s got to mean something.”
“So what does it do?” Rory repeated.
The Doctor paused and glanced at him. His eyes were affectionate and yet sad. “You remind me of someone, Rory. She was always asking how things worked.” He took the screwdriver from Rory and tapped the instrument three times with his finger. “She was a doctor, well, training to be a doctor.”
“Where… where is she?” Rory didn’t know if this was the right question. He and Amy had come across a room in the TARDIS where the walls were lined with pictures of people, mostly women but some men as well (and a robot dog). They had names underneath them but no dates and all the pictures were in colour.
“Home. Earth. With her family and her husband. Fully qualified.” The Doctor moved away to the other side of the engine and Rory followed him.
“So she’s… alive? Not dead or…”
“She was very much alive the last time I saw her,” the Doctor said and looked up. He was still smiling but the sadness in his eyes had become even stronger.
Rory experienced a dizzying moment of déjà vu. When they were growing up, he had seen this look of sadness and loss come into Amy’s eyes so often, but he had to be careful and try to comfort her without her guessing. If she realised what he was doing, she would push him off and be all bright and brittle, telling him that she was fine, she didn’t need a hug; in the worst case scenario, she would go and find Jeff and pretend that she and Rory were ‘just friends’ for the rest of the week.
Rory had no idea how the Doctor would react, but he reached out and put a hand on the Doctor’s arm. The Doctor turned and somehow they were hugging. That was fine. That was good, hugging. They were the same height, so there was no need to bend down, and the Doctor had this peculiar smell about him, a mixture of mint, oil and tweed that was old-fashioned but not off putting. The Doctor shuddered, a tremble rising up through his spine as his body released some sort of weight or tension. Rory patted his back. This was familiar, too.
The Doctor drew back and looked at him. One moment, he was smiling, his features soft with affection; the next, the smile had sharpened, his features had tensed, his eyes had become piercing, pinning Rory to the spot as effectively as a snake pins a bird. Rory had no idea how it happened but the next moment, the Doctor had leaned forward and their lips were pressing together.
The Doctor had become adept at shutting down certain parts of his brain. At this moment in time, he shut off what humans might call ‘a conscience’, the part which looked into the future and the part which looked into the past. He was operating purely on present time and instinct and certain ideas which had been percolating in another area of his brain. He felt the prickle of stubble above Rory’s upper lip (Rory shaved twice a day and still managed to have a five o’clock shadow), he felt the startled gasp as Rory’s mouth opened in surprise. He took the opportunity to slide his tongue carefully between the parted lips and then instinct fully took over as he clasped Rory’s head between his hands and kissed him properly. It was like a sip of Asgard mead, it was the first bite of that golden apple, it was Rory standing here and kissing him and the soft boom of the TARDIS around them.
Rory felt his cock leap and press against the zip of his jeans. He pulled away, shivering, and shook his head. “What… what was that?” He pushed his hands into his pockets. All he wanted to do was turn and leave and forget that this had happened – and maybe get rid of this hard on while he was at it – but the Doctor never did anything without a reason. Of course, he didn’t answer, just kept watching Rory with those eyes as if this were some sort of test or exam (he was always testing them somehow).
“Was that… was that a Time Lord thing?” Rory asked. “Is that something you did with other Time Lords?”
The Doctor experienced a moment of terrible temptation. This was Rory and he knew Rory. He knew that if he said ‘yes’, then Rory would accept that and there would be a possibility they could do this again and maybe go a little further (stop it, stop it right there, you dirty old man). On the other hand, this was Rory, Rory who was standing there, even though he wanted to run away, standing there and looking him right in the eye, almost daring him to lie. Giving him the same look from when he’d first stood inside the TARDIS, the same look from when he was a plastic centurion who’d just killed the love of his life. Brave and honest and yet full of doubt about himself. The Doctor gave in.
“No,” he said. “It was a ‘me’ thing.”
“Oh.” Rory still didn’t move. “I thought you liked Amy.”
“I do like her, Rory.” The Doctor reached out and ran a hand down one of the TARDIS’s pipes. “I like both of you. I’m sorry, I should have made that clear before now.”
“No,” Rory said in confusion. “Honestly, it’s… fine. I’m used to… I’ve had people tolerate me to get close to Amy before, that’s all.”
The Doctor ignored the pain in his chest at all that implied. “Rory, am I people? Do I even look like people?” he demanded.
Rory looked him up and down, eyes lingering on the bow tie. “No,” he said. “You don’t look like people.”
“Precisely!” The Doctor grinned. “When I like someone, I like them for themselves. Understood?”
“Right.” Rory nodded. “Got it.” All the same, he thought, he wouldn’t mention it to Amy. She would either be upset or ask if she could join in next time and he wasn’t sure which prospect was worse. She might be happy to share but he wasn’t. “What next?” he asked.
“Well, the quantum mechanics circuit needs some work, so follow me!”
That wasn’t really what Rory had meant but he was willing to let the Doctor dance away from the subject for now. He was patient, he knew how to wait and he had all the time in the universe.