Because I am a canon-whore, I can't really see Roy and Riza having an actually relationship during or previous to the present manga timeline. However, I am a fan of Royai, so this is my fanwank.
This story is a little OOC, but not really, because I guess Roy and Riza were different before, right after the war.
I also stole the plot device of Roy bringing Riza white roses after the war from someone, but I can't remember whom. I did not come up with the white roses plot device and I definitely do not own Fullmetal Alchemist.
Chapter 1: The first time
He brought her a dozen white roses after the war.
"Here's to us, to victory and life," he said, with more flippant irony than bitter sarcasm in his voice. He was amazingly young then. He didn't look like someone who had gone to war, much less killed anyone, much less killed so many.
She was silent as she cradled the roses, white and clean and pure.
He watched her, slumped against the wall, as she placed the flowers in water. The look on his face was that of satisfaction, of relief, like coming out of the desert and seeing a cool veranda and knowing everything would be quiet and calm now. It was the look of someone relishing in something precious before he went to claim it.
She looked back at him, there in her dim and dusty apartment, and walked to the entrance of a hallway and waited. He walked toward her and put his hands on her face and kissed her. As his hands traveled down her neck and into her blouse, they fumbled a little, hesitant, as if his hands knew that if you tried to hold onto a dream too tightly it would disappear. Yet at the same time he pressed forward with the eagerness of one who had yearned for something for far too long.
Riza Hawkeye herself kissed back slowly and deliberately and walked just as deliberately backwards down the hall. She had been tired for a long time. She had also waited a long time. There was no need to rush things. She suspected that Roy Mustang was a virgin. Perhaps he had been too busy studying alchemy in his former life. In the bedroom she helped him undress, first her, then himself. He lay silent and dormant for a moment as she ran her hands over his unfettered flesh before his instincts took over. He had been waiting for this too: he had been waiting for the right time, the right place, the right courage. He wasn't going to hesitate anymore.
Afterwards he awoke to moonlight streaming in through the window. Outside he could see Eastern Headquarters. He moaned and buried his head into Riza's shoulder, blocking out all that was real with the scent of her hair. He truly wondered for a moment, that if he stayed there long enough, if it would all go away, forever, leaving only Riza. The woman in question reached up to stroke his hair, run her hands down his back. Roy shifted his head to kiss her, deeply.
"I'm going to quit the military," she said.
Roy had a moment of unbridled panic.
"Don't worry: I'll still be in Eastern. I have family here."
"Hmm," was his reply as he bent his head to nibble at her neck, avoiding her unspoken question.
"What are you going to do, Major?"
With a sigh, he replied, "I don't know. I don't like to think about it. I think I really am the military's dog now. Even though I hate my master for what he's done to me, I'm still waiting, I'm still in limbo, until he sees fit to give me another order." Pause. "I don't think I have the will to go on anymore, on my own. I don't know what to do."
"Don't be like that. You're going to stay with me."
That sounded like the best scenario he had ever heard. And she had said it in such a matter-of-fact way, as if it were obvious. He loved that. So he gave her another kiss.