Mal knew that after everything, they would leave. The life he led - no roots, no nothing -wasn't the life that kept people. Kaylee found a great life on some planet with soil that grew strawberries like they were weeds; she ran an engineering school with her husband and kids. And when Zoe and Inara found each other, Mal had ordered Zoe to leave the ship and make a better life for them. Inara thought he was being a gracious ex, but truth is, Mal did it for Zoe. She was too loyal to leave Serenity but too good a soldier to refuse an order, so if Zoe was going to get a chance at happiness after Wash, then Mal was making damn sure she took it.
So for the longest time, it was River, Jayne, Simon, and him. But when the girl decided that she needed to spread her wings, not rot on a rickety ship under the constant watch of big brother, she made a fortune gambling - was psychic, after all - and bought her own ship. She hired Jayne to be her head of security with a big sack of gold coin, and as she left, she winked at the now two-man crew of Serenity, and said, "You boys enjoy yourselves."
Mal knew that his crew would dwindle down to almost nothing. He was grateful that is was mostly with leavings and not killings, but he knew that it was only a matter of time before his ship got emptier and emptier. There's only so much a hollow hunk of metal can do to keep people together, especially people that got better options.
Which is why Mal in a million years would never have guessed that it would come down to him and Simon.
Mal told him once to leave. Simon answered that if Mal found a crew that stuck around for six months, then he would get out of Mal's hair. They both knew that Mal wouldn't settle for anyone less than his old crew, though, so that was as good as telling Mal to go rut himself because Simon didn't intend on going anywhere.
Mal wasn't sure why the doctor was there. The man had taken to providing free medical treatment to the planets they did business on. But he seemed to like not having to make long term commitments to anything other than the ship. Didn't seem interested in setting up some profitable practice somewhere.
That's what Mal figured, anyway.
Or maybe, Mal sometimes thought when he heard the nightmares Simon woke from (since Mal was awake from his own anyway), Simon wasn't ready to join the world yet. Maybe the two of them were just in retreat. They were strong when they had to be, but now the battle was over, they wanted to curl up in a place no one knew they were.
They wanted to be no one. Just two tiny bodies floating around in an old ship.
It worked, for them. Mal kept waiting for Simon to figure out he wanted to leave. Instead, Simon read books on ships mechanics and learned how to pilot. Turned out, Serenity did okay with a two-man crew (the money River sent Simon from her new businesses helped too).
So they took jobs but not the riskiest ones. And they travelled.
And they didn't say much to each other, never really talked about matters of import. Just got used to each other as the only company. Empty men, empty ship, empty black, empty conversations.
One trip, planetside on some lush green globe, they got caught in the rain in the middle of a field they were walking (smuggling) through.
A sudden storm, and they were soaking wet, running in the wet dirt to the nearest dry spot under some trees.
As they huddled to stay out of the wash of pouring water, Mal noticed Simon shivering in his soaking clothes, nice shirt and jacket sopping against the outline of his muscles. Without thinking, he leaned in and grabbed Simon's face, kissed his lips.
Simon kissed back, a point of heat on his mouth amid the cold skin dripping with the rain still dripping from their hair.
Simon pushed away, looked up at him. "This won't fix us, you know," he said, and he seemed old, suddenly, so much older than the smug boy Mal let on his ship years ago.
"Don't care," Mal mumbled and kissed him again, urgent. This time, Simon moved his hand up to Mal's head, ran his fingers through the back of Mal's hair, and grasped tight.