At first she hadn't been a ship so much as a liferaft. Something to hang on to, to focus on, the keep him afloat on the vast sea of memories and thunder and screams. Something to nurture, though that wasn't a word he would have used back then.
When she could fly again she truly became his ship; somehow more so than when she was dirtside. A self-contained world with all he held dear, little as it was. He liked best to be far out, alone in the black. He'd named her Serenity because you could never leave Serenity, it stayed with you, and it was no use trying. The ship was both kinds - the good and the bad, and freedom besides, and it was home in a way he never expected to find anymore. Malcolm Reynolds wasn't stable, not by a long shot, but the ship under his feet compensated him with her motions, evened him out, grounded him even as she took him flying.