Time To Realise
It takes time for him to realise just what she means to him. Their relationship has never really been labelled before and so he hasn't been certain about where he stands. Friendship is possible but then, he's never been good at talking to people and has probably scared her away by now.
And so, when he sees her, gun in hand and terror in her eyes, he is stunned by the wave of emotion that rushes over him. He is sure it is more than the usual amount of fear one feels in such a situation. He doesn't just fear for his own life and River's, but hers and the rest of the crew. He fears for her innocence and that this will be the thing that takes the last of it away.
He swallows hard. The gun in his own hand is smooth and too cold. This doesn't feel right. But then, nothing about this is right. They are fighting for their lives here and the Alliance, the government, is at fault. If it wasn't for their need to make people better, they never would have added the Paxilon Hydroclorate to the air processors.
They never would have created the Reavers and he, Kaylee, River and the rest of the crew would not be here right now.
He lets out a sigh, not defeated but rather accepting of their situation. This may very well be the end for some of them (or all of them, more likely) and there's nothing more to hold him back.
"I never planned anything," he tells Kaylee.