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She loves Dean, of course. He's her son, even so much older and bigger and rougher; he has almost the same green eyes as when he was four, and she couldn't not love him.
But it scares Mary, too, watching him. Scares her and she's not sure if it's a mother's fears for what's become of her little boy, or the more instinctive wariness of a dangerous man. Because Dean is broken, the way hunters can be. There's something present in his voice and missing in his eyes. He's human; they're both all human (he tells her, as if it's a point of concern. It is a point of concern, though she doesn't want to admit it.) But this is the truth of hunting: No matter how good you are, the things you hunt eventually will shred and shatter and tear you apart. If you're lucky, they'll just get your body first.
Dean is gentle with her—too gentle; it's too much like John, who didn't know that he didn't have to be, only Dean does know. Dean somehow knows she was raised a hunter, but the only explanation she's gotten is that it's a long story. There are a lot of long stories and Dean isn't eager to tell her any of them, and Mary isn't sure yet that she wants to ask. Not only because they have more important things to do now, or that she doesn't want to push him into even further silence.
Dean is broken, and Mary isn't ready to know whether she could have stopped it, could have saved him, before it was too late. If she'd been more careful, if she'd run farther. If she'd returned sooner. If there were anything she could have done, to change it so that when Dean smiled, it reached his eyes. So that when he put his gun to a man's head, his knife to a woman's throat, he would hesitate, even for a moment.
But it's too late now, Mary thinks, and despairs, silently, whenever Dean looks away. She's met enough hunters to know what can be fixed and what can't be. Even if she's his mother; even if she loves him.
Then they've finally made it to the basement of a dilapidated farmhouse, and Dean is bent over a man tied to a broken chair, and his hand holding the knife is trembling as he slices through the ropes. He's talking, more words crammed in a minute than Mary's heard from him in the past days, "Sam, how are you doing—hey, Sammy, you with me? Don't move, I'll have you loose in a sec—"
The man—he's huge and lanky and shaggy, but when his head tips back, hair falling from his face as he squints up at Dean, all confusion and wonder, he looks so unmistakably like her little baby boy that Mary can't breathe—Sammy blinks and mumbles, "Dean?"
And Dean grins, green eyes bright and whole, as he says, "Right here, Sammy."