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He can tell she's trying to hide from him – she won't meet his eyes, and she keeps insisting she is okay. But her protests and evasions only make him more concerned for her. Her face is battered and bruised, and her chin is trembling. She looks like a lost little girl, hiding behind her hair. He has never seen her like this before, and it makes his heart ache.
"Mulder, I'm fine," she says quietly, still not looking at him.
Bullshit, Scully. He knows this entire case has been deeply disturbing for her, although she's done her best to hide from him how she's been feeling. Thus far he's allowed her to keep her distance; he's respected her need to appear strong and in control even though he knows she hasn't been feeling that way. But not now. I'm fine, she says. Like hell she's fine. The only time he's ever seen her less fine was when she was dying in a hospital bed.
He brings his fingers to her face and gently tips her chin up. She moves her head up very reluctantly, keeping her eyes downcast as long as possible, but at last she's forced to look him in the eye. Again he is struck by how young she looks, by the vulnerability he sees in her face – a vulnerability that she has never allowed him to see before this moment.
Their eyes meet for only a second, but that is all it takes for Scully. Her face crumples, and he allows her to move her chin back down as she begins to cry.
He takes her in his arms and she allows him to hold her, though she keeps her arms crossed in front of her as though some part of her is still resisting his comfort. He strokes her hair as she begins to sob in earnest. He's never seen her cry like this before, and he feels his own throat tighten in empathy.
After a few moments, her arms come out from between them and clasp themselves around his waist. He holds her tightly, one hand still resting in her hair, and lets her cry.