You can't tell a story like this without some sore spots; she can imagine staying with his father wasn't easy for Mulder, and she's primed herself to see this as a story about not doing what Bill Mulder wanted, anyway.

She can't help wincing at the idea of him in captivity-- but maybe all's well that ends well. Maybe it was a nosy neighbor or something. Whoever called the cops, Scully is grateful to them.

"And here you are, G-man."