There's a not-insignificant bit of relief at the fact that she isn't currently being subjected to the world's worst proposal. It's followed up with annoyance, and a little bit of guilt; it's unfair to expect him to take hints, when she isn't pushing. Mulder has plenty of reason to think it's impossible for her to be pregnant.

She shuts her eyes and lifts her chin, taking a calming breath, hand over her belly in an unconsciously protective way.

"Mulder, whose baby do you think I'm having?"

She had a whole speech half on the tip of her tongue-- I don't want you to feel pressured, I know this isn't what you agreed to, but you're the one who told me not to give up on miracles. I wanted to believe you'd be happy about it for yourself.

But all of that follows on the assumption that he realizes he's the father.