"He'll probably be glad to hear from you," Mulder says, mostly because he doesn't really know what else to say. And it's true, Skinner's probably worried about both of them, under the circumstances. He'll want to hear how things are going, and Mulder has the feeling it'll sound better coming from the time-traveler in their midst.

And since it's next, Scully can tell Skinner anything she wants without being overheard. Dish all the dirt on Mulder. Scully wouldn't do that unless things were really bad, and he's convinced that he's mostly fine - but there's no denying that she could.