Milagro is really rich in the meaning it assigns to space. You're absolutely right that Scully seemed completely at home in Mulder's apartment, as though she had moved in. Her comfort level with him in his apartment was extremely high (symbolized by their sitting close on the couch) as was their harmony as long as they were together in his space. Except when she disputed the psychic surgeon theory at the beginning, I think all the discord and doubt occurred in other places. It is significant that Padgett's apartment is the mirror-image of Mulder's, reversed so as to say that desire is the reversed reflection of the cerebral. This is symbolized in the fact that the only furniture she doesn't touch in Mulder's apartment is the only furniture she *does touch in Padgett's: the bed. Scully is fascinated by Padgett's space, by its sparseness and therefore its quality of absolute focus. The brick wall (which is a symbolic element since that is actually the direction of the street) serves to further concentrate the space by giving it no real external landscape. The symbolism of the brick wall applies especially strongly to the message about writing, but there are really two foci of Padgett's apartment: writing and love, the desk and the bed. Scully enters the space warily, curious but not certain that she wants to be there, interested in the mind of the writer, but ending up testing the space devoted to love. Although she is not comfortable occupying it with Padgett, she tries it on for size, knowing full well that her partner is on the other side of the wall. Despite her anger at Mulder's intrusion (essentially at his failure to trust her), she is quickly on his side again. Although she retains belief in Padgett's innocence, she is fully at home later in Mulder's apartment (no continuing anger) where she participates without a squeak of protest in the surveillance.

The space is equally powerful for the two men as it is for Scully. Mulder and Padgett each violate each other's space and attempt to steal what is most valuable. Mulder erupts into Padgett's apartment breaking the attempted seduction, taking the book and arresting the author, violating the privacy of both writing and desire in virtually the same movement. He also spies on him through the wall, pulling Padgett's actions electronically into Mulder's territory for judgment.

Padgett violates Mulder's territory indirectly in luring Scully away from Mulder's door to his own, preempting Mulder's claim on her time and loyalty. Her visit to Padgett's psychic space at least sways her toward his innocence, although she feels he warrants surveillance for his uncanny ability to predict the murders. Second, Padgett violates Mulder's core in the most vicious and irrevocable way by staging the Nacimiento's attack on Scully in Mulder's own physical and psychic space.