She has known since almost the very beginning, since after that fateful meeting with Blevins, but before her first trip to the basement. Blevins' unspoken ultimatum made her nervous, and drove her to seek out his personnel file. What was it about this man that made the upper echlons of the FBI hierarchy so nervous that he had to be shut down?
She found nothing extraordinary about him; contrary to popular belief, Dana Scully's first impression of her eccentric partner was not one of mad attraction. His official photo was unflattering at best, and as she methodically skimmed through his file, she giggled to herself at her first thought, which was: "My, what a large nose."
Of course, her opinion has since been revised.
The fact that he had been married did not surprise her then. The only thing Dana found out of the ordinary was the identity of his spouse--a former partner. There was an official reprimand on his file for 'inappropriate fraternization', and Dana remembered thinking how cold that sounded, and how the romantic in her had frowned when she read that his wife and partner had been reassigned internationally in response. The woman had apparently loved her job more than she'd loved her husband, because she'd taken the assignment and the marriage was terminated.
Nearly a year later, when she had become "Scully" instead of "Dana", she'd been sitting in his apartment, sipping her Diet Coke when she saw it. He was waving his hands animatedly, discussing their latest case--a pair of psychotic cloned twins had committed several murders, and Mulder was still wildly fascinated by the almost psychic connection they had shared.
"Did you know, Scully, that there have been reports of twins with psychic ability all over the world? If one twin is intense pain, the other can feel it, even if they're miles away. Think about how much that must be intensified with the Eves. There is still research that could be--"
Scully rebutted mechanically with her now-customary skepticism, but she didn't pay much attention to the argument itself. She was too busy watching him to care much. His eyes were warm and radiating energy, and his handsome face had the most endearing expression, as if he were a ten-year-old discussing his Christmas list instead of a grown man discussing homicide suspects. Even as she watched, Scully admonished herself for the schoolgirl crush she had on her partner--it was unbusinesslike, and would never work anyway, as Mulder had a penchant for making Scully want to curse him with the same breath that he stole with his boyish smile.
He was sputtering a reply to her rebuttal--the contents of which she couldn't remember anyway--when she saw it glittering in the lamplight. Earlier in the evening, Mulder had removed his jacket, belt, and tie, rolling up his shirt sleeves and unbuttoning the top three buttons of his shirt. Now, as he talked to Scully animatedly, she could make out a thin gold chain around his neck, and when he leaned forward to get his point across, she noticed a man's wedding ring dangling from the end of it, and she remembered what she'd read in the file.
He'd been married, once.