She used to work with Mulder in 1991. Two of them reopened X-files and started to work with paranormal again after some years. They probably have had some relationship (some think they were even married (in a flashback episode to 1991. Mulder is seen wearing a ring)), but they were good friend for sure. When she came back at the end of 5th season, we could see that she wasn't loyal only to Mulder or X-files. She was working with CSM and probably taking part in covering up experiments on humans and abduction stuffs.
She tried to restore her relationship with Mulder and to became Mulder's 1st person, but fortunately she didn't succeed in it.
She was real bitch, but in episode Sixth Extinction 2: Amor Fati, she finally has done something positive. She gave Scully a book and pass and helped her to save Mulder. She did right thing, but she gave her life for it. But who knows. Maybe she'll come back. Who knows...