Given the context you provide, I interpret her words to mean, "I'm here, on the job just like you, because I work for the FBI just like you, and got assigned to this case just like you, etc." Basically, she is "there" under the same conditions, circumstances, and reasons he is. Mulder, of course, believes she is there for different reasons, i.e. as a pawn who is playing a part of some conspiracy against him.