Why doesn't the FBI want Scully and Mulder working together?

Sorry just became a fã (because I was 2 when the show started..) . I rented a dvd with 8 episodes and they don't go in order. I'm confused because they went from working together in the episode where her Father died, and now I'm at a episode where they can't work together and its a big parasitic thing.. I'm just curious and confused any help would be welcomed :)