To be honest, the story line of the movie kind of just reuses the bees and black oil from previous episodes and presents them, well at least the bees, as something that Mulder and Scully haven't witnessed before, even though they have. They also add an alien aspect to what is going on with the conspiracy that I can't quite figure out how it's connected with the black oil in the time frames they show. The black oil seems more like parasitic/host stuff while the bees are more like the facehuger approach.