According to series head Ron Moore, "There is a tie from [the movie] into the events in season four. ... It's an opportunity to set up something for the fourth season that had not been told to the audience and that the characters themselves hadn't realized, and then go into the fourth season." (In fan-speak, that's called a "retcon.")
Fresh from last night's controversial season three finale, fans are speculating like mad about the fallout. Now the writers have more time to tell whatever story they intend, probably heavily-based on the recent revelations. Whether or not that's a good thing is in the eye of the viewer. (If Number Twelve turns out to be Ted McGinley, heads will roll.)