Depends on how general you want to get.
Excluding DS9 for a moment, I have one plot.
A. Crew encounter alien/bad Earthperson
B. Alien/bad Earthperson causes trouble for crew
C. Crew solves problem/rectify situation and lose 0 or more crewman/crewwomen
D. Crew goes on their merry way - others may suffer but meh we don't really know them