There are ALOT of differences between the movie and comic books, the list will be endless...
The few that come to mind are:
a) Sabretooth is not on the Brotherhood of (Evil) Mutants
b) Magneto did not lead a Brotherhood of (Evil) Mutants with Mystique in it
c) Lady Deathstrike is not mind-controlled by Stryker, she worked for another group known as The Reavers
d) There was a story arc where the Brotherhood of (Evil) Mutants tried assassinating Senator Kelly, but the X-Men intervened.
e) Senator Kelly was not transformed into a blob of goo/ Mutant.
f) Wolverine DID kiss Rogue to save her life, but it was in an entirely different story arc.
... and the list goes on.
The Movies are based off famous storylines
X-Men is based (loosely) on "Days of Future's Past"
X2 is based off "God Loves, Man Kills"
X-Men: The Last Stand is also based (loosely) on Dark Phoenix Saga
If you want to find out what the X-Men are doing RIGHT NOW, read Regenesis, and then proceed with the current Marvel Crossover, Avengers Vs. X-Men
If you want to have some background information about WHY the X-Men are in their situation right now, Read Messiah Complex, Second Coming and Messiah War. The Messiah Trilogy is collected in three separate TPBs or you can hunt down the individual issues.
If you want to know X-Men from a more classic point of view, pick up the 3 TPBs the movies are based off, they have pretty good story lines (but a bit dated too).
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