They change the time line.
The villain travels back through time and does things that alter the Star Trek universe. Director J.J. Abrams is given a clean slate to work from. Even better he is given a clean slate with a variety of characters to revisit and re-imagine in a new way. So far Abrams is doing it right.
This film is superior to the first one, in part, because it requires a limited amount of set up. We know the universe has been changed. We know the Vulcan home world has been destroyed. The cast we know from years of Star Trek geekdom but it is great fun watching the new interpretations of these characters--especially by Chris Pine, Zachary Quinto and Simon Pegg (although not necessarily in that order). Quinto's Spock and Pegg's Scotty are the real standouts. In defence of Pine, however, both Spock and Scotty have more to work with for an actor than the heroic leading man that is Captain Kirk.
Even now, after you should have seen the movie, I won't give away any twists or secrets. That is just wrong. It might even be wrong to let you know that there ARE twists and secrets but by this point you know at least that.
This movie is one to see on a big screen and in 3D. It looks great and the 3D, while not intrusive, is done well enough to add something and not just give you a headache.
It is to be hoped that Star Trek doesn't fall into the trap of each movie requiring larger and larger roles for the bit players in the film, that they do not succumb to the fear of killing off characters in the movies and that they use the universe Gene Roddenberry to its fullest.
So far it is all good. Maybe Abrams can even pull the Star Wars universe out of the trash can George Lucas' last three films dumped it into.