Star Trek Online has posted a helpful chart to let players know how the game and the movie interact. The background story for the chart also talks about alternate reality created by Nero when he travels back in time and how that some of the events that take place in that reality have affected STO. To learn more about the aftermath of some of those events check out the Path to 2409 page on the STO site.
Here's the background story for the STO timelines and a link to the timeline chart:
How do Star Trek Online and the new movie interact, and where does the timeline diverge?
In the movie, two characters travel back in time from the year 2387. When Nero arrives in the year 2233, he disrupts the time continuum, creating an alternate reality from the point of his arrival. Star Trek (the new movie) takes place in this alternate reality. This is explained in the film in a conversation between Uhura and Spock on the bridge of the Enterprise.
Star Trek Online is set in the "prime" Star Trek reality. This is the timeline of the five television series and the first 10 movies. It is the world in which the Gorn attacked Cestus III, Kirk fought Khan in the Mutara Nebula, Picard explored the galaxy, the Federation fought the Dominion War, Voyager was stranded in the Delta Quadrant and Captain Archer and the crew of the NX-01 showed us how it all began.
Events in the movie that happened in the prime timeline (the destruction of Romulus, and the disappearance of Spock and Nero) have affected STO. You can learn more about the aftermath of these events in the Path to 2409 and in STO itself.
So how can the movie and STO be in different realities? When working on Star Trek, screenwriters Roberto Orci and Alex Kurtzman referenced the theory of quantum mechanics, which allows for the simultaneous existence of parallel timelines and universes. Parallel universes are self-contained, separate realities that exist as a consequence of different choices and outcomes. This concept was explored in the TNG episode "Parallels," in which there were thousands of alternate timelines (and thousands of Enterprises!). It also is seen in the Mirror Universe, which is a darker take on the world of the Federation.
There are many, many stories to tell in the prime universe. The fallout of the destruction of Romulus and the upheaval that causes in the Alpha and Beta quadrants creates storytelling opportunities that we at Cryptic didn't even imagine when we first began working on STO. We're excited by the possibilities, and fans should be as well. The best is yet to come.