STAR TREK/LEGION OF SUPERHEROES tells the tale of the original crew of the Starship Enterprise, who beam down to a planet only to discover that the planet isn’t their intended destination, or even in the right universe. At the same time, a group of “Great Darkness Saga” Legionnaires inside a time sphere find themselves cast into the 23rd century, but it’s not the 23rd century as they know it, either. STAR TREK/LEGION OF SUPERHEROES is a galaxy-spanning adventure that draws both teams together to face a menace that includes Khunds, Klingons, Borg, and other threats that aren’t quite as they should be. The egalitarian United Planets in one universe and a United Federation of Planets in another is now the Imperial Planets of Terra, a dark empire focused on war and conquest, and that’s just the beginning for this special series.
The series will be written by Chris Roberson, with art by Jeffrey Moy, inked by Philip Moy. As ever there will be a variety of covers, with Phil Jimenez providing covers for the entire series, plus covers from Legion of Super-Heroes artists such as Keith Giffen, Steve Lightle, and Mike Grell, and IDW talents such as Gabriel Rodriguez.
Comic Book Resources has posted an interview with Roberson about the series, here's how he describes the setup:
The crew of the Enterprise has returned to Earth so Kirk can give the commencement address at Starfleet Academy. Various other members of the bridge crew are beamed down to do other things, but when they materialize on the surface, it's not the Earth they know. Something has happened to history, and the universe at large, while they were dematerialized. Meanwhile, a group of Legionnaires are returning from an unseen mission in the past to the 31st century and run into an eddy in the timestream, and the time bubble they're in basically crash-lands in the 23rd century. But the 23rd century is not one they know from history, and they are immediately forced to deal with a very unfriendly population of a very changed Earth.
Roberson has compared the alternate reality story to something like the episode Mirror, Mirror, and explained:
In the altered universe they find themselves in, what's happened is that both of their histories have been obliterated by a change that's happened somewhere in the past. So the bifurcations that would have given rise to both their universes didn't happen. Elements of both their universes exist in this blended one.