The article from the mag contains the following description, which reveals a few new details from the plot.
SPOILERS ahead..
..With Earth under terrorist attack from Benedict Cumberbatch’s ex-Starfleet employee John Harrison, Kirk is this time forced into a rash decision that breaks a critical Starfleet command, puts his crew in danger & costs him his captain’s chair. Now out of uniform and dressed down in space civvies of black leather jackets and boots, our three heroes have separated from the Enterprise and headed off on a mission to try and rectify his mistake…
In Summer 2013, pioneering director J.J. Abrams will deliver an explosive action thriller that takes Star Trek Into Darkness. When the crew of the Enterprise is called back home, they find an unstoppable force of terror from within their own organization has detonated the fleet and everything it stands for, leaving our world in a state of crisis.
With a personal score to settle, Captain Kirk leads a manhunt to a war-zone world to capture a one man weapon of mass destruction. As our heroes are propelled into an epic chess game of life and death, love will be challenged, friendships will be torn apart, and sacrifices must be made for the only family Kirk has left: his crew.
Be sure to pick up this special 2013 preview issue of Empire when it hits stands December 27th.