My current theory (subject to change in the next five minutes):
The Enterprise is sent to hunt down a rogue Starfleet ship in Klingon space, whose crew includes Captain Peter Weller, Dr. Elizabeth Dehner (Alice Eve) and Ben Cumberbatch.
It'll turn out this ship's senior staff are all Section 31 members and they're up to no good, trying to hurt the Klingon Empire somehow, probably involving bombs in volcanoes. It will be discovered that Cumberbatch is an Augment superbaby that S31 had hatched and tried to domesticate (similar to Gary Seven's attempts with Khan in the Eugenics Wars
books that Bob Orci mentioned reading during the movie's development) and that Sulu is an S31 agent on the Enterprise (as per the possible recruitment scene in the comics) who will have to decide where his loyalties lie.