Here's the official, not-terribly-well-written synopsis for Star Trek Into Darkness:
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.
So what does any of this mean?
First: the bad guy probably kills Kirk's family. As of Star Trek, it seemed like his mother and brother were still alive, so if the crew is the only family he has left, the Big Bad must off them. Also, this is a cheap and easy way for lazy screenwriters to create tension and stakes in a story. And you saw Star Trek - they killed Kirk's dad and blew up Vulcan in an attempt to raise stakes, so killing mom and Sam Kirk is a no-brainer.
It says this is a personal score to settle for Kirk. Obviously the deaths of his family would be enough to make that so, but what about if the villain were a character from Kirk's past? He's 'from within,' and a 'one man weapon of mass destruction,' and so Gary Mitchell, who is in the second Star Trek pilot, Where No Man Has Gone Before, is a possibility. I doubt it, as Mitchell was already used in a tie-in comic book, and supposedly the comics are canon.
Could it still be Khan? I guess. But now I have a new hope for who Benedict Cumberbatch's villain will be:
Finnegan. He was an upperclassman who tormented Kirk in the academy (in the original continuity Kirk was a big nerd in school). He - or a simulacrum of him, anyway - showed up in the episode Shore Leave, where he and Kirk fought and rolled on the ground for a good long while.
It's likely not him, though. Khan seems less likely now that we know the villain is from Starfleet. I'm not entirely sure who, out of the many Starfleet characters, it could be, and whether or not the film will reach into Next Generation for characters (the first season Conspiracy episode introduced some mind worms that almost destroyed the Federation. Could they be behind it all?). This is a good time to begin guessing again - we do know that the villain is a canon character, but that's it.
And what's the war-zone world? I'm willing to bet this is a canon planet as well. Just a guess here, but how about Neural, the planet from A Private Little War? That had Klingons arming locals, and we know Klingons are in this film. That planet also has the Mugato, the horned white ape that is one of the most recognizable Star Trek monsters. I can see that getting a CGI update.
It's all speculation. So I guess it's your turn to speculate below.