I just posted a comment
in a different thread that got me thinking about this and I wanted to follow up on it in more detail.
What if Cumberbatch's John Harrison is not the actual villain in this movie? What if he's just an operative for the real villain who somehow betrayed or abandoned him and now Harrison has returned to "have his vengeance" with Starfleet and the planet Earth caught in the crossfire? What if the real villain is actually being played by Peter Weller, the one major cast member who has yet to be identified and has remained so far under the radar he's almost been forgotten?
As tempted as I am to dismiss the Section 31 speculations, knowing how well steeped Orci and some of the others are in Trek esoterica does make me wonder. I can imagine a scenario in which John Harrison is a Section 31 agent, perhaps genetically augmented, and Peter Weller is the head of Section 31, operating from a secretly built, technologically advanced starship, maybe the one with the darker interior we've seen in the previews, and maybe even the one we see crashing into San Francisco bay.
We know the opening of the film (SPOILERS AHEAD) involves the Enterprise crew intervening to save a primitive alien culture from destruction by a catastrophic volcanic eruption, but a dilemma arises when Kirk has to choose between letting Spock die and violating the Prime Directive by revealing the Enterprise to the natives. Of course we can guess which option Kirk chooses and, by some accounts, gets in a degree of trouble for it with Pike and others at Starfleet. This sounds to me like the perfect setup for a confrontation with an organization like Section 31 whose very existence is antithetical to the Prime Directive.
John Harrison could be, as 137th Gebirg
commented on my original post, a "Jason Bourne-style character gone completely off the reservation." Or perhaps someone more like Raoul Silva in the latest James Bond flick, Skyfall,
a deadly former agent hell-bent on revenge against the head of MI6 who sold him out and left him for dead. I'm guessing he's somewhere in-between, disillusioned both with the shadowy organization he works for and the people who have no clue or appreciation of the sacrifices he has made to protect them from a dangerous galaxy. Go back and listen to his voiceover in the teaser trailer and consider it in that context.
It's even possible that Harrison redeems himself before the end. Perhaps he realizes the damage he has done and seeks to atone for it. Maybe this has something to do with the scene, presumably in the ship's brig, with hands on two sides of the glass that supposedly belong to Spock and Harrison. Or maybe Harrison actually sacrifices himself in order to defeat Weller's character and this is a moment of understanding between former enemies. Lots of possibilities.
Here's one more: What if Weller not only plays the real villain, but that villain is actually someone we are all well acquainted with? What if the writers' comments about the "villain" being a canon character from TOS were accurate after all? What if Section 31 was actually founded by a very familiar character, one who was a product of genetic engineering and selective breeding but was not
Khan, one who's very purpose in life was to intervene in human events for the supposed betterment of mankind?
What if the real villain of Star Trek Into Darkness
is Gary Seven?