"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.The waiting to learn who the villain is in the this movie begins, a mystery that's going to be killing me 'til May or until it's leaks on to the net. My personal belief along with many others is it is Khan Noonien Singh, my theory is in this new timeline the Federation found Khan and his ship full of genetically engineered followers years before James T. Kirk took command of the Enterprise and has been using him to do off the books black ops mission until he is betrayed and left for dead which leads him to return with a grand plan to destroy the Federation. My evidence is in the trailer as we see the villain jumping down from an extremely high height, swinging around a very big weapon effortlessly, and showing superior and powerful martial arts abilities, and then in the extended Japanese teaser trailer he has the additional quote of "Is there anything you would not do for your family?" which I think is talking about his fellow genetic augmented brethren being held by the Federation as leverage for Khan to do their dirty work.
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."
The official synopsis even says: "Captain Kirk leads a manhunt to a war-zone world to capture a one man weapon of mass destruction." , sounds like a genetically engineered super warrior to me. "an unstoppable force of terror from within their own organization" I believe points toward the shadow cabinet of higher-up Federation officials that's behind all the darker and secret events that keeps the Federation as a major power but still appear peacekeeping and exploring, perhaps Section 31. I also believe Peter Weller plays a member of this cabinet, perhaps maybe Commodore Decker, Weller did say in an interview he has his own ship.