We also think the comic book series is likely hinting toward who Benedict Cumberbatch's character is. In Star Trek Countdown To Darkness #2, Captain Kirk and his crew encounter Robert April on the planet Phaedus IV. Robert April was once a captain of the Enterprise, but he left his ship to help one race that was being slaughtered by another race on the planet Phaedus IV. While Robert April’s action would seem to indicate he’s a good guy, his actions went against the Prime Directive of not interfering with any civilization that has not evolved to the point of interstellar travel.
At one point in the Star Trek Countdown to Darkness comic book, Kirk tells April, “I’m getting my men back – as quickly and quietly as possible – and then I’m taking you back to San Francisco in a holding cell.” Of course, Benedict Cumberbatch’s character appears in a holding cell and wearing a Starfleet uniform in the previews for Star Trek Into Darkness. Could it be that Benedict Cumberbatch is actually playing Robert April?
Even though we're still not convinced, the comic book definitely seems to be hinting in that direction. One holdup though is that in the Super Bowl trailer, Kirk appears to ask Benedict Cumberbatch's character, "Who the hell are you?" If Cumberbatch was Robert April, then Kirk should already know who he is. Unless, maybe something else is masquerading as Robert April, and Kirk could be asking who the person that appears to be Robert April really is.
One other possibility though is that Robert April mentions someone is supplying the dominant race on the planet with heavy artillery, and whoever that is has not been revealed yet. The person helping the dominant race could also be Benedict Cumberbatch’s character. One way or the other we have a feeling we'll have a pretty good idea of who the Star Trek Into Darkness villain is by the time the prequel comic series is over.