One rumor going around is that the Federation finds Khans ship the 'Botany Bay'. Spock 'prime' already knows what could happen and it is decided that Khan must die. Cumberbatch is Khan's second in command and seeks vengeance.
Again... just a theory.
Better to be the bastard child of a king and his whore than to be a ****ing peasant at the shite homer trough.