I'm thinking actually (given the shot of the room with the stasis canister things) that at some point someone in Starfleet - or Peter Weller in his ship - found the Botany Bay, lost in space since 1996, and decided to create their *own* supermen - either with the assistance of some defrosts, or autopsies and study - and that Harrison is one of those... Weller's character is presumably the guy in charge - and either literally or conceptually Harrison's "father"
I think this could be heading in the right direction. I'm wondering though if the "pods" or "coffins" we saw in the teaser are Khan's enhanced "family" that are essentially being held hostage. If John Harrison doesn't work for Starfleet, then they will disconnect power from the pods and kill his family. Weller finds the BB adrift in space and realizes their potential.