If I remember correctly, didn't Kirk find Khan and his crew floating in space in a some kind of container? They were all cryogenically frozen, and Kirk picked them up, thawed them, and Khan tried to take over the Enterprise when Kirk finally marooned them on a planet.
That's what I remember, but I could be wrong. Anyways, why can't they show that part where they first discover Khan? Things can play out differently now since there are some differences in characters due to the changed events.