The instant he says “I relieve you” at the change of command ceremony, the new Captain assumes 100 per cent responsibility for everything and everyone on that ship. It is his responsibility to qualify the personnel that will handle the ship during their watch. By definition, if they are deficient in carrying out their duties, the Captain is deficient in carrying out his responsibility. That is how our Navy operates. These issues of watch qualification will be examined during the investigation and will be discussed at the Courts Martial if one should occur.
I agree the Captain’s Navy career is likely to be over with. That said, when accepting the position of Captain he has generally accept that most people know what they are doing. I suspect the XO and a few other department heads careers are over as well.