Seeing as the CO was a Commander, I don’t think there was a “junior Captain” on board.
Yep. The Navy does not have junior and senior Captains on a ship. There is only one.
I heard the call the other poster was referring to. The caller said “junior officer.” I believe the poster mangled that one detail in describing the call.
Probably means the "OOD" or Officer Of the Deck. This is the person the Captain puts in charge of the ship when he goes to bed.