[Drew68]

Seeing as the CO was a Commander, I don’t think there was a “junior Captain” on board.

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.

[Bull Snipe]

There is an OOD on the bridge of a naval vessel 24/7 when the ship is at sea. This allows the Captain to attend to all of the things he has to do as the CO. Even when the Captain is on the bridge the OOD handles the ship, and it navigation.