It's commander in the sense of "commanding officer" or "officer in charge", an 'appointed' title, and not the actual naval rank commander (which would be 「中佐」 in Japanese.)
It's pretty much the same title that RTS games use when they address the player as "commander".
I'm not familiar with military/navy rank. What's 司令官 -- Commander? General? Admiral?
一緒に昼寝してあげる -- "let's take a nap together."
Well, 司令官 isn't really a rank in the navy. It's just as the word being used to translate it, "commander", means that it's using to adress the "officer in command" or more like "leader in a group of military men".