Not sure of the characters exact job description but it could be any number of things. Probably not orders to return fire as that would not be the purview of a low level pencil pusher like a Lt. Commander, but rather more mundane things that keep the military machine rolling like casualty reports, supply receipts from the opening of stocks and the like.
All armies (and navies) run on paperwork and 1940's US was certainly no exception to that. It just comes with having a level of organization beyond that of a pitchfork and torch armed mob and it must be done by those whose job it is even when the bullets start flying or it all grinds to a halt.
It would not be that officers job to abandon his desk for a helmet and rifle unless Japanese forces were marching up the street and even on that dire situation he'd probably be tasked with destroying paperwork (and would probably have to sign for the destruction at some point too if he manages to survive).
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Flanked by life and the funeral pyre. Putting on a show for you to see.
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