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In the Department Heads section of the Duty Officers interface, you can choose which Bridge Officer fills which Department Head role. Each career path has two Departments which an associated Bridge Officer may be Head over, and a Bridge Officer may be Head of one, both, or neither. Additionally, any Bridge Officer (regardless of rank or career path) may be selected as First Officer.

Does this make any difference at all, or is it purely aesthetic?

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I think it determines who talks to you during various bits of scripted missions, but I don't really know. – Argyle Aug 20 '12 at 18:55
@Argyle Interesting thought, and it would be nice to know for sure if that is true, but I'd file that under "purely aesthetic". – Iszi Aug 20 '12 at 19:43
@Iszi That feature - last I played - was partially bugged, but as the Foundry shows/showed, triggers in the mission cause the dialogue to be associated with that officer. (Not adding as answer, cause I haven't loaded it up in quite a while so I can't even confirm it right now.) – user98085 Apr 14 '13 at 2:21

As far as I know this is purely aesthetic and has no effect on which missions are offered. It's where you are that counts for duty officer missions.

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