You may be overcomplicating things. Take it from a more basic level: 1) You need an Operations crew. They decide where the ship goes, who reports to whom; they are the diplomats, the head science guy, the head of engineering, the head of the military/security crew, etc. - the head staff. 2) You need an engineering crew, the folks who make the ship run. 3) You need the science crew. Or as someone put it, unless you're exclusively a military ship, someone to justify what you're doing out there. 4) You need the military crew, or at least a couple of guys to protect the other idiots in the crew.
So if you were to draw boxes around those people, you'd have a box around Operations, who are usually in charge of everything, and then the separate People-in-Charge of their departments would then ultimately report to the captain of the ship. It's not that different than a corporation in that regard.
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1) You need an Operations crew. They decide where the ship goes, who reports to whom; they are the diplomats, the head science guy, the head of engineering, the head of the military/security crew, etc. - the head staff.
2) You need an engineering crew, the folks who make the ship run.
3) You need the science crew. Or as someone put it, unless you're exclusively a military ship, someone to justify what you're doing out there.
4) You need the military crew, or at least a couple of guys to protect the other idiots in the crew.
So if you were to draw boxes around those people, you'd have a box around Operations, who are usually in charge of everything, and then the separate People-in-Charge of their departments would then ultimately report to the captain of the ship. It's not that different than a corporation in that regard.
Hope that helps!