Owen brought up a good question: What do you do when a player takes a disadvantage and doesn't roleplay it? Negative Renown is the first thing I would do to the character, and I'd make sure that the character's reputation affected his interactions with NPCs. For a violation of the Starfleet Code of Honor, the character would lose the respect, confidence, and trust of all who know about his violation of the code, and I'd make sure that everybody who's anybody in the campaign knew about it. If that wasn't enough to make the player change his roleplaying style, I'd tell him that he'd have to buy off the disadvantage with his experience points immediately or as soon as possible.
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LUGTrek isn't really dead. Not as long as we remember it.