Mark,
I have a few questions/comments that might shed some light upon this topic.
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Okay, I have a dilemma. I have a player who's concept of a Star Trek captain seriously differs from mine.
So what? Not intending to offend you or the player, but if your views were the same it would become rather boring now wouldn’t it?
Just a few questions about your group dynamics- Do you and the player “play well together?” Are the two of you adversarial when you play other games? He could be sabotaging your game on purpose in an effort to “wreck your game.” It is rather typical in some groups were a player will feel that it’s “Me Vs. GM” and that if he can be problematic that he is “beating you.”
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I had a recent adventure where the crew encountered a strange alien life form. After investigating and learning to comunicate with it, they needed to protect it from a Klingon patrol.
However, this captain decided it wasn't his problem and refused to investigate this "strange new life". Dispite the complaints of the other players, he insisted that it wasn't something that his character take part in.
Speaking as a person who embraces Star Trek and its philosophies:
No Starfleet Captain would ever do this. It goes against the basic principles of respecting all sentient life forms. He would probably be court-martialed and stripped of command. (More details would be needed, but unless this alien was destroying/hurting the ship and its crew in some way…)
Speaking as a GM:
During our next session, I would bring in a JAG team to investigate. I would temporarily relieve him of command and bring in a real pain in the @ss Admiral “I will Make Your Life Hell” to take over the ship while the investigation is going on. Think Fleet Admiral Alynna Nechayev on a bad day.
Also, you could make the alien important to the storyline in that they were trying to initiate first contact and, instead of the Federation, it is the Klingons who will gain the area of space the aliens call home.
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So how do you deal with a player who insists on creating a character who refuses to "boldly go where no one has gone before!"
I personally would not allow such a character. If the player in question is justifying his actions by “Well that’s what character would do???” then I would suggest he makes another character. He has NO CLUE what it means to roleplay in a Star Trek campaign.
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How can you justify this character having made it through Starfleet?
It would be rare that he would pass ANY exams that deal with respect for life.
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How do you write "Star Trek" adventures for someone like this?
This is a big mistake on your part. You are not writing adventures to cater to one character. Think about your group and what types of games they like to play and go with that. Enjoyment of the whole group is what you are shooting for. It sounds to me like this player is either going to help or hinder your success as a GM. If he comes around and actually helps your adventure, keep him. If not, and he continues to sabotage your adventures, get rid of him or play a different game that requires little or no roleplaying.
Hope this helps.