What exactly can you do about if they take the ship and go rogue? Happened in a Star Trek movie.
Then you have a new setting. It is the same as if a Paladin led party in a save the world game changed sides. You have to reset the entire campaign.
I not saying that is can't happen but if they want to stay in character and run a special campaign then there is a narrow structure on how it is run. You are changing the entire game when you change the parameters your talking about. It is like if your group had decided to play a game as PI's who solve murder mysteries, that is one setting (or what ever you want to call it) then suddenly they head out into the wilderness and start being explores.