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Well, Mutiny just says that the ship is no longer under your control. Why shouldn't the enemy be able to reprogram your Master Computer (just a little virus...)?
Well, you could be right about that. But I was thinking, since that intel project is called 'CREW insurrection' how does a spy insurrects a crew if there is no crew... or crew quarters... or life support. Also, I suppose there would be some security systems on board that could detect his presence (since there isn't anybody else on board), unless he pretends to be a floppy disk to avoid those measures

. But seriously, that computer reprogramming shouldn't be so easy and should fall in a different intel project (a Version of ship sabotage), not CREW insurrection. It is just misleading people in thinking that they are safe against those projects.