Re: Does card text override the normal rules-example with a Klingon crew
I assume you mean VAGH. I do not see anything specific about this card in my playtesting notes and I cannot recall if we had this situation during our games. So....
First, losing influence is only (normally) caused by your opponent using an Influence action. It does not have anything to do with opponent's ships in the location that you control. You just cannot take an Influence action in a location if any of your opponent's uncloaked ships are in the location.
I would allow the crew card to use its ability.
1. Page 14 of the rules state "It [the cloaked ship] may not take any actions other than Cloaking Actions unless a card or ability allows it to." I think this qualifies as a card ability that allows it to (even though the ability does not require an action).
2. Crew card abilities are permanent bonuses so they do not require an action to use them. The only requirement for Vagh is that the ship he is assigned to must end its movement in the location, not just move into the location.
3. Even if VAGH was on an uncloaked ship and it was in the same location as an uncloaked Federation ship and the location has a Federation Influence token on it, I would play it as allowing VAGH to remove an influence marker. That is his special ability and not an Influence Action.
The Federation should probably capture VAGH (Transporter action) or destroy the ship he is assigned to if the Federation is trying to complete a mission dealing with Influence.
Let me know if that clears things up.