Every ship has a secondary bridge. Deck one could be destroyed, environmental systems disabled. So for those of you who need a mission to take place 'on their bridge' make up a reason to send your captain to the battle bridge (or secondary, which ever you want to call it) and there you go. He/she is still on their ship and you can have a mission on a bridge.
heh, that's a pretty cool idea. Is there a map that shows a bridge that's taken battle damage? If so, that could be used too...like, your ship is disabled and you have to do stuff to get it back online.