Some obvious examples
- the holodeck gets a fatal software error and people are stuck in a classic novel
- a shuttle breaks down and crashes into a habitable planet
- the federation loses a space battle, but thankfully there's some space jungle (nebula, asteroid field, etc) to hide out in, thankfully within sub light distances
I would love to see an "Upper Decks" series of some kind. Set at the admiralty, have it be about the decent ethical admirals who are going out of their minds trying to rein in their crazy colleagues.