Title: "When the Captain's Away..."
Setting: Starship in orbit of a resort colony, or in spacedock where there are no other ships...
Era: Any
The ship is up for a minor refit, or an upgrade of some secondary systems, or something similar. The Captain, XO, and whoever else is higher rank than the PCs, take this rare opportunity for shore leave, likely with some pushing and shoving from the Ship's counsellor or CMO.
They're not at hand - either spelunking in a cave where transporters don't work, or they've shuttled to somewhere else, when the ship, in stardock, gets a fairly routine request for assistance from a ship with a failure in its warp drive. The starbase commander OK's the ship going out and tugging the damaged ship into the starbase, as they are the only starship on hand.
Of course, the others are playing possum, and try to take over the PC Crew's ship, which suddenly has junior officers in charge during a very real crisis... overpower them, and then they'll find they're at the hands of a fairly hostile race - but it doesn't want to kill the junior officers, they want to steal something from the Starbase - and now they have a way to do it...
So they have to overpower their invaders, and then retake their ship, and warn the Starbase that the ship they're "tugging" is armed and dangerous!
The Doc