Title: Shadows of Ourselves
Era: TNG or later, better with post VOY "Doctor" type EMH
Setting: Starship, Holodeck
Start the story normally as a "Day in the life of Starfleet people," and then have the ship receive a very tangental, weak, distress call from a planet along the border with the Romulans. They go in, and see that the Romulans have attacked the colony, and they did so lightning fast and quickly eradicated the civilian's abilities to call for help. More importantly, they've set up dampening fields around the system - loud static-makers so that a signal isn't possible until the ship leaves the system - which would be abandoning the colonists, many of whom are about to be killed en masse.
Likely, the captain would be OK with sending an away team, and make that the players, specializing their skills to why they were sent to this particular planet. Once the undercover stuff starts, all is good...
...except they start to get odd bits of intuition. THey suddenly "know" things, like: there's a Romulan around the corner. I need to go into that particular building (where they find the Romulan plans), etc. And suddenly, the Romulans are frantically looking for them, even though the crew haven't done anything to be "spotted" yet. More information falls magically into the minds of the crew to keep them one step ahead - what is going on?!
Well, the ship has been boarded by Romulans, and the players aren't playing their characters - they're playing holodeck simulations of their characters. Indeed, the Romulans downloaded the pysch profiles from their very own ship into the holodeck simulation they're now running, complete with their plans for takeover of the nearby colony world.
The "help" they're getting in the form of intuition is information the Holodoc (or ship's engineer somehow) is downloading into their holomatrices, in an effort to get the simulations sentient enough to clue in that they're simulations, and that they've for more going for them than they think: the trapped crew (or the Holodoc) have given them command codes.
Then it gets fun: holocharacters need to defeat the Romulans from within the Holodeck and sickbay (or shipwide if they can on their ship - ie: holoemitters), with the full knowledge that they're not who they believe they are... Might be fun if one or more of the engineer/science types just download themselves into the ships computer to play havoc with the Romulans..
The Doc (who likes throwing "you're not who you think you are" stories at his players)
So you think, 'Might as well,
Dance a Tango to Hell,
at least I'll have Tangoed at all.'
-- "Rent," Jonathan Larson