It's a pity that the game doesn't let you play the encounter to its logical conclusion:
"So, you work for Section 31 and this is a holodeck?"
"Whoops. Darn that loose trigger. Too bad I always keep my tetryon rifle set to 'disintegrate...'"
2nd time through, my group spent more time coming up with reasons to kill Drake than actually doing the bridge encounter.
Though we did the Captain because, within the terms of the simulation, it's more logically him. But there are other things that point to a simulation (even without the yellow bars in map view). One of the more amusing ones is that we're in a nebula of over-thick Tang and the viewscreen shows a clear starfield.