What system(s) do you have in mind?In You only live twice there is a scene where Bond fights across Kobe docks defeats all comers, girl safely in tow then just when it looks like he's won, a mook steps out from behind some crates bonks him on the head and lights out - captured. If you tried this, your players would be fully justified in protesting it would just feel like I don't care what you do this is the way the story is going. GM ex machina.
In Burning Wheel, this would be a versus test - maybe the mook's Stealth + Weapon skill vs the PC's Observation. The dice would determine what happens.