Not only is this a moving, shocking, and all-around incredible quote about the consequences of blindly accepting authority, but it also represents one of the single most insightful statements ever made about videogaming in general.
Cut scenes are a form of gameplay slavery. They rob the player of control, take him out of the moment, and force him to passively witness as the events of the game -- the events he is supposed to have some degree of local agency over. Ken Levine knows this, and chose to exploit it in creating one of the most memorable story twists of all time.
When the player finds out that he has been subliminally controlled by Atlas throughout the entire game, he or she experiences a very sudden, shocking reassessment of values. Having gone through the game thus far with the single-minded intent of beating Andrew Ryan to a bloody pulp, the player is suddenly forced to ask a question most other games would never dream of proposing to the player: "Why am I doing this?"
Why, upon first entering Rapture, do you inject a Plasmid into his veins for seemingly no reason? Why do you follow Atlas's every instruction? Why do you kill the innocent, nonviolent-unless-provoked Big Daddies? Why do you want to kill Ryan? The answer is depressingly simple: you did these things because you were told to. Not because you necessarily had any personal investment in the action, but because someone asked you nicely. Even after realizing this, the player remains completely powerless to stop himself.
In an older article I wrote ("Exploring BioShock's storytelling flaws"), I had this to say about the final "would you kindly" cut scene:
Noninteractivity is used brilliantly within the context of the scene: for perhaps the first time in the entire game, the player doesn’t want to kill Andrew Ryan, but Jack’s violent nature and refusal to question his orders are too much and the player is forced to watch, horrified, as he mercilessly and uncontrollably batters Ryan to death.
It stands as the single greatest noninteractive cut scene in gaming history. Ever. As a storytelling device, noninteractivity is used as a weapon against the player: you don’t want to question why you’re doing what you’re doing? Fine -- you’re nothing better than a mindless, robotic slave, and you have essentially given up the human gift of choice. Having control taken away is, within the context of the story, a tangible punishment for accepting things on face value and blindly following orders.
BioShock wants us to question authority and instruction not just for the big stuff -- politics, work, education and so on -- but for videogaming, as well. When Cortana asks you to pistol-whip a bunch of aliens in Halo, why not stop for a moment and really think about why you're doing it?
One might suggest that questioning authority in a videogame, where structure is more or less mandatory and even the most nonlinear games still have an inescapably linear storyline, would be an ultimately meaningless gesture. But if you're willing to take everything a videogame presents you with at face value, how much more are you capable of accepting without question? If the player is asked to mow down armies of faceless baddies simply because they are "evil," what does that even mean?
For these reasons, "would you kindly" is, quite simply, the most meaningful videogame quote of all time. It deeply affects the player on both emotional and intellectual levels; not only that, but the intensity of the former inspires the latter. As the player feels hatred and betrayal from his amiably-worded induction into slavery, he becomes much more likely to take Andrew Ryan's dying words to heart:
A man chooses; a slave obeys.