Note: This post is going to gleefully spoil a crucial scene from Bioshock. It will absolutely ruin the enjoyment of much of the plot if you haven't played. So if that's the case, and you're interested in playing it at some point, delete this from your feedreader and/or scroll past it. I'll try to stay fairly vague, in case your eye wanders, and try not to edit it too much.
I actually thought I had been spoiled for the twist in Bioshock before I played it, because I already knew that Jack (the main character) is actually Andrew Ryan's illegitimate son, suspected that Atlas was not who he seemed to be, and had heard that Jack was being manipulated somehow during the events in Rapture. In other games, these would be the twists.
Which is not to say that they're not in Bioshock, to some degree. The method by which Jack is controlled, along with flashbacks through the game to drive the realization home, is played for natural dramatic effect. Likewise, the game feeds you clues as to Jack's identity gradually enough that--even if you don't realize the full extent of his relationship to Ryan--you feel clever about figuring it out.
But the real killer scene is when, after revealing the method by which Jack has been manipulated throughout the game, Andrew Ryan uses it to take control of him. He delivers a short monologue (in the best tradition of his inspiration, Ayn Rand), repeating again and again that "A man chooses. A slave obeys." He demonstrates his ability to control Jack (at this point, and for the remainder of the scene, Bioshock takes over input and disables the gamepad).
And then, that plot point is still being digested, he hands Jack a club, and commands him to kill. The player is only able to watch helplessly as his alter-ego slowly beats Ryan to death, with Ryan shrieking all the while: "A man chooses! A slave obeys! Obey!" It's a tremendously shocking and disturbing tableau. I would argue that solely as a game, Bioshock doesn't provide much in the way of novelty. As a narrative, however, it is absolutely brilliant, and Ryan's death is the peak of that brilliance.
(If you don't plan on playing the game, or you want a refresher on what I'm talking about, you can watch it here. If you haven't played it, however, I suspect it'll be robbed of most of its context and resonance.)
There are several really thought-provoking things about the scene, the most obvious of which is its decision to make the player powerless. You could write the same scene in a movie, or in a book, with Jack unable to stop himself from murdering Ryan. But it's really only in a game, where the player is used to interaction, that the point can be fully driven home--a tendency Bioshock encourages by only very rarely using traditional cutscenes, generally eschewing them in favor of Half-Life's now-ubiquitous scripted events.
Immediately after Ryan's death, interestingly enough, Jack is given a new mission using the same mental control mechanism--but this time, the player is back behind the wheel. I suppose you could choose not to follow orders at this point, but you'd be forced to sit forever in a small room with no-where else to go and no plot available to you. Which is a neat way of forcing the player to bow to the plot convention, as well as a sly commentary on the nature of videogame storytelling--of course you're going to do what you're told, chump, because you literally have no choice. Interesting, too, that Jack is unknowingly coerced into following the game's missions, instead of allowing for the possibility that the player would have gone along out of altruism or curiosity if given a choice. Not to mention that no-one has to issue any commands before the player kills practically everything in sight (although I doubt this view of Bioshock's violence was intentional).
In his defense of the game against its detractors, Kieron Gillen seems to argue that designer Ken Levine is trying to send two messages in Bioshock: A) don't follow any ideology blindly, and B) killing (the Little Sisters) is morally wrong. The second point is a nice thought, but entirely speculation--Levine has stated bluntly that he never wanted to add the "bad" ending for players who harvested the Little Sisters instead of rescuing them, which would have left the game morally ambiguous if he'd had his way. The first stands on stronger ground, but I wonder if it's not undermined by the circumstances of Ryan's death. After all, if Ryan never forbade contact with the surface (a governmental control of the kind he claimed, as a Libertarian demagogue, to detest), Frank Fontaine might have never risen up to challenge him via a smuggling empire. The game isn't a ringing endorsement of Objectivism, but it's no refutation, either.
Levine himself is on record, I believe, as saying that he wanted the game's narrative to focus on how so-called perfect ideologies are invariably let down by imperfect humans. Again, I'm not sure that the narrative actually backs that up--in no small part because I believe it's a flawed premise from the start. My reading of it, backed up by Ryan's assisted suicide, is more along the lines of "be careful what you wish for." Ryan sets out to create an Objectivist state where laws are ignored and industry rules all, and Fontaine is the embodiment of that state--to Ryan's dismay (particularly since it moves him to betray those ideals in order to combat Fontaine). In the end, it's Ryan's own runaway ideology that threatens him, and rather than change his ways and live, he allows it to kill him.
Regardless of these interpretations, the fact that Bioshock can invite such investigation is a testament to the writing and the depth of characterization throughout. It's on the strength of that writing, and the uniformly excellent voice acting, that Bioshock truly succeeds, above and beyond the bare mechanics of the game itself--killing the same splicers and hacking the same machines over and over again soon becomes tedious. The promise of Rapture's secrets, on the other hand, may carry it past those problems more effectively than any straightforward gameplay could have done.