Morality and the illusion of choice in games and virtual worlds

As game as increased in complexity the concept of choice and allowing players to create their own stories and feel the affects and consequences of moral actions has become an integral aspect to many games. This helps create a deeper level of immersion within the game and gives the players actions more weight as they connect to our emotions and real world beliefs and not simply to prescribed goals within the game. However there is a counter argument to this belief and it brings up a unique question in game design. If a game is designed to allow to make choices based on your morality, did you actually make a choice? Or simply follow one of several paths created by the game designer? Can choice ever actually exist in a world where every action and choice must be created by a person programing the ability for you to make those choices, and therefore all those possible choices are simply illusions made by an invisible creator, rendering the player into nothing more a puppet being manipulated by the game creators.

In an attempt to better express the concept of choice in games, The game Bioshock created what is considered by many people in the game community one of the strongest statements on morality in games ever made. Bioshock has at its core a very simple story of a man being trapped in a strange underwater city and he wants to escape. You control the character as he tries various plans to escape. During the game however their is a very infamous twist near the end of the game based around the players ally, a character named Atlas. Atlas is the only ally the player has for the majority of the game, he gives the player information about their situation and advice on what to do and where to go, a common function of AI companions. He is also very polite and always asks "would you kindly" before asking you move on to the next part of the mission objective.
Near the end of the game it is revealed that Atlas is in fact the antagonist of the game and every time he says the words "would you kindly" you have no choice but to follow his orders. This is explained not to the character you are controlling but to YOU the player. You are not in control of the game, the game has lied to you, it has betrayed you. when you thought you were make choices based on your own morality you were in fact nothing more than a puppet on rails.
The only comparison I can give to this moment in another medium would be the novel "The Murder Of Rodger Ackroyd" when it is revealed the narrator did it.

Bioshock the game

An explanation of Would You Kindly