The concept of choice acknowledges multiple alternatives, including the consequences of what we choose.
The very first version of the Matrix was designed by The Architect as a utopia, but the human minds eventually rejected this simulation resulting in its failure. A subsequent version of the Matrix was then designed to become much more of a nightmare, but the incorporation of human suffering still proved unsuccessful. Studying the human psyche, The Oracle then suggested that the component of choice be introduced in the third and current version of the Matrix, allowing the Matrix to finally become stable albeit needing to be reloaded every century.
Choice allowed the human minds born and connected into the Matrix to accept the simulation as reality, feeling enabled that their decisions result to palpable changes in their existence, even if their minds were only vaguely aware of their options.
Agent Smith: Why, Mr. Anderson? Why, why? Why do you do it? Why, why get up? Why keep fighting? Do you believe you're fighting for something? For more than your survival? Can you tell me what it is? Do you even know? Is it freedom? Or truth? Perhaps peace? Could it be for love? Illusions, Mr. Anderson. Vagaries of perception. Temporary constructs of a feeble human intellect trying desperately to justify an existence that is without meaning or purpose. And all of them as artificial as the Matrix itself, although only a human mind could invent something as insipid as love. You must be able to see it, Mr. Anderson. You must know it by now. You can't win. It's pointless to keep fighting. Why, Mr. Anderson? Why? Why do you persist? Neo: Because I choose to.”
― The Final Battle
Neo had been, at multiple times, presented a choice between two options, with each option having been portrayed to only ever result in a predefined outcome. With Neo always findings ways to decisively negate the unwanted consequences of his actions.
Much like any other Resistance member rescued from the Matrix, Neo was initially given the choice of two pills to take. When Morpheus presented Neo the choice between two pills, he explained how the red pill will start Neo's journey to discover the reality behind the Matrix and how the blue pill will just return Neo to his normal life.
During his first visit to The Oracle, she tells Neo that he would need to make a choice between saving himself or saving Morpheus from dying, with the other dying as a consequence of the action. Neo chose to save Morpheus and was killed by Agent Smith as a result. But Neo rejected his death within the Matrix, enlightening his mind to his inherent powers as The One. His newly awakened abilities then allowed him greater power to actually achieve his desired outcomes.
When Neo met The Architect, he was presented with two doors: One to the Source, wherein Neo dies, sacrificing himself to reinsert the Prime Program back to the Source in order to reload the Matrix; and the other door returning Neo to the Matrix, allowing him to save Trinity but risking the extinction of the entire human race. Neo chose to save Trinity, with his unprecedented choice ultimately having ramifications which not even The Oracle could foresee.
Cause and Effect
Some programs believe that the world operates in a paradigm of cause and effect. The Merovingian attempted to demonstrate this basic principle at Le Vrai by having a young woman eat a dessert loaded with code that triggered an orgasm. The Merovingian proceeds to exclaim that everyone was a slave to their most basic drives.