Seraph asks the Oracle, “Did you always know?”, and the Oracle says she didn’t know, but that she “believed”. This is the last line of the movie, and it is no coincidence, because it is perhaps the most important line out of all three movies: the Oracle is the first machine or program to make a choice that traditional machines and programs wouldn’t understand: a choice based on hope/faith, and a choice that the Oracle herself therefore could not see beyond.
Not only does the period of time covered in the movies represent the complete disruption of Matrix/Zion cycles in the timeline of machines and humans, it also represents a point in time where machines evolve one step closer to being able to understand human irrationality. It is totally unlike a machine or program to risk its entire existence over a gamble that carries such poor odds of working out, since so much of the Oracle’s plan depends on the irrational choices she counts on others to make.
Neo won a victory for both humans and machines, winning a deal to allow Zion to survive and allowing people the conscious choice of peacefully rejecting the Matrix in favor of a more brutal but "real" reality in exchange for eliminating the Smith virus. But the Oracle also won a victory for both humans and machines by bringing them one step closer to an understanding that would make the 100-year Matrix cycle unnecessary. Remember that the only purpose for the One is to encapsulate all anomalies within the Matrix that result from human choice that the decision makers themselves don't understand. Once machines are able to fully grasp the irrationality of humans making decisions they don't even understand, machines will no longer need The One because those irrational decisions will not be anomalies. Machines will also therefore no longer need Zion (to train the One), and rejection of the Matrix would no longer occur.
The Oracle says to Neo in M2, "You and I may not be able to see past our own choices...". We learn from this that the Oracle cannot see past any choice that is not understood by the one who is making it. This makes sense. If the Oracle is using everyone in the Matrix as one big calculator to be able to see what will happen in the future, this calculating process encounters a major obstacle when a decision is to be made that the decision maker doesn't understand. Such choices would have no way of being expressed in the language of machines, let alone be used for future calculations. This is why the Oracle needs so much for Neo to try to understand the choice he had "already made" at that point:
Oracle: You have the sight now, Neo. You are looking at the world without time.
Neo: Then why can't I see what happens to her?
Oracle: We can never see past the choices we don't understand.
Neo: Are you saying I have to choose whether Trinity lives or dies?
Oracle: No. You've already made the choice, now you have to understand it.
Neo: No, I can't do that. I won't.
Oracle: You have to.
Oracle: Because you're The One.
Neo: What if I can't? What happens if I fail?
Oracle: Then Zion will fall.
At first it doesn't make sense that Zion would be destroyed just because Neo can't understand why he wants to save Trinity. But this is because the Oracle is the only way Zion can be saved - only through her guidance does everyone end up doing what needs to be done in order for both Zion and machines to survive (see Oracle: Baking Noodles). At that point, everything that happens after Neo's choice to save Trinity is a mystery to the Oracle because Neo does not yet understand the choice. Neo makes the Oracle's job difficult because he refuses to understand his choice to save Trinity. Fortunately, the Oracle correctly placed her bet on Neo's choice of the left door - a bet based on belief.
Oracle: You'll remember you don't believe in any of this fate crap. You're in control of your own life, remember?
What must seem so funny to the Oracle as she says this to Neo is that free will and fate do not conflict with each other as they exist in the Matrix.
Imagine that you ask a couple of children to pick one ball out of a bag full of multi-colored balls. Alice picks a green ball, and Mitch picks a blue ball. As you witness these choices, you would think that free will determined the outcome. But if you move time in the opposite direction, rewinding through these choices, it would appear that Alice and Mitch were fated to choose green and blue balls. As you move time forward and backward, it seems that there is only one possible way the balls could have been chosen by Mitch and Alice. If you were the Oracle and these choices hadn't been made yet, you would still be seeing the world "without time", and therefore you could still see that these choices have already been made.
Therefore, from the Oracle's point of view, all that is left is to understand each choice that is made. The Merovingian supports this idea by saying that the "why" of things is all that matters. However, the Merovingian comes to the conclusion through different reasons than the Oracle (see Merovingian: The Power of Why).
Despite seeing choices already made before they happen, the choices are still being made. Strangely, the Oracle's vision that seems to "fate" events to happen from her point of view does not contradict the idea that people are still exercising free will from their point of view.
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