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"nearly 99.9% of all test subjects accepted the program, as long as they were given a choice"

How could the humans have rejected the program if they had no choice? Isn't that a paradox? You cannot reject something if you have no choice, otherwise you would have a choice.

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    I don't understand what you mean, are you inferring from the above that people given no choice rejected the program? That sentence gives no evidence for that per my understanding. – TheLethalCarrot Jan 16 at 11:17
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    @TheLethalCarrot earlier in the same monologue Smith talks about failures of early versions of the Matrix where "entire crops were lost" which suggests everyone rejected the program. Oh wait, the 99% quote is from the second film, with the Architect speaking... – Jontia Jan 16 at 11:37
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    @TheLethalCarrot The decision to give people a choice to accept or reject the program really only makes sense if they were rejecting it when not given a choice, and doing so in larger numbers than when given a choice. – Anthony Grist Jan 16 at 15:18
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    The current answers follow my initial interpretation of this question, but I'm starting to wonder if we are all mis-interpreting it. I'm starting to suspect the question may be about the logic of what the architect says about the previous versions: how can people attached to the previous versions reject the program if they have no choice? – abathur Jan 16 at 16:27
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    It's like the body rejecting a transplanted heart. It's not a conscious decision. – Paul McCarthy Jan 17 at 14:38
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It's important to note that the Matrix isn't actually that convincing a simulation of reality. It glitches regularly, the physics is weird, it requires periodic rebooting (including regular brain-wipes for the occupants) and is, for those that are aware that they're inside a simulation, immediately apparent to be a fake. In short, people are prone to noticing that they're in a sim and keep trying to find ways to get out of it, initially on a subconscious level, but eventually by actively trying to subvert the Matrix and find ways out. As Smith says,

... The perfect world was a dream that your primitive cerebrum kept trying to wake up from.

The problem, as defined by the Architect is that all the glitches in the Matrix eventually become so apparent to the subject that they eventually realise, on a conscious level, that they're in unreality and reject the system. They end up mad, dead, suicidal or actively trying to subvert the system and eventually tell more people that the system is fake which creates a cascade of problems.

The Oracle came up with a solution, namely the Choice (with a big c). If people are periodically polled on a subconscious level to see whether they're happy with their reality, even despite the fact that it's obviously a dud, the vast majority will accept their reality. Conversely, a small number will choose otherwise and they can be safely ejected from the program and subsequently murdered.

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    It's not entirely clear to me what for "rejecting" would take without someone from Zion there to help out. There were a couple of Animatrix shorts which suggested a way out without outside help, but only the short conversation between Neo and Kid bridges these into the main films. – Jontia Jan 16 at 13:30
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    @Jontia - We see someone who couldn't (or wouldn't) leave in the Matrix Comic A Life Less Empty. In short she suffers from depression and seems to be suicidal – Valorum Jan 16 at 13:37
  • And in the Matrix Comic Survivors, we learn that a mind that is shown (or discovers) the truth in adulthood simply dies in agony – Valorum Jan 16 at 13:38
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    @Herrsocke: It's a prison that the prisoners are mostly onboard and content with. – Ellesedil Jan 16 at 18:00
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    This answer involves a lot of speculation. Which is entirely unnecessary, because (as explained in @Jontia's answer) the answer is given in the movie, in the exact same quote mentioned by the OP. – BlueRaja - Danny Pflughoeft Jan 16 at 21:41
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The entire quote from the scene, which is Neo's discussion with the Architect in The Matrix Reloaded.

ARCHITECT: Please. As I was saying, she stumbled upon a solution whereby nearly 99.9% of all test subjects accepted the program, as long as they were given a choice, even if they were only aware of the choice at a near unconscious level. While this answer functioned, it was obviously fundamentally flawed, thus creating the otherwise contradictory systemic anomaly, that if left unchecked might threaten the system itself. Ergo, those that refused the program, while a minority, if unchecked, would constitute an escalating probability of disaster.

Everyone is given choice, but most are not aware of it, and this is obviously flawed. Both logically and as a method of actual control, as the Architect points out. And leads to the rise of the anomaly "The One" who left unchecked would make the choice conscious by exposing the Matrix to everyone inside.

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  • Neo was already doubtful, so his choice was quite apparent in Morpheus's offer. – Cees Timmerman Jan 17 at 15:38
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Per my comment on the answer, I started to wonder if the question is actually more like: how can people attached to the previous versions reject the program if they have no choice? Adding this answer just in case, since the other answers don't address that interpretation.

I suspect this just comes down to the use of language/terminology that has different meanings in different contexts.

Both Smith and The Architect use the word "accept" here. I think it's fair to read "reject" as the correct antonym, but I don't think they mean accept/reject in the sense that you might choose to accept/reject a gift or job offer.

I think they're using accept/reject in roughly the same way medical discourse describes whether a body accepts or rejects transplanted tissue.

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  • As in "this world is too good to be true." – Cees Timmerman Jan 17 at 15:41
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    Yes, this was my understanding, as well. The host has rejected the implant, it’s just that in this case, the implant was a simulated reality instead of a kidney. – Ian MacDonald Jan 18 at 1:00
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Let us remember that the entire movie took place within the Matrix. Zion was never actually in the "real world".

Case in point: "The Kid" brought back the spoon from the Matrix to give to Neo. This is only possible if "the real world" is also within the Matrix itself.

Humans were only given a choice within the Matrix to keep them from realizing the actual truth: there is no choice, only the idea of a choice.

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  • I'm not too familiar with Matrix but I've read this a few times and I'm not entirely sure what your answer to the question is. Could you edit it to clear this up? – TheLethalCarrot Jan 16 at 15:36
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    While this may be the only logically consistent explanation, it has been explicitly rejected by the writers. Zion is the real world. – OrangeDog Jan 16 at 16:13
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    "Later, when Neo was about to leave Zion to see The Oracle again, Kid caught up with him to give him a gift, saying "I just have to give something to Neo. A gift from one of the orphans. He made me swear to get it to you before you left. He said you'd understand", which, when unwrapped, turned out to be a spoon, showing that Spoon Boy had been freed from the Matrix." – Herrsocke Jan 16 at 17:54
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    So just to be clear, @Herrsocke, your point is that the spoon gifted has nothing to do with the Matrix spoon, it's a different, symbolic, real spoon. Contradicting this answer which claims it was the same (virtual) spoon in both the Matrix and Zion. – ShadowRanger Jan 16 at 22:45

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