I've never been clear on this, even after seeing all three Matrix films.

I understand that there's been a cycle where some humans don't do well and don't actually accept the Matrix and break out and start living in and building Zion. I know this cycle has been repeated, so what there is of Zion wasn't just built by the rebels in the current cycle. This also means Neo is only "The One" for this generation, that there's been previous versions of "The One," and after each rebellion, the cycle starts over again.

Why is this cycle necessary? When given a choice, do so few humans opt to stay in the Matrix that the Machines can't survive on the power they supply? Is there a reason the Machines and humans can't create an equilibrium, where those that want to live in Zion can live there, while all other humans stay in the Matrix?

Is there a reason the humans and machines have not agreed to a long term truce that allows free humans and Machines to live without interference and allows humans that prefer the Matrix to live in it and power the Machines?

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    They are machines. if (bSubjugateAndKillHumans == true) { ... KillHumans(); ... } else { bSubjugateAndKillHumans = true; // developer note, add code for peace someday } – Jack B Nimble Feb 29 '12 at 16:59
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    SPOILER that's exactly how it ends. – Kevin Feb 29 '12 at 17:05
  • As Seraph noted - "You do not truly know someone until you fight them". They keep the war going to learn more and more about humans until the day that the war is no longer necessary because all humans accept Matrix version X. – Justin C Feb 29 '12 at 21:26
  • @JustinC: That's an interesting point. Why not post it as an answer? – Tango Feb 29 '12 at 21:28
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    @Kevin: I'm not sure what you mean by ends. It's a shame they never made any sequels. xkcd.com/566 (bottom strip) – fire.eagle Feb 29 '12 at 22:45

It's not a matter of necessity, it is a matter of caution. In similar fashion to BSG, the war is driven by machines that do not benefit from the passage of time and its erosion of human memory. If you watch the Animatrix it shows that the foundation of the war was the humans' inability to see robots as a valid form of life, and the humans' attempt to eradicate the now sentient machines.

However unlike humans and various exterminations of our past, these events did not ocurr to some distant ancestors of the current machines, it happened to THEM. In their eyes humanity had a chance for equality that failed, the only other option was to eradicate.

Then humanity scorched the sky.

Now they had a two fold problem, how to deal with the humans, whom can not be trusted, and how to continue to survive on limited power. Thus we arrive at the solution they have. You can not convince them human kind has "learned". We are the same race that tried to wipe them off the earth, twice. We are the same race that destroyed the life giving powers of our own planet, assuring our own eventual destruction, simply because we could not stand to let the machines have power, their one city.

The Architect is not burdened by human emotion, he does not see forgiveness or redemptive value in humans, all he sees is problems, and solutions. And those problems are absolute, and sustaining.

Personally, I think they should have exterminated the entire human race and just used cows. But then again, I am a Cylon (spoilers).

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    Damn Cylons look like humans now. – Xantec Mar 1 '12 at 1:31
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    Cows would be no more useful than humans, unless you were marketing a motion picture trilogy to them. scifi.stackexchange.com/questions/1263/… – Chad Levy Mar 2 '12 at 0:39
  • we know from the movie there is a clear sky up there, and we know the AI can build amazing tall towers. they should logically choose tall towers with solar panels. why they did what they did means they "need" humans and are flawed – simpleuser Feb 25 '16 at 21:03

Some people would say that Zion and the "real" world are just another layer of the Matrix. If true this would mean that the war really is over, the machines have unequivocally won and the humans are continually tricked into thinking they are still fighting for something.

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    I don't know if this is the official answer (I think it isn't, actually), but this is the only interpretation of the Matrix movies that makes sense to me. Especially since it rules out Neo's real-world superpowers, which I never liked. – Andres F. Feb 29 '12 at 17:34
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    It was a dream the whole time! – Ashterothi Feb 29 '12 at 17:40
  • If this is true, all machines are not real in this "fake real world", they are just a computer program. How are the real machines? – Rodrigo Feb 29 '12 at 19:24
  • This is called Matrix-within-a-Matrix (MWAM) theory and there was a discussion of this on another Q. – DVK-on-Ahch-To Mar 1 '12 at 15:12
  • Alas, the MWAM theory has been debunked. – Valorum Mar 25 '16 at 10:42

Because they are machines they likely behave in a binary way. The all or nothing mentality (true or false). A peak into the original AI source code might reveal this:

if (bSubjugateAndKillHumans == true) 
    bSubjugateAndKillHumans = true; // developer note, add code for peace someday 

But really it might boil down to the flawed logic of the machines. Once the humans are perceived as a threat, they might always be perceived as a theat, until such time as an extraordinary event happens to flip the switch from ON to OFF (such as Neo offering himself as a sacrifice).

Humans are also emotional and irrational creatures. They basically killed their planet in an effort to win the war against the machines (by darkening the skies). It could be the machines decided they could never trust humans. The Architect says as much:

The Oracle: What about the others?
The Architect: ...What others?
The Oracle: The ones that want out.
The Architect: Obviously they will be freed.
The Oracle: I have your word?
The Architect: What do you think I am? Human?

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    Silly dev, should have used //TODO:. Then it might have shown up in the search before release. – fire.eagle Feb 29 '12 at 22:48
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    Even today, computer systems, and especially A.I. are not black-and-white. They are much closer to probabilities, which are the opposite of binary. Also KillHumans is pretty far from what they actually did (well, Revolutions got a bit messy). – bitmask Mar 2 '12 at 10:47

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