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Part of the Prophecy of The One involved the destruction of the Matrix. The prophecy as explained by Morpheus is:

When the Matrix was first built, there was a man born inside who had the ability to change whatever he wanted, to remake the Matrix as he saw fit. It was he who freed the first of us, taught us the truth - As long as the Matrix exists, the human race will never be free. After he died, the Oracle prophesied his return and his coming would hail the destruction of the Matrix, end the war, bring freedom to our people. That is why there are those who have spent our entire lives searching the Matrix looking for him.

The prophecy was part of the Machine-engineered Path of The One so the Machines knew the Matrix would not be literally destroyed but rather simply reloaded. But some Zionists like Morpheus believed in the prophecy and presumably that the Matrix would be literally destroyed.

Now, if the Matrix was destroyed it seems quite possible that all the blue pills would die. From the blue pills' perspective the destruction of the Matrix would be the destruction of the world, which could easily lead to their deaths. It is well known that someone who dies in the Matrix dies in the Real World, so the literal destruction of the Matrix could result in many blue pill deaths.

But even if the blue pills did not die from the destruction of the Matrix I do not see how most of them could survive in the Real World. There are billions of blue pills in the Matrix versus hundreds of thousands in Zion. I don't see any way the billions of blue pills could survive with a scorched sky in the Desert of the Real. So, either way, it seems that the literal destruction of the Matrix would result in the mass deaths of billions of blue pills.

And if that's true then who really has the moral high ground -- Zion or the Machines? At worst the Machines are guilty of "enslaving" the blue pills, but even then we are told the blue pills make an unconscious choice to accept the Matrix. On the other hand, Zion would be guilty of murdering billions.

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    The attitude towards individual innocents within the Matrix seemed to be pretty casual - 'shoot them before they turn into agents', though what that implies for groups of innocents is not clear.. – Andrew Thompson Sep 11 '14 at 0:16
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    @Mazura That's weak. Defending civilisation by murdering billions in another civilisation certainly does not give you the moral high ground. – Lightness Races in Orbit Sep 11 '14 at 14:23
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    @Richard The Matrix was redesigned so that most humans would accept the program at an unconscious level. Blue pills by definition have accepted the Matrix. Who are you do decide that their deaths are acceptable 'collateral damage' under the guise that you (Zion) are 'freeing' them? – Null Sep 11 '14 at 14:29
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    @Gaius - The "Matrix within a Matrix" theory is a fan - theory, not established canon. – Valorum Sep 11 '14 at 14:53
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    @Mazura - I'd say indiscriminate bombing of cities was indeed immoral, but in that case defenders can at least argue that the number of soldiers saved might be greater than the number of civilians killed. In this case you're killing billions of civilians to save a few thousand people, I think if you have any kind of general principles about which tactics are OK and which aren't (as opposed to saying anything goes or going with gut feelings) this would be wrong--for example it wouldn't meet the "proportionality" requirement in just war theory. – Hypnosifl Feb 16 '15 at 23:09
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In The Matrix Online Morpheus admits that he (and presumably the rest of Zion) thought that a human victory would result in the deaths of the blue pills in their pods. The relevant quote is:

We thought... I thought... we could win this war or lose it. If we won, yes, millions would die in their pods, but our days and years would be spent saving those we could, and reclaiming the surface. Instead, we have peace. Neo found a way to save them all...

The video of Morpheus saying this is on Youtube. In case the video is no longer available, here is a screenshot with the quote from Morpheus as a subtitle:

enter image description here

What this implies about the moral purity (or lack thereof) of Zion and its operatives is left as an exercise to the reader...

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    Under the circumstances, I think you'd consider those still inside the Matrix as being casualties of war. – Valorum Feb 16 '15 at 20:58
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    @Richard At some point mass homicide of non-combatants goes well beyond collateral damage and becomes a war crime (note that Morpheus underestimates the loss of life in millions rather than the more likely billions). The whole objection to the Matrix is that blue pills are enslaved and must be "freed" -- so how is killing them a preferable solution? – Null Feb 16 '15 at 21:15
  • There's a couple of levels here; 1) From a moral (and legal) perspective, it's acceptable to kill civilians if the target is primarily military (e.g. collateral damage). 2) Those humans that are still inside the Matrix are, with a small number of exceptions those that have chosen to accept machine control. Killing the machines, even if that results in the death of every inside the Matrix would allow the free human population to continue. – Valorum Feb 16 '15 at 21:43
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    @cde - I'm sticking with point 1. The intention wasn't to kill the blue pills, that was simply an unfortunate side-effect of defending themselves against the machines. – Valorum Feb 16 '15 at 22:29
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    @Richard 1) The Matrix is a population center of non-combatants that doubles as a power plant for non-military as well as military uses by the machines. It is not primarily a military target. 2) Even if you consider the blue pills allied with the machines, that is not an excuse to kill them. – Null Feb 16 '15 at 22:54
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First off, as you noted, considering that the whole search for The One was a quest designed by the Oracle and the Architect to retain stability in the Matrix, it is more likely than not that this parable, as told by Morpheus to Neo, also originated from the Oracle.

And the "You're not The One, Neo" Oracle is known for Obi-Wan-Kenobying the truth.

As far as the point of view of those who believed the prophecy:

  • It's quite possible that they interpret the prophecy in a way that the coming of The One would turn all the blue-pills into red-pills, as The One would convince them to quit the Matrix. At least, that would be the most obvious rationalization.

  • Those billions of blue-pills already survive on nutrients supplied. Which means the logistics and the means of making them survive exists, scorched sky or not.

  • The prophecy must be taken with a grain of salt, for sure. It was, after all, a control mechanism for the Machines. Nonetheless, Morpheus seems to think that the Matrix must be destroyed -- I quoted him saying "As long as the Matrix exists, the human race will never be free." That's not part of the prophecy, that's his commentary. – Null Sep 11 '14 at 0:47
  • I agree that your first bullet point is the most obvious interpretation. But that still leaves the issue of keeping all the recently ex-blue pills alive. The Machines would have lost their energy source but would undoubtedly unleash a final, massive attack on Zion and all those ex-blue pills. – Null Sep 11 '14 at 0:50
  • +1 for the second bullet point. The issue with that, I think, is that the blue pills survive by being fed from the liquified dead. I don't think that would go over too well in Zion. That leaves harvesting humans' thermal energy with the Machines' "form of fusion", but all that machinery is connected to the Matrix. What are the recently ex-blue pills going to do all day? Sit in their pods? They might as well plug into the Matrix while they're waiting... – Null Sep 11 '14 at 0:53
  • @Null Not to mention that it doesn't really seem like the Zionists have anything to rebuild the world. There's no hope like "we'll fix everythign" - they no longer have chicken or cows, wheat seeds or even grass... They might be free, and start "reclaiming" the world, but people who lived their whole lives in the Matrix will probably not be very happy about the apocalyptic environment with no hope of ever fixing it. Only the humans and machines survived - the rest of the planetary ecosystem is essentially dead. – Luaan Jun 24 '15 at 9:01
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    @Luaan - sorry but I'm stealing that for a question if you don't mind :) – DVK-on-Ahch-To Jun 24 '15 at 10:40

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