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For context, I've only seen the first film, and only all the way through at a social event.

When Neo is unplugged, he's leaving a sterile or at least very isolated environment, getting dunked in sketchy standing water, and being exposed to other people for the first time in his life. When you increase the size of your real life social group dramatically, even if you have a completely healthy immune system, you're likely to catch something, a la fresher's flu or con plague. Why doesn't this happen to him?

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    He probably did, but when all you do is effectively lie down with a really fancy VR headset on all day, it doesn’t matter. Aug 14, 2021 at 17:53
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    @PaulD.Waite Pretty sure they had giant underground Discos in 2. And he had already bathed in stagnant "Dead human corpse recycling" water. Aug 14, 2021 at 18:19
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    @Christopher yeah zion discos mean anything contagious has hit everyone a long time ago. They are way past herd immunity. Aug 14, 2021 at 18:27
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    @Christopher with a few exceptions, corpses actually aren't all that good at transmitting disease. It's a poor enviroment for germs that are adapted for the enviroment of a living body.
    – Mae
    Aug 14, 2021 at 19:04
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    How do we know that immune systems work the same way in the Real World? scifi.stackexchange.com/a/3822/21154
    – Milo P
    Aug 16, 2021 at 16:08

4 Answers 4

21

Answer attempt, assuming nobody finds a book or interview answer:

When he leaves the tank, he has completely atrophied muscles. Given he has never used them in his entire life. They treat him for that. It is safe to assume they also give him a "Immune System buildup treatment" while they are at it.

Keep in mind the whole of Zion is part of the overall machine plan. The need to reboot the matrix and restart Zion is worked into the overall system. So any such knowledge would be provided with the Zion reset.

Edit: While the authors had propably no way to consider it, it is possible that the machines intentionally introduced some pathogens into the lifecycle of a pod human. It turns out that pathogens are so important, our own DNA encodes for releases of some during our Embryonal phase.

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    The matrix wasn't based on a book
    – Valorum
    Aug 14, 2021 at 18:16
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    @Valorum Neither were any Star Wars Episodes, yet they all got companion books - that differ in some details or explain some stuff further. Aug 14, 2021 at 18:17
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    The Matrix films have not been novelised
    – Valorum
    Aug 14, 2021 at 18:38
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    @Valorum But, they do have various non-novelisation books, such as compiled books of the official comics, and "The Art of the Matrix", which contains art, storyboards (including of 3 deleted scenes), and commentary. I presume that Christopher was throwing a CYA, in case either the commentary or comics in the books contradict him. Aug 15, 2021 at 15:48
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    Movies still have writers. Aug 16, 2021 at 15:38
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As Morpheus said.

That you are a slave, Neo. That you, like everyone else, was born into bondage... kept inside a prison that you cannot smell, taste, or touch. A prison for your mind.

One of the benefits of being kept in a prison that you cannot smell, taste or touch that isn't mentioned a lot is it works well as social isolation. Most human transmissible plagues wouldn't get a chance to pass on since the humans are isolated from each other, and would be eliminated and as such it's reasonable for the film creators to ignore this aspect of real life.

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    Exactly. I question the assumption that, in a world where nearly all life has been snuffed out and humans have been isolated for generations, illnesses caused by microbes would still necessarily be a significant problem.
    – trlkly
    Aug 15, 2021 at 23:21
  • I don't remember seeing any animals either, which also aid in disease transmission.
    – rtaft
    Aug 16, 2021 at 12:13
  • @trlkly we've had viruses with us from early agriculture at least (smallpox is around 11,000 years old) and things like influenzas and rhinoviruses are pretty much constant moving targets. Zion's also bigger than a lot of historical (preindustrial) cities, so it's not like there aren't enough hosts.
    – Mae
    Aug 16, 2021 at 22:23
  • Smallpox evolved from a rodent virus. It's doubtful that many rats or gerbils are alive with the disappearance of the sun.
    – Nepene Nep
    Aug 17, 2021 at 9:12
  • @NepeneNep What I mean to say is that it's difficult to make a group of humans so small that disease is no longer a concern. Zion is 250,000 people, and while it likely wouldn't be spitting out current-level plagues every century like the modern world does, it's probably enough to keep some of our pathoegenic frenemies kicking around and mutating. & it's not like you could wipe out ALL the things we call "a cold", for example.
    – Mae
    Aug 17, 2021 at 21:24
3

Although I've found nothing to back it up yet, I always just assumed they had immunity because they were all inter-connected via the 'vats' before they were released.

The machines would not want their 'battery system' (ahem) to be destroyed from within, so it would only be logical for the humans to be kept immune from infection while within the system, so why would that immunity not continue after they were freed?

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    I'm actually curious, what are the odds that their batteries do catch a disease from an external micro organism, when they have no contact with anything outside of their pod. I also wonder if that liquid is renewed in some way, and if it's "treated" beforehand.
    – Clockwork
    Aug 14, 2021 at 19:09
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    I don't imagine that they were connected in a way that would allow for the spread of disease. The machines certainly wouldn't want to intentionally do so, because that means one infection could take out the whole lot. Having some exposure to foreign organisms may improve your immune system, but it certainly doesn't make you immune to everything.
    – NotThatGuy
    Aug 16, 2021 at 17:15
-5

As any answer is speculation, I provide my favorite take on the series. There are so many plot holes, particularly in the later films, that the most reasonable explanation is that Neo never escapes the Matrix. He simply transitions from one level to a deeper level that imagines he has “escaped.”

So no need to wonder about immune systems or why Skynet doesn’t use potatoes as batteries. Like Total Recall, it’s all in the head.

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    The idea that the 'real world' in the films was just another layer of the Matrix is a popular theory among fans, but is there any clear indication that this is what the filmmakers actually intended? Aug 15, 2021 at 8:09
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    @LogicDictates - Debunked thoroughly
    – Valorum
    Aug 15, 2021 at 11:40
  • @Valorum I don't think it's possible for a simulation theory to be disproven, which is kind of the problem. It can be a "valid" theory for basically any work of fiction (or for real life... which I suppose is also the plot of The Matrix). Of course some works may explicitly suggest this interpretation, but plot holes don't really do that.
    – NotThatGuy
    Aug 16, 2021 at 17:40
  • @NotThatGuy - The Matrix-within-a-Matrix theory was moderately compelling around the time of film #2 in the series, but basically debunked by the end of film #3, not least because if Zion was simply another form of Matrix ("it was all just a dream"), it would utterly invalidate the films, and what filmmaker would want to do that to their baby?
    – Valorum
    Aug 16, 2021 at 17:58

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