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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?

fez
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Mae
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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. – Paul D. Waite Aug 14 '21 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. – Christopher Aug 14 '21 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. – lucasbachmann Aug 14 '21 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 '21 at 19:04
  • Here’s another thing to think about: when Neo asks Morpheus about taking injury and that he “thought it wasn’t real”, Morpheus confirms so that the mind makes it real for the body, even death. One could assume that perhaps the mind experiencing sickness in the matrix caused the immune system of the human in the pod to adjust itself accordingly and learn naturally as it should, thus meaning Neo’s immune system actually was just fine. It was just his muscles that were in bad shape due to disuse. – MissouriSpartan Aug 16 '21 at 02:55
  • The simplest answer is that it's not important for the story. So just make something up and be happy with it - The Matrix isn't LOTR, nobody thought that hard about the pedantic details of the world. – J... Aug 16 '21 at 11:47
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    How do we know that immune systems work the same way in the Real World? https://scifi.stackexchange.com/a/3822/21154 – Milo P Aug 16 '21 at 16:08
  • @J... Well yes, but it's not really a FUN answer, is it? :P – Mae Aug 16 '21 at 22:24
  • @Mae Remember, all I'm offering is the truth. ;) – J... Aug 17 '21 at 12:35

4 Answers4

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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.

Clockwork
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Christopher
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    The matrix wasn't based on a book – Valorum Aug 14 '21 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. – Christopher Aug 14 '21 at 18:17
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    The Matrix films have not been novelised – Valorum Aug 14 '21 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. – Chronocidal Aug 15 '21 at 15:48
  • @Chronocidal - Oh sure, there was some artwork cruft and other bits. Nothing that explains any element to the plot, tbh – Valorum Aug 15 '21 at 17:26
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    Movies still have writers. – DeepDeadpool Aug 16 '21 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.

Nepene Nep
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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 '21 at 23:21
  • I don't remember seeing any animals either, which also aid in disease transmission. – rtaft Aug 16 '21 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 '21 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 '21 at 09:12
  • @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 '21 at 21:24
  • Humans overcome colds in a few weeks. Any humans who entered the matrix with colds would quickly become immune in the paradise matrix loop. With no humans with active cold viruses, they'd die out.

    By the time they get to Zion they've had several rounds of quarantine.

     – Nepene Nep Aug 17 '21 at 22:44
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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?

WolfieSmith
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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 '21 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 '21 at 17:15
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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.

Carl B
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