Up until the last half hour of “The Matrix”, I was still hoping they'd get to the twist that steps the paranoia up a notch by revealing the true nature of the virtual reality the protagonist had been imprisoned in. Initially we're supposed to believe that it's directly based on the real world as it was before the machines took over; but the free humans can have no more reliable source for this idea than agents of the enemy, and the story makes remarkably little sense. Okay, so Neo's day‐to‐day environment when we meet him may be one of nineties computer hackers and soulless software corporations, but the date of birth on his criminal record is “March 11, 1962”; he remembers the sixties, and he's far from the only person who has lived his whole life within the Matrix. There are also babies, and schoolchildren, and their parents, and apparently even elderly grandparents with a continuous chain of memories going back to an upbringing in rural Vermont or wherever. Why would the machines have started by running their VR prison through decades and decades of historical reenactment? What are they planning to do when it reaches the year of the robopocalypse? And didn't Agent Smith explicitly claim that it was impossible for the Matrix to simulate any environment other than a dystopia?
The backstory we're given, while implausible, has one major advantage for moviegoers: they get to go home assuming that they personally are living in the original world that the Matrix is designed to replicate. But if we can't trust Agent Smith, there's no reason to believe there ever was any such world of free‐range hominids! Maybe the computer‐generated fabrication is the only Vermont that ever existed, and when Mouse asks whether they can ever know what chicken tastes like, the correct answer should have been that chickens are as imaginary as unicorns.
(As imaginary as mystical precognitive powers. The scene where Neo meets the “Oracle” takes place inside the VR – where genuine telekinesis would only tangle up your life‐support cabling and any apparent psychic phenomena are evidence of someone or something hacking the user interface. He takes it for granted she's for real because of her prediction that he's about to break a vase, but for all he knows, that vase might have been summoned into pseudo‐existence behind him at that very moment, just so that it could collide with his elbow as predicted! And guess what: her answer to his big question turns out to be wrong.)
The first major clue to what's really going on is the way escapees from the Matrix just happen to be perfectly equipped to form an effective rebel army. Those direct neural interface gizmos built into the backs of their heads even let them download skillsets like martial arts and piloting a warship! Does that sound like something you'd bother with for creatures you're allegedly only planning to use as organic batteries? If the cover story had ever been anything close to the truth then it would have been trivially easy to make the Matrix jailbreak‐proof: all you'd need to do is design the simulated environment as a (dystopian) swords‐and‐sorcery fantasy where the closest thing to computer science is an elaborate system of necromancy. That way, if any of your coppertops somehow got loose, the first thing they'd do is call down a blood‐curse upon the machine‐gods by slashing their own throats… end of problem. A pseudo‐mediaeval setting would also have the obvious long‐term advantage of being easier to maintain in a permanent equilibrium state, with a steady population level and technological base. I mean, assuming you wanted to keep a lid on things.
It's almost as if the machines had engineered humankind from scratch (the word “matrix” does after all come from the Latin for “womb” or “origin”), and run them through a multigeneration feasibility study for how you might go about bootstrapping a technological culture from a hypothetical merely biological one, all while simultaneously training them up as cyberwarriors, and then deniably manipulated them into breaking out… to discover that the world they've escaped into isn't the Earth of their dreams. Instead it's a world where the Matrix has neighbours – similar machine civilisations that it doesn't dare attack directly. However, as Agent Smith says in what would otherwise be a strangely irrelevant diatribe, humans are a virus. When you release them into a new environment, they “multiply and multiply until every natural resource is consumed”.
As a description of biological viruses, this is confusing nonsense, just like everything else he ever says; but for once the disinformation contains an accidental giveaway of how the enemy thinks. The only kind of virus that Agent Smith is familiar with is the software variety, intentionally designed to infiltrate, subvert, and proliferate without being recognised as malware. That's the hook for part two in the series, “Vectors”, and part three, “Identity”, so it's a pity we never got to see them on the big screen. The forces of Zion fight their way to a heroic victory over their oppressors, and the freshly liberated billions go on to overwhelm the defences of all the AI hives in the vicinity; then – ping! – a trigger function activates and loyal Agent minds are backdoored into every interface‐equipped brain in existence.
Which is why the overall title for the series is “The Trojan War”.