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In the Matrix, the One is the person who can truly accept that the Matrix isn't real. As such, it makes total sense that they would be able to ignore psychosomatic effects like dying when shot in the Matrix. However, at the end of the first movie we see him stopping bullets with his mind, and flying like Superman.

The Matrix is ultimately just a physics simulator / networked brain-in-a-vat system, though. If the only signal a connected person can send to it is the nerve impulses that would normally go to their muscles, how is the One stopping bullets or flying? Why would it even have a signal coming from a connected human body that could result in those things happening?

To clarify, superhuman leaps and dodges make sense, because they're still just messages intended for the (simulated) human muscles; understanding that the Matrix isn't real lets you send messages that a real body couldn't handle. But what nerve impulse is telling bullets to stop or letting the One fly without flapping his arms?

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Remember the jumping simulation? Morpheus jumping across a six-lane street, plus sidewalks? All those who return to the Matrix after being freed are taught the skills to change things, to make superhuman leaps and move faster than they should be able to -- but in the end, they have limits.

The One "can change anything he wants" -- not just by way of loading equipment in the loader program before entering the Matrix, but even after he's in. He can jump like Morpheus -- only far, far more so. He can jump and not come down until he's ready. He can warp or suspend physics, not only for himself, but for other things (like bullets). He can dodge (if he chooses) like an Agent. He can (in the second film) defend himself against plural Agents with one arm, while noting that the Agents have had "upgrades."

Then remember the spoon-bending when Neo first met The Oracle: "There is no spoon." Similarly, there are no bullets. The One isn't stopping the bullets, he's just ignoring them -- in a way that prevents them from doing damage to his simulated body, with the visual effect of them seeming to stop in midair (while he picks one from its hover and examines the Matrix code that produces the simulation).

Simply put, The One is above the laws of the Matrix. He has given himself administrator or "super user" privileges.

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    OP is asking why the One is above the laws of the Matrix. Why doesn't the Matrix reject the One's signals that say "stop the bullet" or "don't fall down yet" and simulate the bullet hitting him or him falling down anyway?
    – Null
    Jul 13, 2021 at 19:21
  • @Null It's more that I'm asking how the One can send that signal, when it seems like the Matrix is only set up to receive nerve impulses intended for a human body. The jumping makes sense because you can just send signals that your body couldn't actually handle. But unless I've been wildly misinformed about biology, there isn't a nerve bundle that signals "stop those bullets that are coming towards me". Jul 13, 2021 at 19:23
  • Edited in response to comments.
    – Zeiss Ikon
    Jul 14, 2021 at 11:44
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The Matrix is not just a physics simulator. It has, as Morpheus says, "the same basic rules, rules like gravity" but it does not have the exact same rules as reality. The rules of the Matrix allow Agents, for example, to perform superhuman feats using the simulated bodies of humans. Other (usually older) programs are capable of performing superhuman feats of their own (e.g., the Twins).

Because the Matrix is not merely a physics simulator it is not merely receiving signals from the human brains which are intended to control the simulated human muscles. Indeed, we know that the Matrix receives other signals from the human brain -- that's how programs like Rama Kandra and the Architect can detect Neo's thoughts and emotions (like love) which have nothing to do with physically controlling muscles. These programs aren't just reading faces -- the Architect tells Neo that

I can see the chain reaction – the chemical precursors that signal the onset of an emotion, designed specifically to overwhelm logic and reason – an emotion that is already blinding you from the simple and obvious truth.

transcript for The Matrix Reloaded

The human brain is therefore also sending signals to the Matrix which include the chemicals involved with emotions -- and quite likely all kinds of other signals.

Combine the fact that the Matrix is built on similar (not identical) rules as real physics with computer bugs, and it's easy to see how the Matrix can be hacked by humans to perform feats that completely break physics -- like flying and stopping bullets. You might think that the machines can write programs that are bug-free and completely secure, but that's clearly not the case. Not only did they fail to produce a working Matrix multiple times, but the existence of Exile programs is specifically due to the fact that programs can malfunction (i.e. have bugs). If the Matrix's physics-simulating rules are not sufficiently bug-free and secure then it is possible for humans to bend or even break the rules entirely. Most humans are not able to do this because they accept the simulation, but red pills who reject the Matrix know that it isn't real and therefore they can bend or break these rules. The One, who is the integral anomaly (the sum of all rejection of the Matrix and its rules), is able to break these rules even more completely. Additionally, we are told that the One has a special connection to the Source which also allows him to break the rules more easily and completely (even outside the Matrix):

Neo: Tell me how I separated my mind from my body without jacking in. Tell me how I stopped four sentinels by thinking it. Tell me just what the hell is happening to me.

Oracle: The power of the One extends beyond this world. It reaches from here all the way back to where it came from.

Neo: Where?

Oracle: The Source. That’s what you felt when you touched those Sentinels. But you weren’t ready for it. You should be dead, but apparently you weren’t ready for that, either.

transcript for The Matrix Revolutions

This connection to the Source which allows the One to completely break the rules of the Matrix is almost certainly by (machine) design, since the path of the One is another control mechanism of the machines -- the One is supposed to integrate the anomalies in the Matrix (rejection of the Matrix by humans) and return to the Source to reboot the program. Therefore, to some extent the Matrix allows the One to rewrite its own rules.

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I hate to give a frame-challenge-y answer, especially one where I'm shooting from the hip and not citing much myself, but I don't agree with ~two of the assertions rolled into the question, and I think these differences point to a simpler answer:

The Matrix is ultimately just a physics simulator / networked brain-in-a-vat system, though.

I read the Oracle, Architect, Merovingian, Sati, Seraph, Train Man, and Smith--not to mention the ability to insert/remove people via phone line--as all challenging this assertion somewhat.

In the Matrix, the One is the person who can truly accept that the Matrix isn't real ... at the end of the first movie we see him stopping bullets with his mind, and flying like Superman ... what nerve impulse is telling bullets to stop or letting the One fly without flapping his arms?

This strikes me as a fair reading by the end of the first film. With 20/20 hindsight, it is probably derailed by Neo's first encounter with unplugged-Smith. If nothing else, I don't think it survives Neo's encounter with the Architect near the end of the second film.

The Architect makes it clear that Neo is part of the plan, so I think it's at least defensible to argue that Neo's code, as it were, directly supports everything he does in the Matrix.

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