In The Matrix Revolutions, when Neo and Trinity are trying to get to the Machine City, when the Machines launch weapons against them, Neo is able to destroy some of the incoming weapons.
This is in the real world at this point, not in the Matrix. How does Neo have any powers against the machines outside of the Matrix?
Addendum: I'm looking for in universe answers only. I would think that would be obvious, but I'm adding this after an answer that is essentially, "It's a movie..."
The explanation given within the films is that Neo (as the One) has a special connection to the Source which allows him to control machines in the real world. Neo asked the Oracle how he was able to stop Sentinels in the real world and she gave him the answer:
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.
The Matrix Revolutions
Neo was able to destroy the machines' weapons in The Matrix Revolutions in the same way. The films never explain exactly how Neo was able to control the machines in the real world, but it's worth noting that Neo was designed by the machines to carry machine code that enabled him to perform the function of the One. As explained by the Architect:
The function of the One is now to return to the Source, allowing a temporary dissemination of the code you carry, reinserting the prime program.
...
Your 5 predecessors were, by design, based on a similar predication - a contingent affirmation that was meant to create a profound attachment to the rest of your species, facilitating the function of the One.
The Matrix Reloaded
We know machine code carried within a human body can affect the real world because of Smith's control over Bane in the real world. Thus, the code carried by the One undoubtedly gave Neo a connection with the Source in the real world as well.
The biggest question is how Neo manages to communicate orders via the Source in the real world, and the films don't explain how. Presumably he communicates wirelessly using his head jack. Zion's use of EMPs should disable the head jack, but the EMPs apparently only disable head jacks temporarily: humans can't be connected to the Matrix during an EMP blast but they can re-enter the Matrix after the blast, and Smith/Bane is put in a coma by his EMP blast in The Matrix Reloaded but eventually regains consciousness. Machines like Sentinels are permanently disabled by EMPs, but evidently the human body acts as a "battery" to re-start the head jack.
As an aside, the Matrix-within-a-Matrix (MWAM) theory is an understandably popular fan theory which easily explains how Neo controlled the machines in the real world. However, it suffers from several notable inconsistencies with known facts. For example:
Okay, but what if the "real world" is a Matrix controlled by different machines? In other words, what if the machines we see in the films were themselves products of Supermachines which control the Matrix of the "real world"? Presumably the machines in the films would just be another level of control for the Supermachines and the machines wouldn't be aware of the Supermachines; the machines would think that the "real world" was real and not just another Matrix. This would explain some things like why the machines acted threatened by the loss of their power source in the "real world", but there are still inconsistencies with this Supermachine theory. For example:
The Supermachine MWAM theory is a complicated theory which assumes that there is another race of machines controlling another Matrix (and possibly more) which is completely unknown to both the humans and the machines. In contrast, the dialogue from the films suggests that Neo communicates wirelessly with the machines in the real world, and only a few minor assumptions are required to explain how that's possible: that Neo's head jack is able to communicate wirelessly with the machines in the real world, and that the head jack can be rebooted after an EMP by its human "battery". By Occam's Razor, the MWAM theory is less likely to be true.
Both versions of the MWAM theory also suffer from another, out-of-universe problem: if MWAM is true then all the events in the entire Matrix franchise are ultimately meaningless. The story starts with the humans imprisoned in multiple Matrix levels, a lot of things happen, and the story ends with the humans imprisoned in multiple Matrix levels.
One of Morpheus's first lines references Alice in Wonderland. But, just how deep does the rabbit hole go?
I am of the opinion that Zion and the rest of the real world isn't actually the real world. Humans are rebellious by nature, so what the Architect said about Zion needing to exist makes sense. But as long as the humans believe they escaped from the Matrix, why does it need to be real?
Remember what Cypher said in the first movie? As I recall, it was quite a popular quote for a while:
Well you have to. The image translators work for the construct program. But there's way too much information to decode the Matrix. You get used to it. I...I don't even see the code. All I see is blonde, brunette, red-head. Hey, you uh... want a drink?
Why does that matter? Well, remember this scene from the end of Matrix Revolutions, Neo walking through Machine City with his eyes wrapped up? At that point, Neo had also learned/figured out how to see the code, and no longer needed his eyes:
("Real" world)
(Seeing the underlying code/structure)
So while Neo may have gotten one level closer to reality, he wasn't there yet.
Ok... to me this seems pretty simple. Neo is able to affect things in the matrix that normal people can't - he has escalated privileges, superuser access even above that of the Agents. Why shouldn't he be able to affect other parts of the machine infrastructure beyond the matrix simulators?
Then the only question is how are his wishes communicated to the machines? Well, he still has a machine-implanted jack in his skull - who knows whether it contains some kind of wireless backup link?
Yeah there's no evidence I know of in the movies for this, but it's certainly a simpler explanation than a whole nother level of simulated reality.
There are a couple of in-universe theories that have been written about before (see #4 here).
We've previously told you about a popular interpretation which holds that the "real" world of Zion is still part of the Matrix; Keanu had just moved up to another level of simulation, like in Inception.
But this more elaborate theory is more interesting in my opinion.
Zion is a Matrix-like simulation, but one made by humans for the purpose of creating better machines. In this scenario, Neo and his "enlightened" fellow humans were actually machines all along, and the baffling, recursive fight scenes they experienced in Matrix Reloaded were software implanted by the humans designed to teach them to understand human pain.
The movie canon doesn't hint at either of theories; although they aren't directly refuted. Unfortunately, the real answer is probably out-of-universe: the Wachowskis brothers made a Lucasian blunder and wrote in something into the plot that doesn't make sense within the universe they'd previously created.
This is a lot easier than what you guys have articulated. Think of Neo as a machine's version of A.I.
Neo is a pod human. All pod humans are created by the machines. Since he's the one, the way he was created by the machines allows him to do things (i.e. fly and stopping bullets) in the Matrix that no other human can do.
The only way he can do the ^ isn't because his RSI in the Matrix grants him "master user status," it's because his physical body was uniquely created when the machines made him. Therefore, the reason he can do things in the Matrix that others can't is because the machines made his physical body differently from those of other humans and that physical distinction allows him to also do things outside of the Matrix (i.e., in the real world) that others can't do (i.e., the ability to see the energy machines have and stop them, presumably through wireless powers).
Think of Neo as a machine's version of A.I.:
Lastly, to analogize it, think of Neo as a machine with A.I., the machines are humans, and the pod humans are thoughtless machines (like a dish-washing machine or a lamp).
The machines use humans to help them live (similar to why humans, generally, created machines) and the machines created A.I. (in this case, Neo) as another means to survive (in this case, to make sure the Matrix is fail-proof). Though humans created A.I. to allow them to survive, but screwed them over in the end, the same happened when the machines created Neo. Just like A.I. f@@@ed humans over, Neo f@@@ed the machines over because he's not like every pod human they created; he's got self-control, just like A.I. Hence Neo used his "outside the Matrix" powers, which were granted to him by the machines, against his creators, just like the A.I. machines used their powers (in this case, intelligence), which were granted to them by humans, to rebel against their human creators.
I would say it may be something telepathic. From the scene where he got kicked back into the matrix and had to get out. He developed the ability to affect the machines. It even goes back further to when he jumps into Mr. Smith. Mr. Smith later says something along the lines of I became a part of you and vice versa. It first showed itself when he killed the squids but it is more impressive when he blows up all the missles
Another theory, based on the expanded universe of the Matrix Online game: just like when he was in "digital" coma, his consciousness was held in the digital world and the body in the physical world, when he's awaken some part of himself may still be in the matrix at all time.
This would explain why he would still retain some degree of power, only on machines of course, while being disconnected: he may not be able to directly communicate with his "digital counterpart", but the digital counterpart may well be aware of everything about his physical counterpart via the machines (eg, when the missiles are launched towards Neo in his flying ship towards Deus Ex Machina, the digital counterpart is already informed and can work to take down the missiles).
This is kind of confirmed by Matrix Online, where the corrupted RSI (residual self image) of Neo re-appeared even through Neo was dead (since the events of the game happen after the movies), and it was in the process of being repaired before the game ended, thus implying that the digital counterpart could be separated and even survive the physical counterpart.
However, this does not explain how Neo could "feel" the machines, but it may well be just a residual feeling from his sentiment that some part of him has been detached to stay inside the Matrix, just like a phantom limb.
It is simpler than Inception kind of stuff. As shown in movie somehow he remained connected with Matrix even in the real world unlike others. He felt the machines because they were a part of Matrix as well.
His indirect connection with machines allowed him to interact with them. He stopped them by thinking about it (just like he did in simulation) and was able to sense them (see them without eyes) because of his connection.
When Smith occupied the brain of Ben, he would have been able to do the same.
Neo is a cyborg, he was created by machines - as the chosen one. Or maybe he's just genetically modified, as he has no parents (they were machines). There is no facts behind that, though, but remember that he almost doesn't have life in the matrix - no family or friends, it seems as he was reset and plugged into the matrix a while ago .
You could actually already ask this question about the way he shut down the Sentinels at the end of Reloaded, and the answer is probably the same. While one explanation surely is the uber-Matrix mentioned in another answer, a much simpler explanation comes to my mind:
As the Architect revealed, Neo's being The One (or at least, someone becoming the One every now and then) is part of the Matrix programme. Therefore it is not unlikely that the machines actually still have a weak wireless connection to the Redpills and thus know what Neo is attempting to achieve - and his purpose is
to betray those who trusted him by selecting 23 others to rebuild Zion instead of saving everyone (of course, he refused to do so)
so it is conceivable the machines actively helped him, even his meeting the Architect especially once
Smith wrecked havoc,
which would also explain why he suddenly could "see" again after having being blinded.
Of course, you could even manage without a wireless connection, when you assume that in order to be The One, Neo had a slightly different Physiology (maybe something about Delta Brainwaves) that allowed him to actually first emit and later detect electromagnetic waves independently of his eyes...
I have to say - Tinch's argument is the one I've seen here which differs from my own, but shows a lot of originality in its analysis and I think it's interesting.
The machines use humans to help them live (similar to why humans, generally, created machines) and the machines created A.I. (in this case, Neo) as another means to survive (in this case, to make sure the Matrix is fail-proof).
While I could see this being justified in-part due to canon, where the Architect explains that the "one" is a systemic-anomaly that basically embodies all the leftover subconscious rebellion from the Human psyche, and a depository for incompatible algorithms. Which must be re-inserted into the Matrix so that people will be able to "choose," once again, if even on an unconscious level (as he explained about the Oracle, or "Jesus'" idea). The answer was simple to me even from the first time I saw the conclusion to the Trilogy. Remember, Agent Smith was able to supersede the matrix by taking that phone call - thus using the digital-translation mechanism of the telephone, in order to get into that other character's mind - becoming his consciousness. This brought Agent Smith out of the Matrix, since while inside the matrix a consciousness is virtual, anyway (whether you're Human OR machine). So why couldn't it work the other way around? It's not coincidental that at roughly this same time in the second installment, Neo has grown so accustomed to the "sense" of how the Matrix operates (after-all, being able to see in code and everything), that in a way dualistic to how Smith escaped, he is actually able to use Matrix-like powers against them from OUTSIDE the virtual-construct.
Keep in mind, the Matrix was constructed by these very machines - so it's not surprising that while Smith has the ability to transcend the "virtual world" into the real, but the flip-side of that is Neo being able to transcend the "real" world's limitations directly through his accumulated interface with the nature of these same machines. Remember, when he entered Smith's avatar in the dramatic conclusion of the 1st movie? Well, I believe that's a CLUE to what the Architect would ultimately confirm in the second movie, and that is Neo is somehow integral to the survival of the Matrix. So there's no reason to object to the possibility that this fundamental connection couldn't supersede that virtual form - after-all, the minds behind the Matrix have a physical basis OUTSIDE of it as much as the actors jacking into the Matrix do as well. It's the opposite of bleeding in your chair when you get punched too many times while connected to the program, basically.
It's no coincidence, therefore, that Smith in Bane's body ends up lying in the medical-bay directly (and oppositely-positioned) from Neo, after this manifestation of his intrinsic connection to the Machines outside in reality actually drains him of all his energy - hey, I'd be exhausted too after something like that.
