We've gotten a lot of great email from readers, with a lot of fun explanations for what's happened in Reloaded, and what may happen in Revolutions. Two of the most talked-about scenes in Reloaded are when Smith is downloaded into Bane, and when Neo stops the Sentinels by waving his hand. We know a lot of the ideas on this site are from our point o f view, so some people agree with them, and some people don't. We figure it's a good idea to let our readers have a say so we can show other points of view. If the author's name is linked, they'd be interested in hearing what you think of their theory.

I have a possible explanation for Smith's existing in the Real World. As we all know Bane, Neo, Morpheus and many more were once a part of the Matrix, hence the holes in their arms and legs. They can still get Plugged or Unplugged from the Matrix. This is possible because of the holes. Therefore, all these people are not 100% human. They have circuits in their bodies which make them part Machine. When Smith copies himself onto Bane, and Bane returns to the Real World, he carries the Smith program with him. The program can survive in the Real world as Bane also has the circuits inside his body which makes part of his body machine. The Smith program has overwritten Bane's program of being a human.

I support my theory with the following information from the first Matrix, where Tank tells Neo that he is 100% pure human and hence has no holes in his arms and legs. People who are plugged in the Matrix are not 100% human. Even Morpheus tells Neo that Humans are no longer born they are grown.

I have my own theory about the two scenes in Reloaded that defy analysis, based on my suspicion that the Wachowski brothers don't understand The Matrix any better than you or I do.

I think one of them said to the other, "Wouldn't it be cool if Smith could somehow exist in the real world?" And the second brother might've said, "How can we justify that?" To which the first would've replied, "Don't be silly. We can leave the explanation for later... or maybe we won't even try to explain it."

Same thing for Nero's real-world powers. One says, "We need Neo to stop the Sentinels somehow. How about if he starts to use his Matrix powers in the real world? And, since we don't have any more time for exposition, we'll just let him suddenly understand, or intuit, that he has those powers." And the inevitable reply comes back, "Sure! Great idea! Write it in now, and explain it later, or not at all. Our fans are good at coming up with justifications for all of our off-the-cuff decisions. They haven't guessed yet that we put in the dance scene just because we love rock music." The first one exclaims, "And sex, too! Don't forget, we needed more sex!"

In support of my theory I offer the confusing title, "The Matrix Reloaded", which can't possibly mean what it says. The Architect tells us that Zion has been reloaded five times, and he assumes it will be again. The Matrix hasn't been, and won't be. Furthermore, no reloading of any kind occurs during the time spanned by the first two films. The title's just an(other) example of fuzzy thinking.

I believe it may be the result of his merging with Agent Smith at the end of The Matrix. The merging has changed them both and this is reinforced by Reloaded. Smith has incorporated some of Neo's 'humanity' and is now able to control humans directly in the real world. And Neo may have incorporated some of Smith's 'command programming' (for want of a better computer equivalent to humanity) and is now able to control computers in the real world, especially considering that The Ones are given special treatment, software, (and most likely hardware) by the computers in the first place.

Another obvious point I thought of, in regards to Neo stopping the squiddies, was the scene where a message is delivered to Neo from Smith. Neo takes possession of Smiths earpiece that the agents use to communicate, command and control. If we consider that Neo himself and the earpiece, when in the Matrix, are no more than highly complex programs, then it is not a big stretch to acknowledge that while Neo is in possession of the earpiece that the two pieces of software are in some way attached. And further if he exits the Matrix while still in possession of the earpiece could the piece of programming be stored in his brain like say, the instructions for flying a chopper? So considering "The Ones" are give special treatment i.e. software and possibly hardware, Neo may be able to use the earpiece programming to communicate directly to the Matrix. Though he would have to emit a signal. And this is the heart of the question, if the Matrix is not nested and Neo is indeed in the real world, to talk to the Matrix, his body still has to emit some form of signal. I wonder if answer lies in the body's bioelectrical field.

I'm just going to suggest something along with what Arc said about Neo carrying a part of Smith and Smith a part of Neo. Could it be that when they "melded" that they did exchange abilities to some extent and Neo carried the ability to command machines and programs with him outside the matrix, like he would carry knowledge of Kung fu or helocopter piloting? How would he be able to command the machines if not verbally? The machines are able to see humans? or do they sense the heat human bodies give off? Or do they sense and read brainwaves? How did the robots originally communicate with humans before the war? I wonder if the sentinals have sensors that take input from human brain activity and interpret those signals. Neo's newfound ability to command machines combined with a line of 'wireless' communication to the sentinels allowed him to stop the sentinals. As far as proof that robots can read and understand human thought, refer to the animatrix episode where the humans retrain robots in their own psycadelic matrix.

I believe the Matrix trilogy are movies about perception concerning the theory of phenomenalism. One of the "possibles" in the first Matrix, more specifically the bald kid who bends the spoons with his mind, quotes "There is no spoon." What he is saying here is there is only your perceptions and that you can do what you believe you can do. While this definitly holds true for Neo in the Matrix, it could possibly and, by all rights, should be true for Neo in the "real" world, hence he figured out he can stop the Sentinels dead in their tracks just by believing he is the "one", which actually pertains to the theory of solopcism, a more extreme form of phenomenalism.

The Logic Explanation
Submitted by Mario Pitalua

There are a lot of amazing ideas and opinions on this website. Some of them are more based on what we can get directly from the movies and from theory derivation. The part about Smith overwriting Bane's memory (brain) can be explained with plain logic facts that we are shown in the movies instead of speculation. Consider the following and draw your own conclusion!

In the first movie, The Matrix

• Neo is awakened to the Real World thanks to Morpheus and his crew. In the Real World, Neo remembers his life inside The Matrix. This fact is evidence that the cable plug to his head is a device to read and write information into his brain.
• It is the single cable on the back of his head that is unplugged in a very specific and controlled way when he is considered disposable by the machines, and is the only one that they plug in to get inside the Matrix.
• In addition the fact that this cable cannot be unplug without following specific procedures to avoid killing the human denotes its importance. That's why they have to go back in the Matrix to rescue Morpheus from the Agent complex.
• It is thru this cable that new skills and knowledge can be loaded into the brain.
• Tank trains Neo in the whole universe of Martial arts in only one day by just copying the knowledge into his brain. This method of learning is amazing, and especially useful inside the Matrix where someone does not need to backup this knowledge with a superior physical condition to perform things correctly.
• Another example of this is when Trinity needs to know how to pilot the helicopter in the first movie and, in the second movie, when she asks to know how to hijack the motorcycle.
• In the first movie the agents overwrite themselves into humans when they are plugged into the Matrix, It is unclear if the Agent programs choose where to go or if the SYSTEM moves them to the place where they are needed.
• Agent Smith shows his desire to get out of the matrix, when he is interrogating Morpheus.

In the second movie, The Matrix Reloaded

• Agent Smith knows how to overwrite himself onto other programs if he gets access to the correct media. This is shown when he overwrites other agents. He comes back like a computer virus.
• It is not shown at this moment that he had been overwriting persons that are still plugged into the Matrix, but the fact is shown when he is fighting Neo and Smith is incapable of winning. He just starts bring more replicas of himself into the fight.
• It was just a matter of time for Agent Smith to find someone like Bane, a crew member from some Hovercraft, who will be unplugged and wake up in the real world.
• Morpheus and Neo are the members of the crew who understand and can keep a clear mind inside The Matrix. They are the ones who can recognize most of the time the world inside the Matrix is a dream over which they have some influence. The other members are not that skillful in this matter. This is why Bane could not fight being overwritten as Neo did. Morpheus shows this skill in more than one occasion in every movie, examples are the Fight with Neo, The braking of the restraints and his jumping during his rescue from the Agent complex, and the fight with the Twins and the Agent. It is this awareness of being in a dream world that allows Neo to do some amazing things including flying, and saving Trinity at the end of the second movie. Bane does not share this power.

In the third movie, The Matrix Revolutions

• Neo is able to influence the machines without being plugged into the Matrix. This is not as weird as it may look. It is well known that there are persons who can alter the normal behavior of electronic devices just by their presence. Once the person moves away the device will perform normally. This has been shown in other media. In this case, the only difference is that Neo can do this at will by focusing his mind. Although there is a limit as shown in the race to machine city.
• Neo evolves from movie to movie and learns to use his mind to the fullest potential. This explains how he is able to see different kinds of spectrums that the human eye cannot interpret for us. The basic step is how everybody on the crew can see images thru the famous Matrix screensaver. They develop a skill to process information much faster and in great volumes.

In the first Matrix, when Neo is pumped full of useful things such as various martial arts manouvres, he wakes, sees Morpheus, and says "I know kung fu". He's not in The Matrix at this point in time, but he is one of the "new" types of human, with computer holes which enable their brains to be programmed. Whether in The Matrix or out of it, Neo knows now how to fight. Also, people who are killed in The Matrix are killed in real life. What this tells us is that computer programmes, and Matrix-related events are not isolated incidents, but stay with humans throughout.

Thus when Smith possesses Bane, it is not really surprising that Bane takes on the thoughts, actions, and even the speech of Smith. It is conceivable that were he to be jacked back into The Matrix, he would once again be one of the many duplicated forms of Smith. Smith's goal was to possess and take control of a human so he could manifest himself both in The Matrix and in the real world. Smith wants to kill Neo, so Bane wants to kill Neo. There doesn't have to be a Matrix within a Matrix. Just as people can die in The Matrix, because their real world body believes it has been killed, so Bane can become a real world part of Smith's army because his brain believes he is in fact a manifestation of Smith.

Everything Morpheus teaches Neo about The Matrix (i.e. what he can accomplish within it), he and the rest of the characters fail to learn about themselves in the real world.

Morpheus wants to open Neo's mind in the first film, but in fact it is Neo's mind that ultimately becomes the most open.

The abilities that the likes of Neo, Morpheus and Trinity have whilst inside The Matrix, they develop thanks to a safety net. As The Kid says - there is no spoon. They all believe that The Matrix is a mere programme and that is why they are able to fight and move at unrealistic capacities. They do not attempt any of this in the real world because that is the real world, and not The Matrix, and humans don't REALLY have the capacities to do that sort of thing.

Maybe not the likes of Tank and Dozer, but Neo et al represent a new type of human. If, thanks to a computer, they can be programmed to be able to fight, hotwire motorcycles and fly helicopters, what else can they do? Neo is the only one who takes Morpheus' words to have a double meaning - he realises that if his mind can give him the power to do the unthinkable inside The Matrix, then why can't that same mind give him power outside of The Matrix? He is outside the safety net, the concept that he can do anything because "none of this [The Matrix] is real", but he is the only person who transfers the mindset he has from within The Matrix back outside it. That is why he can stop the sentinels and why he is the first 'One' to end the war between the machines and humans. Neo represents the potential that every human mind has if they truly believe in themselves.

I was thinking about your explanation for how Neo is able to stop the Sentinels at the end of "Reloaded." I've struggled with this question a lot and I think you're explanation of him being changed by meeting the Architect is correct. Here's why:

1) Let's assume that the Sentinels are actually physically real as well as Zion and everyone in it. Hence, it's not a "Matrix within a Matrix" situation.

2) Just before Neo confronts them, he pauses and says, "Something's different.....I can feel them." Note that he says he can feel them....not that he can see them. What I think is being implied is that he's becoming aware that his mind is still tapped into the Matrix on some level.....most likely as a result of returning to the source and then re-entering the physical world. This idea is further confirmed at the start of "Revolutions" when the Oracle says he's separated his mind from his body and is in Limbo.

3) Therefore, he's able to stop the Sentinels because his mind is still in the Matrix....or rather, it's in the computer network and he's making the choice to exercise control over the software which in turn controls the hardware (the sentinels). This is very significant moment because Neo is realizing that his mind is much bigger and more powerful than he imagined. It's one thing to be able to control the Matrix when your body is physically linked to it by a physical interface (being "jacked in"). But he's just taken the huge step of realizing that his mind can go there at will regardless of his body's state.

This whole idea is rather Buddhist in thought. It could be thought of as a metaphor for the meditative state where the goal is to free the mind from the concepts of being connected to the body, and allowing it to return the "Universal Mind" or "Source." Upon our return to normal consciousness, we're drastically changed because our mind has experienced something that's totally beyond our conventional understanding.

I've got an idea I've been kicking around: WiFi.
Neo is the anomaly, the One. His brain is so able to interact with the digital information of the matrix once he is able to see it for what it is, that he can actually manipulate the digital code of it. In the real world he still has that same brain. The human brain is made up of electrical signals and it is vastly agreed that we hardly use more than a small percentage of our brains. Pigeons have the ability to sense the earth's invisible magnetic field through the way it interacts with their brain. What if Neo's brain can actually pick up WiFi, radio transmissions, and such from the machines? What if when he stops the sentinels, he is somehow hacking into the machine network wirelessly and ordering a shutdown?

This would also explain his later sight. How can he see without his eyes? He could very well still be linked up via brain WiFi to the machine network. This would allow him access to the blueprints of the machine city as well as any current movement or motion or machine activities as long as we assume said movement/activity was also linked to this same network (and I think that is a safe assumption).

I've read other theories and the only others I have seen are the Matrix within the Matrix and the idea that he is somehow changed after meeting the architect. As for the question why he can suddenly do this now, I'd say he is growing in his understanding of his own capabilities and necessity breeds creativity (and sentinels rushing straight at you seems to have done the trick!)

I read the explanations written above about Neo stopping the sentinels, and all of them were interesting yet most entries tried to explain and see the act from a spiritual point of view. I do strongly agree that the Matrix Trilogy has a lot of spiritual roots yet some events are far from being related to any spiritual meaning there for they can simply be explained in a computer meaning.

That being said what I think best explains Neo stopping Sentinels in the real world is simply what we call nowadays remote connection. Neo can tap into the matrix without him physically being jacked in. Mike McGee already mentioned that what Neo was able to do is he tapped into the Matrix wirelessly something that the Machine world already have setup we all see throughout the trilogy that sentinels are connected and send and receive data to and from the machine main frame. How do they do it (radio waves, wifi,…) is not important but what important is if the Machines can do it Neo can too.

This brings us to the question why can Neo do it? Well we all know that Neo was born inside the Matrix this by itself gives him accesses to everything, he is part of the system. Let me elaborate, Neo being from that same system he can move in and out of any hardware and software without triggering any alarms he is not considered an outsider. To a computer program he is compatible. (if we have a wireless connection, before u can connect and be able to send and receive the device needs to authenticate without a key or a password the authentication will fail) Neo does not need that since he is already part of the Matrix and he is granted that accesses. This matter can also be explained as follows. If we introduce a foreign object to the human body it’ll be rejected and attacked by our immunity system if the object is born within our body even if it’s defective it won’t be attacked and will not be recognized as a defective organ “cancer”).

I have more thoughts about this but I didn’t want my first post to be very long but I will add more based on peoples' responses.

I believe Mike McGee is right in his assessment of Neo being changed after seeing The Architect but the 'why' seems to still be a bit elusive. I think it's because of the reloading of the Matrix that Neo is left with a part of the Source code inside him. As soon as he enters the room of The Architect, the machines have already scanned him and are making ready the re-insertion of his code. It's like a program download or install; by going into the room, Neo has started the process of information being read and space being tagged for code to be copied onto. Now, I think it's important to take into account what the machines believe will happen. They 'know' that The One will always choose to restart the Matrix because it's simply logical. They engineer a scenario where there can only be one logical choice. Knowing this, they already start preparations for the next cycle because as soon as the One enters the room, they've won. Except, they need to give him a choice. Knowing that humans need a choice or they'll reject the program, they need to give the One the ability to choose the continuation of the cycle. Still, so confident in the perfection of the scenario that's been created, The Architect doesn't conceive of any One choosing the end. In this context, giving a human access to the Source code of the Matrix is a huge risk. Why take that risk? Well, it goes into the mechanics of how the One is created.

On the screens in the Architect's room, Neo's possible reactions/choices are shown. I don't think they are window-dressing, I believe they are actual scenarios the program is running. If the program was not ready for Neo to, say, give the old man the finger then Neo would think of the action but there would be a delay as the program writes and loads the code to show him the action being performed. This lag would create a problem in many humans who sense that something is not right if they should be able to think and do simultaneously. So, many scenarios are written but only once choice is made. This can be seen by Neo's realization when he says "Choice. The problem is choice." He can react a number of different ways to the same thought; anger, denial, rebellion but he chooses to remain calm and voice his realization. So, what of the other scenarios? They are dumped into the machine's "recycle bin". Trashed, erased but not gone. Eventually, these random pieces of code create a glitch in the system that is The One. After they're little rebellion, the One is led to the Source and is inserted into the system again. This time, the bending of the Matrix is done within programming parameters because the One's unique code has been installed and the system has restarted, absorbing that change. He is not a true 'One' anymore because he is being allowed to manipulate things, whereas the prophesied One is out of the control of the machines because he is a glitch. It is part of the Architect's role of balancing the equation.

Now, the last piece of the puzzle. Thinking of it in terms of computers and programs being written/rewritten and rebooted I think it's pretty easy to see how Neo is able to hold onto part of the Source code that was downloaded into him when he went into the room. It's not a real room, it's not a real person sitting in front of him. It's all still Matrix code streaming down in front of Neo's eyes. The room, person and doors are all there for Neo's (and the audience's) benefit. It's a port, connecting Matrix and Source. The connection is made, the exchange of information already taking place, it just needs the One or the user to click "OK" to complete it. Which, of course, he doesn't. Which breaks the connection and leaves Neo with partially downloaded code and a 'backdoor' in his mind into the Matrix which strengthens as he remains jacked in and trapped at the in-between.

Neo and Smith are opposite sides of the equation. The purpose of the Architect is to the balance the equation. The Architect is not an intuitive program like the Oracle and as the Oracle said he (the Architect) can't see past any choices. So the Architect is blind to the consequences of his balancing actions. The Architect perceives an imbalance and acts to balance the equation, sees another imbalance and acts again; he is reactionary.

Smith is a program within the Matrix and has power, like Neo, to bend and break the rules of the Matrix. The Architect sees to it that the abilities of Neo and Smith remain relatively equal, that is his job to balance the equation ("we are all here to do what we are all here to do").

Smith takes over Bane; he overwrites Bane's consciousness with Smith code just before Bane jacks out of the Matrix. Now Smith, a program, has power to act as Smith in the real world as well as in the Matrix. The Architect sees this and works to balance the equation. In order to balance the equation now Neo must have power to act as Neo in the real world as well as in the Matrix.

Like all actions to balance the equation the process does not happen immediately. The recipients of newly granted equation balancing abilities (Neo and Smith) tend to learn about and grow into the abilities in a given amount of time rather than suddenly exercising a new talent. Does balancing the equation take time? So at the end of Reload Neo feels that something is different. Neo begins to feel the existence of power to act in relation to the machines in the real world as Neo acts in the Matrix. Neo acts to stop the Sentinels in the real world in exactly the same manner as Neo acts to stop bullets in the Matrix (extended arm with hand open toward the threat).

This delay or time lag in the balancing process may also explain why Neo still has abilities in the real world after Neo kills Bane, effectively deleting Smith from the real world. With Bane's death Smith has now lost his power in the real world and the equation needs to be re-balanced. The Architect just hasn't had the time to complete the process before Neo goes to the machine city. So Neo still retains his power to act as Neo in the real world long enough to get to his meeting with Deus Ex Machina.

We're not sure exactly what the machines have done to the human body. There are plugs and cables that connect into the body's nerves and the mind can be convinced into believing a perceptual reality. Perhaps there is more to this than what meets the eye. The Architect tells Neo that part of the Matrix's source code is written on him... on him where? Perhaps each person is more mechanized than we actually know. Perhaps every person's digital self exists on a hard-drive implanted on the body, or even in the brain. So, if Neo is part machine (not made of metal, still flesh and blood of course) and has the ability to jack into the Matrix "wirelessly" and to turn off the Sentinels... is that really so much different than a wi-fi connection or even a bluetooth connection on a laptop? I don't think there's any magic to it. Nuts and bolts and nerve endings. Who knows what we'll be capable of installing on the human mind hundreds of years from now?

I pose several theories in this composition, but the big one is explaining how Neo stopped the sentinels, and the defense of that theory. The end bit is just a whole bunch of loop-holes that Neo could have exploited to beat the system and have survived the entire ordeal many times over.

In the first movie, it is kind of underplayed that Neo is different in the real world. First, there is no physical deformity that would give him away, nor a personality flaw that would spell out his difference from anyone else. The machines wouldn't have made any obvious changes to his outward personality or physical state, because they would fear --if they can-- that someone might catch on.

However, there is evidence of his being different, although it is delivered to us while he is in the matrix. When fighting Morpheus, Mouse is the only one (and, to be sure, there is no real reason for anyone to do this) to look at Neo's neural readings, and stares, confusedly at the readout, while everyone else's eyes are locked on the fight, as the Wachowski bros. wrote in the script 'like a game of Mortal Kombat' and once Neo and Morpheus start fighting again, he tells everyone (and is promptly ignored by everyone) that Neo's 'neuro-kinetics are way above normal' No one had looked at a scan of Neo's brain at all up to this point, that we know of, and it is not likely to be one of the tests they regularly conduct, as the machines would discard brains that were not functioning, or, even if Neo's brain was odd, it functioned just fine for them, so it wasn't a problem. An explanation of this could be that one of the machine's steps in the 'process' mentioned by the Architect in the third movie is that Neo's brain is rewritten or rewired in some way to improve his 'processing speed' in essence, they upgraded his processor.

That's a lot of conjecture, one might say, but notice what Neo's job was. Neo was a software designer/excellent hacker. And by 'excellent' I mean $2000 a program excellent. That's not chump change. That's the price you'd pay for a hacking system that was untraceable and unbeatable for the program it was written for, until it was finally countered by some ingenious programmer. But to be a great hacker or to be a great programmer, you must be able to think like a machine. You must be able to use logic to go piece-by-piece to get the exact result you want. Neo was obviously very connected to machines subliminally and intelligently.

Neo had code written into him by the machines, namely, at least the code to be the key to the program of rebooting the matrix. This made at least part of Neo's mind a program. In the third movie, we learn that while Neo is in the 'real' world (Not going in to WMAM atm. I used to be a fan, now I don't really believe it. Why would the machines compromise with Neo on Smith if they could just recall or reboot the Zion matrix and rebalance the entire equation?) but I digress, as I was saying in the 'real' world, Neo's brainwaves seem to show that he is jacked in. All that that means is that Neo is operating on the same frequency as the matrix. That's similar to having an RC car and having two controls for it. One is 'jacked in', the other is 'jacked out' most people would have one remote on one frequency, and one on another, but Neo has two that are the same. Basically, his mind is always writing itself in code. Neo is constantly rewiring his brain and operating on the same fundamental 'radio station' that the matrix itself is. He's constantly using the same operating system, instead of most people who need to be converted, in essence, from Windows 1992 to Windows 7. Neo is a native program to Windows 7 --the matrix-- and thus, no part of his programming is misunderstood or corrupted in transfer, as most people who have tried to change the format of a file will have undoubtedly encountered. My thought is that Neo was like this from the beginning, and no one noticed it. (except Mouse, who died... Poor chap) To be sure, the only time one would even see Neo's neuro-kinetics is when he was jacked in. I believe that Neo, when jacked in, is capable of doing what he does because he already has all the tools of Windows 7, while everyone else is trying to word process with notepad. Neo has all the handy formats and functions already available, such as an affinity for understanding code and computers, and the ability to 're-make' the matrix. He's not 're-making' it, he's re-writing it. He is, in function, opening up the file and changing the code, which is what he made a living doing before his mind was freed. Neo could do anything any program in the matrix could do, because he wrote his own code as he saw fit. This would mean that his mind would fundamentally be doing what Bane's did after Smith copied himself into Bane's mind; that is, assimilating code and making it a brain. Bane's brain was human, unlike --assumedly-- Neo's, though, so Bane-smith was unable to operate at the vicious velocity of the matrix's frequency, correcting that hole in my theory. Unlike Bane's brain, though, Neo would be able to process his mental code at the speed the Matrix does, and at the same pattern, allowing him to basically be the One mentally in the 'real' world. Sure, he couldn't fly in the real world, (unless it was another matrix), but he would be a part of the system while outside it. Humans need to be encoded to enter the matrix. Neo doesn't have to go through that step, he's just automatically compatible.

When Neo stopped the sentinels, the sentinels were broadcasting on the matrix' frequencies. Neo's frequency. His bio-electric field would be charged with his transmitted 'code.' Notice that when he stops the sentinels, the first stops first, and the others stop soon after. This could be explained with the potential method Neo stopped them with; my theory is that Neo broadcast into the first sentinel, who was already on a network with the others, a virus, ultimately causing catastrophic failure. Once Neo had done this, he basically copied that code onto the network, and the others all stopped, too as they were infected. Neo hacked the sentinels using their wi-fi connection to make a direct link to one hub of the network, and mass e-mailed it to his friends. Neo fell into the coma because he neglected to pull out of the sentinel before he activated the virus. Neo had not retained consciousness in his own body, because he could not manufacture the virus in his own system before sending it, and could not activate it remotely because he had not the intuition. When Neo flipped the switch, he fried the calamari, but his own mind was picked up by the matrix broadcast, and he went to Mobil station because he would not be permitted access to the link-up the squiddies were using to talk to Daddy. Neo was basically broadcasting from the matrix to his body, as opposed to from a ship to the matrix. Because Neo did not have to be adapted to the matrix code, he suffered no corruption from this transfer, but because of the rules of the system, he could not leave until he had been taken to one of the exit points. Of course, had Neo the foresight to do so, he could have attempted to rewrite the code to permit him to return to his body, although it is unknown whether he was enough machine to handle such a large manipulation, basically whether or not he would be able to alter a system file as opposed to an independent program, such as gravity.

Further defense for this is seen when Neo loses his sight. Once his sight is gone, Neo is capable of 'seeing' the code. What he is seeing is what the machine's broadcast sees. He was seeing the world as the machines saw it, and because they are written with the same programming as the matrix, the code was the same. Neo saw machine city because the entire city would resonate with code. The ship was illuminated because it was electrical, and Neo could extrapolate data to encode based on the familiarity he had with the objects emitting electricity, or conducting it. Neo could not have seen the entire 'world' like this, though. Only where the machines used the same code as the matrix. For example, Zion would be invisible to him.

Neo is never taken out of broadcast range during his coma. This is very important, because if he had been, the connection would have severed, and there would be little chance of Neo returning to his body, as his digital code would change, and his body's mind would be the same, rendering them two separate programs, and potentially incompatible. He would basically have been 'unplugged,' and we saw the deadly efficiency of that in the first movie. Using this theory though, it is equally likely that Neo's avatar and Neo's body would have both retained (or regained, as it were) consciousness once the severance was complete, with the two functioning as now-separate entities, being two separate programs. The difference would be that the digital Neo would have no ability to be 'jacked out' unless he copied onto a suitable host, and the real Neo would have no recollection of the doings of the digital Neo. With this split accomplished, Neo could in effect perform the same viral take-over as Smith had, the power which he always retained, but refused to use (or just didn't realize, because of his morals.) It is conceivable that the real Neo could be jacked in again and the two digital Neos could operate side-by-side, both identical in function, but differential in code, and should the real Neo ever repeat this entire process, he could then replicate a third time, and so on, without ever reaching a limit, as, necessarily, the One Code cannot be deleted, it can only be absorbed once given willingly or deceasedly to the source. In this way, Neo could have replicated to double his side of the equation against Smith (who only ever matched Neo 1:1) and could have both survived and died, or have completely subverted the necessity of the One's path to end entirely. This said, Neo could always have copied himself even without a host, being entirely capable of creating programs if he wanted to. Every crew could have a One. Hell, they could pass them out like candy.