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.