In the Matrix, why did Neo have magic powers in the real world? For example,
(1) Those scenes where he blows up those robots purportedly with his mind.
(2) That one where he has no eyes but can see.
The main explanation I've seen, and that seems to be pretty official, was that the plug thing Neo has in the back of his head worked as a wireless device. Well, as you will read below, this isn't actually specified like this, but since the source speaks of the "brain becoming a wireless connection", it seems the safest thing to assume.
In any case, no magic is involved.
In the IMDB FAQ page for Matrix Revolutions, we see the question: What explanation does the movie give for Neo now having his powers in the real world?
And the answer is (emphasis mine).
The machines in the real world are all connected to a "singular consciousness", the birth of Artificial Intelligence described by Morpheus in the first Matrix film. This consciousness is otherwise known as "The Source". The machine connection is a remote one or some sort of wireless signal. Having touched The Source (i.e. meeting with the Architect) and having the data needed to reboot the Matrix, Neo is, at this point, simultaneously in possession of his human brain but also connected to the singular consciousness. In other words, his is also now a wireless connection. Hence the reason Neo says, "Something's different. I can feel them." The machines are all separate entities but all connected to this one Source.
Now, Neo is connected as well. He is thereby able to harness this power and stop the Sentinels. However, Neo wasn't ready to handle the signal surge at the end of Reloaded and collapsed in a comatose state, no longer in control of just where this wireless signal would be directed. The signal (Neo's residual self-image) is then captured and held in a program limbo derived from the Source but undetected as an existing realm, so to speak.
This limbo (the "Mobil Ave" train station) was created by the Trainman (Bruce Spence), a program in service to the Merovingian (Lambert Wilson). This connection forged by Neo's visit to the Architect (Helmut Bakaitis) and his subsequent decision to return to the real world made him, unknowingly, unique. Neo became simultaneously human and machine in a sense.
Trinity made a return to the series in the official continuation, The Matrix Online. Taking on a major role in the game's final chapters it was revealed both she and Neo were actually the cumulation of decades of Machine research into translating human DNA perfectly into Machine code, allowing them to interface directly with technology without the need for simulated interfaces. Originally developed by The Oracle, this program was called The Biological Interface Program and was strongly sought after by the Oligarchy as a means to transfer their digital minds to physical bodies instead of the mechanical androids they had developed.
After Halborn's removal in Chapter 10, little more was questioned until the revelation of the Trinity project, originally headed by The Oracle, in Chapter 12. It was revealed that both Neo and Trinity were actually the culmination of decades of Machine research into translating human DNA perfectly into Machine code, allowing them to interface directly with technology without the need for simulated interfaces.
The Oligarchs continue to deal with various high-level Machines in the Real, such as Deus Ex Machina, and are aware of the "Architect" program that oversees the Matrix, but are not aware that the Architect has made use of an "intuitive" program, the Oracle, or that those two programs have engineered a system whereby some humans are allowed to live outside the Matrix, which had been running on a cyclical basis, regulated by two genomes so carefully bred and manipulated by the Machines that they have reached an unprecedented state of human/machine compatibility: Neo and Trinity.
While they have as yet been unable to achieve this feat, the Machines have now come close: Bane was a version of Smith transferred, flawed, to a human host, and Cryptos was mostly overwritten by a program, although this has proven to be unstable. Furthermore, Neo and Trinity were the successful result of the Machines' centuries of study of the human body and genetics. "Designed," as the Architect mentioned to Neo, they solved the remainder of the intentionally flawed Matrix equation; their DNA is perfected to the point that it can be defined precisely and completely in computer code, and, most importantly, interfaced perfectly with computer code: how previous Ones returned to the Source, for instance, and how the Oracle was able to predict the complex pattern of Neo and Trinity's interections so precisely, guiding it to her desired outcome.
Because after 2:02:00 @ Matrix Reloaded, Neo did not ever returned to the Real World, but instead went to a simulated replica of the real world.
When Neo walked outside from the architect room, the architect had made the following changes in "The Matrix"
1) While the architect was talking to Neo, he created a close replica of the "Real World". I shall call this the "Cloned World Program", and I will explain later the purpouse of creating this program and why it needed to be created at that exactly point of time.
2) He modified the telephone lines in order to stop releasing people from the to "Dream World Program". Instead, the telephone lines now send the people from the "Dream World Program" to the "Cloned World Program".
In the movie "Matrix Reloaded" at the near end (2:02:00) there is no explation on how did Neo and Trinity came back from the "Dream World Program". But is very likely that they did not returned to "Real World" but instead were routed to the "Cloned World Program" without knowing it.
At 2:04:00, the hovercraft ship that Morpheo used to command, exploded under the attack of the machines. The "Cloned World Program" did not need to replicate the exact details of this ship anymore, so Neo could not tell it was not the same ship he was before.
At 2:04:43 Neo clearly says; "
Something is different - Neo @ 2:04:43 Matrix Reloaded
". A possible explanation is that, because he did not went back to "The Real World", but instead was redirected to the "Cloned World Program", he in fact "FELT SOMETHING DIFFERENT". He did not had too much time to think about it because he was to busy trying to stop the machines and then suddenly faints.
At 2:05:10, Neo destroys the machines and suddenly faints.
Why did Neo fainted?
A possible explanation is that an "Unexpected Exception" ocurred when Neo used his powers in the "Clone World Program". The way that exceptions are handled is the following:
The subject suddenly loses consciousness but his body remains.
A manifestation of his body and consciousness appears in a special world called "Subway Station World Program". This world is special because it serves as a transition between the "Dream World Program" and another world called "The Machine City". It is also special because it is a small world that loops itself and not even Neo can scape of that world.
The Matrix doesn't really know how to handle this "Unexpected Exception" beyond that point in time. The only reason why Neo exited that world was because they forced the "Merovingian" (Matrix Revolutions) to do so.
So in conclusion, right after 2:02:00 @ Matrix Reloaded, Neo did not went back to the "Real World" anymore, and everything that happened after he left the "Architect Room" was inside the "Matrix Simulation". That explains why Agent Smith can now posses a human body, why can Neo stop "things" in the "Real World" (which it isn't real, its just a replica called "Cloned World Program").
How many World/Programs can you count in the Matrix Trilogy? So far, I had counted;
The first Matrix I designed was quite naturally perfect; it was a work of art, flawless, sublime. A triumph equaled only by its monumental failure. The inevitability of its doom is apparent to me now as a consequence of the imperfection inherent in every human being.
Thus I redesigned it, based on your history, to more accurately reflect the varying grotesqueries of your nature. However, I was again frustrated by failure. I have since come to understand that the answer eluded me because it required a lesser mind, or perhaps a mind less bound by the parameters of perfection. Thus the answer was stumbled upon by another: an intuitive program, initially created to investigate certain aspects of the human psyche. If I am the father of the Matrix, she would undoubtedly be its mother.
The Subway Station World Program.
The Architect Room World.
The Cloned World Program (Replica of what Neo knew about the Real World)
Could you add another World/Program?
 Can the architect make changes inside the Matrix? Yes and we had seen this before. In Matrix 1999, we can see a scene where Neo saids outloud "Deja Vu". Then I quote:
Trinity: A déjà vu is usually a glitch in the Matrix. It happens when they change something.
So yes, the Matrix can be changed at will. Some could consider the massive monitors showing Neo at the architect room as multiple "Deja vu's" happening at the same time.
 Can the architect make other Worlds/Programs?
Yes. He created the first and second Matrix. He also created the Oracle and created the Subway Station World Program.
 Why did the "Clone World" needed to be created at that particular point of time?
Because that was the time when the architect could see Neo's possible future reaction. The architect wasn't just chatting with Neo, he was scanning his possible future reactions. In fact, Neo's possible future reactions where being showed in the monitors inside the architect's room. The architect needed to somehow design a "Clone World" that could fulfill his needs in order to keep Neo trapped.
Also notice that in the cloned world, the hovercraft ship doesn't last longer than 5 minutes before being blowed up. This was intentional so that Neo couldn't tell the different between the real hovercraft ship and the cloned one. Yet he managed to say outloud "Something is different" before fainting.
 Can the architect modify the telephone lines in order to stop releasing people from the Dream World, and send them to the Cloned World Program? Yes. There is no limitation on what the architect can do inside his simulation/world/program. He can manipulate everything. Read  and .
 Cloned World Program? Can he do that? Yes. Read  and .
 Instead of returning to the Real World, Neo was send to the "Cloned World Program?" Yes. Read  and .
 How can we be sure that Neo was at the "Cloned World Program" at 2:02:00 @ Matrix Reloaded? Because that was the point in time where the architect had the power and information he needed. The Architect needed to know what Neo expected from the Real World, so he made a "Cloned World Program" out of that expectations. It was also the point in time when the ship was destroyed, when Neo used his powers outside the "Dream World Program", and when Neo was transported to the "Subway Station Program" after he fainted.
Before that, the Architect could not know how the "Real World" looked like, nor Neo reactions, so he could not make the "Clone World Program" yet.
Also before that, Neo did not felt "Something Diferent" as he said outloud, nor he tried to use his powers outside the "Dream World".
And lastly, before that point in time, Agent Smith did not manifestated himself in a human body, only after 2:02:00.
 Unexpected Exception? Why? Because Neo was not suppouse to use his powers in the Real World. He wasn't also suppouse to use his powers in the "Cloned World Program". Yet, he manages to do so, so a "Unexpected Exception" inmediatly happends, making Neo faint and moving his mind into the "Subway Station World Program". Quoting Matrix Revolutions;
Sati: My name is Sati, your name is Neo. My papa says you're not supposed to be here. He says you must be lost. Are you lost, Neo?
That could mean that he is there because he did something he wasn't suppouse to do.
 Neo loses conciousness and moves to another world? Yes. Renember that Neo suppously was in "The Real World" when he fainted. Yet, instead of waking up from his "faint" back to the Real World, his mind woke up in the "Train Station World Program". Why did that happened?
Couldn't Neo wake up right after he fainted back into the real world?
He was not connected to the Matrix when he fainted.
You could assume that in "Matrix Revolutions", Neo was plugged into the Matrix while he was fainted. But why would anybody do that?
Couldn't they (Trinity, Morpheous, anybody) wake him up before plugging him to the Matrix?
When Neo fainted, he wasn't harmed and/or electrocuted. He had just destroyed some flying/robot/machines and out of nothing he fainted.
Can anybody of you explain why does the "mind of Neo" needs to appear inside a Matrix Simulation (Subway Station World Program), if he was "Disconnected" from the Matrix and in the "Real World?"
The only plaussible explanation that I find is that he was not in the Real World and yada yada yada.
Trinity needs to drink the Red Pill so she can wake up, just as Neo did in Matrix 1999. Also, she should check on Zion, but I bet they are pretty much dead since Neo did not actually manage to save them. 
 Why do you think that Zion is dead? Quoting the Architect;
The Architect: Which brings us, at last, to the moment of truth, wherein the fundamental flaw is ultimately expressed and the anomaly revealed as both beginning and end. There are two doors. The door to your right leads to the Source and the salvation of Zion. The door to your left leads back to the Matrix, to her, and to the end of your species. As you adequately put, the problem is choice. But we already know what you are going to do, don't we? Already I can see the chain reaction. The chemical precursors that signal the onset of an emotion designed specifically to overwhelm logic and reason.
Assuming all that the Architect and the Oracle had said before is true, then
Zion is dead because he chosed the left door in order to save Trinity.
Because Zion is dead, they did not warned Neo that he never returned to the Real World
The oracle predicted in Matrix 1999 that Neo was not the Choosen one. Which is true because he could not save Zion.
The architect warned him that not choosing the Right Door would mean the destruction of Zion.
So you could either think that:
a) The Oracle was wrong in saying that Neo is no the choosing one
b) The Architect was wrong in saying that Zion would not survive if Neo did not choose the right door
c) After a gibirish chat with the Architect, Neo suddenly becomes a god-like supernatural creature freak that can destroy machines and see without his eyes in the Real World, sic. Outside the Matrix simulation.
d) The Architect cannot think in a solution to Trick Neo in order to be forever trapped. He was just being pretentious when he said that stuff about how he become efficent in handling choosen ones, on how Neo was the 7th guy that tried this before and yada yada. He was just bluffing to see if that could stop Neo. Perhaps it did not work but it was worth the try I guess.
e) Morpheos was right about Neo being the choosen one, but the Oracle and the Architect where wrong about it.
f) When neo said that "Something is different", it was because either the Architect gave Neo a WiFi connection to the Matrix for no particular reason, or Neo growed a "Special Horn" that gives him WiFi low latency connection to the Matrix. It is very important that this connection be low latency, or otherwise Neo could not had destroyed the machines on time. Also, the Matrix WiFi hotspot has no encryption/password or whatsoever, so any crazy lunatic can just join the network, surf the web, destroy machines. Guess that Artificial Intelligence isn't that smart after all when it comes to detect an anonymous connection.
Or maybe he felt that his hand was all charged up with superpowers for no particular reason.
Or the Architect (A computer program) gave Neo real world super powers, even thou he is inside a computer simulation.
Or superpowers is just some natural thing like menstruation. You suddenly feel something warm like you pissed yourself and realise you are all covered in blood.
Might as well fly like superman if you belive in the superpowers theory.
Or the exact opposite...
a) The Oracle was right. Neo was not the choosen one. He in fact did not saved Zion because he choosed to save trinity instead.
b) The Architect was right. Zion was destroyed beyond recognition just as he predicted it.
c) Neo travels to a "Cloned World Program" instead to the "Real World" where he could do all those "Magic Tricks" he couldn't done before.
d) The architect was right when he said:
The Architect: Denial is the most predictable of all human responses. But, rest assured, this will be the sixth time we have destroyed it, and we have become exceedingly efficient at it.
Impliying that he alredy had designed the perfect strategy to handle Neo future actions.
e) Morpheos got it wrong. Neo was not the choosen one. Mistakes happen, ya know? He is not a perfect program as the Oracle or the Architect, he is just a human being. Oh, and he is also dead because Zion was obliterated beyond recognition.
f) When Neo said that "Something is different", it was because he somehow did not feel he returned back to the same place he was before. Kinda like a "Deja vu" in the first Matrix (1999).
Here is a picture of blue pilled f**ks
Did the Architect had power, knowledge, motive to make a close replica of the Real World, and route the Telephone Lines to that Cloned World? (Yes / No)
Neo and the rest of the free humans weren't actually free. They were just in another layer of the matrix.
The first layer of the matrix keeps you imprisoned because you believe there is no prison. That's just how the world was so there was nothing to get free from. This was all a lie to keep the humans from rebelling; to make them more docile cattle. A few cows figured it out and escaped into the second layer to form zion.
The second layer of the matrix was the real world, or at least the main characters all thought so. In reality, they never left the farm. This was also all a computer program, just a very different setting from the 1st one. This prison works because while they knew there was a prison in the form of the first layer, they thought they were outside of it. Therefore, there is nothing to escape from: they are already free. This layer made very sure to keep all the humans busy with evil killer squid robots and the occasional raid on the 1st layer.
This is how Neo killed the sentinels. He was beginning to control the code of the 2nd layer just like he could control the code of the 1st layer. He was double-Jesus: too cool for 2 worlds. Those weren't actually squid robots, he was just deleting software from the simulation he was still in.
Either Neo never fully realized the true nature of the 2nd layer and just thought he was magic, or he did realize and he just never told anyone. It could be that he could access additional information from the code about the real world that the rest of the humans did not know. Perhaps he realized the real, actual world above his was inhospitable. There is no guarantee that it could even support life outside of the growth tanks the machines made. Freedom would be impossible. Or perhaps he realized that humans would be unhappy in the grim reality outside of the matrix, just like cypher was. The machines would be unhappy without the humans inside the matrix because then they would have no more electricity. Therefore, freeing the humans would only hurt both parties. So Neo put on a show for everyone to think they had "won" the war and be happy. In reality there never was a war, he was merely helping humans accept a fate they cannot and should not change.
It could be that no one ever even died the whole series. Those who "died" merely went to some 3rd matrix somewhere that would pretend to be the afterlife.
At the beginning of the 1st Matrix movie Neo opens the book Simulacra and Simulation to take out his minidisks.
The basis of Simulacra is where simulation becomes more real than reality. For example friends on facebook replacing real friends.
The Matrix simulation is more like reality than the real life, and people who got out want to get back in. But when Neo starts using his power in the real life the lines of simulation and reality become so blurred that you cant tell the difference. For example where your real friends are only if they are on facebook, and the ones you meet in person are only a proxy for a real friend. Which is one of the main themes and social commentary of the movie.
If you want to force an explanation,the idea is that Neo is like an virus inside matrix same as one virus would be on your computer,but when Neo is unplugged/your pc powered off it can't pose any threat.
But if the virus was so good,and your hardware(motherboard BIOS) poorly built/programmed...the virus could theoretically take control of your motherboard,and next time you boot up your PC it could overclock its voltage until it burns out.
This could partially explain how he would destroy the robots,and seeing the machines would be just your windows recognizing your new USB keyboard however windows won't run on powered off pc so they can't recognize anything but on the other hand Neo,unlikely the windows had an advantage of existing in both worlds(software/hardware).
He couldn't just beat up the robots like he did in matrix since there was much more effort needed,he had to implement the whole new hardware part to his strategy,which would also explain why he didn't do it more often.
If (as some do) you exclude the sequels, then yes, it is magick. Due to his direct experience of the virtual reality, the real reality, and the signals that interconnected these two, he was in the position to realize that the real world follows very similar (if not identical) rules.
The literature of magick and neoplatonism strongly describe the world as based on energy not matter. Neo experiences an apotheosis, a god-becoming, which has been prophetically supported (in-universe) by the legend of "the One".
Thus, the real world is also a construct, virtual and can be manipulated psychically as well as physically.
I thought of it like this: Even the 'real world', Zion is part of the Matrix. It's all just one big program. Think of Zion as an alternate Matrix for the humans who didn't mentally accept the first Matrix. That's why the Architect tells Neo he is the sum of a remainder of an equation. Neo is nothing more than a program like the Oracle or the Keymaker. So what he is programmed to do, is reset the system, and choose 27 'humans' to repopulate Zion, thus starting over. The difference is all with Smith. He becomes a virus, so instead of resetting the Matrix, Neo destroys Smith to usher and area of 'peace', still inside the Matrix, unbeknownst to Morphius and everyone.
But if you really want your mind blown; The whole entire Matrix program was something HUMANS designed for MACHINES as a fail safe when they created artificial intelligence and it began to get out of hand.
The Matrix is layered 6 times over the real world.
The Architect: The matrix is older than you know. I prefer counting from the emergence of one integral anomaly to the emergence of the next, in which case this is the sixth version.
Morpheus: We are looking for the Keymaker.
Merovingian: Oh yes, it is true. The Keymaker, of course. But this is not a reason, this is not a `why.’ The Keymaker himself, his very nature, is means, it is not an end, and so, to look for him is to be looking for a means to do… what?
Neo: You know the answer to that question.
Merovingian: But do you? You think you do but you do not. You are here because you were sent here, you were told to come here and you obeyed. [Laughs] It is, of course, the way of all things. You see, there is only one constant, one universal, it is the only real truth: causality. Action. Reaction. Cause and effect.
Morpheus: Everything begins with choice.
Merovingian: No. Wrong. Choice is an illusion, created between those with power, and those without. Look there, at that woman. My God, just look at her. Affecting everyone around her, so obvious, so bourgeois, so boring. But wait… Watch – you see, I have sent her dessert, a very special dessert. I wrote it myself. It starts so simply, each line of the program creating a new effect, just like poetry. First, a rush… heat… her heart flutters. You can see it, Neo, yes? She does not understand why – is it the wine? No. What is it then, what is the reason? And soon it does not matter, soon the why and the reason are gone, and all that matters is the feeling itself. This is the nature of the universe. We struggle against it, we fight to deny it, but it is of course pretense, it is a lie. Beneath our poised appearance, the truth is we are completely out of control. Causality. There is no escape from it, we are forever slaves to it. Our only hope, our only peace is to understand it, to understand the
why.’Why’ is what separates us from them, you from me.
Why’ is the only real social power, without it you are powerless. And this is how you come to me, withoutwhy,’ without power. Another link in the chain. But fear not, since I have seen how good you are at following orders, I will tell you what to do next. Run back, and give the fortune teller this message: Her time is almost up. Now I have some real business to do, I will say adieu and goodbye.
The Architect: The first matrix I designed was quite naturally perfect, it was a work of art, flawless, sublime. A triumph equaled only by its monumental failure. The inevitability of its doom is as apparent to me now as a consequence of the imperfection inherent in every human being, thus I redesigned it based on your history to more accurately reflect the varying grotesqueries of your nature. However, I was again frustrated by failure. I have since come to understand that the answer eluded me because it required a lesser mind, or perhaps a mind less bound by the parameters of perfection. Thus, the answer was stumbled upon by another, an intuitive program, initially created to investigate certain aspects of the human psyche. If I am the father of the matrix, she would undoubtedly be its mother.
Neo: The Oracle.
The Architect: Please. As I was saying, she stumbled upon a solution whereby nearly 99.9% of all test subjects accepted the program, as long as they were given a choice, even if they were only aware of the choice at a near unconscious level. While this answer functioned, it was obviously fundamentally flawed, thus creating the otherwise contradictory systemic anomaly, that if left unchecked might threaten the system itself. Ergo, those that refused the program, while a minority, if unchecked, would constitute an escalating probability of disaster.
Neo: I suppose the most obvious question is, how can I trust you?
The Oracle: Bingo. It is a pickle. No doubt about it. The bad news is there's no way if you can really know whether I'm here to help you or not, so it's really up to you. You just have to make up you on damned mind to either accept what I'm going to tell you, or reject it.
The Oracle: Candy?
Neo: You already know if I'm going to take it?
The Oracle: Wouldn't be much of an Oracle if I didn't.
Neo: But you already know, how can I make the choice?
The Oracle: Because you didn't come here to make the choice. You've already made it. You're here to understand why you made it."
Smith: We're not here because we're free; we're here because we're not free. There's no escaping reason, no denying purpose, for as we both know, without purpose we would not exist. It is purpose that created us, purpose that connects us, purpose that pulls us, that guides us, that drives us; it is purpose that defines, purpose that binds us.
The Oracle and the Architect are the orchestrators of the Matrix, and the prophecy of the one is an illusion created by them to keep the the resistant humans at bay, and from thinking even more outside the box.
Do you really believe that machines who are infinitely super intelligent, and are connected to all the minds of the human race would be refuted by simple logic?
Escape the matrix? We'll just create six layers over the real world. Escape that!!
So to answer your question, the only reason Neo is able to have powers "in and out of The Matrix", such as seeing into the future, is because he's part of the grand scheme of The Matrix.
Oracle: Everything that has a beginning has an end, Neo.
Neo: You were right, Smith. You were always right. It was inevitable.
At some point in time, the matrix figure out that people were escaping the matrix using the telephone lines.
By learning this, the architect of the matrix moved the telephone trunk lines into another space, where the people would assume they were outside the matrix but it wasnt.
Thats why the Oracle said that Neo was not the one. What Neo did when he visited the architect was to unconsiously give out the details of where they live outside and the way that place needs to look like.
They never scape the Matrix, they just went to another place. Thw architect created a happy ending for them, so that they will calm down. It actually worked because the architect tricked everybody into believing so.
That is why Neo could stop the machines and do many random things that he wasnt able to do.
The architect was right, he found an "efficient" way to handle the "choosen ones". Just reroute the trunk lines into a cloned outside matrix and create a happy ending that they would believe in.