The Matrix/Headscratchers

The Dark Storm
So, the humans had the means to deploy a vast layer of nanomachines, covering the world in perpetual darkness. The nanites must be either self-replicating or self-repairing since the storm is still there after centuries. Also, the machines (ANY machine, for that matter) can't touch it, since doing so pretty much kills them.

... uh, so why not simply use a fraction of those nanites ON Zero-One, easily shutting down the whole machine empire in a swift strike? What's the logic of having such a weapon, and then use it in the most contrived, indirect, and outright inefficent way possible?
 * Also, another point never really touched upon is quite why the machines relied exclusively on solar power in the first place. As has been mentioned elsewhere on this page, other generation techniques clearly existed in the pre-war world (and now) so quite why they went from exclusively sun-based to exclusively human-based is an amazingly strange choice on the parts of the writers. As is Humanity's decision that ultimately dooms all organic life on the planet outside of the Matrix.
 * if i remember correctly from watching the The Animatrix, the reason the machines used solar was due to it been renewable energy.

Just tell the truth!
I don't see why the machines couldn't have just up and told everyone "Yes, this is a simulation. But the real world is a radioactive ruin and in this one you can download knowledge and use superpowers!" It's perfectly true and it would solve everything!
 * Human nature: we want to know reality, and we rebel against authority. Even blue-pills would if they knew, and they would handle it worse.
 * Normal human beings value their individualism and freedom, and are not eager to be held prisoner in a gilded cage "for their own good".

The machines of the machines?
Here is something that has always bugged me. The Squiddies and similar physical machines, are they slaves to the AI programs we see in the Matrix? Are those a ruling class of some sort? I mean, the programs are quite self-conscious about their existence and mortality, whereas the Squids are mindless and suicidal, being destroyed by the handful without any reaction by their peers. Matriculated, one of the Animatrix shorts, shows that the machines do have an AI that could be liberated, and that they possess a "residual image" (not sure if the term even applies) that is much different from the humans and the programs. So, does that mean the sentient machines are basically using slaves to do their bidding? Would be quite ironic.
 * Judging from how in-Matrix programs treat each other, it doesn't seem likely they'd have a problem treating other machines as slaves, sentient or not. It doesn't actually look like they have a concept of ethics at all, which isn't surprising. The main thing they have that machines in our world don't is a drive to surivive.

Powered by People?

 * Does anyone know of ANY identifiable source for the comments that the Wachowski's original Matrix concept used humans for neural networks instead of power generation, before Viewers are Morons set in? Neil Gaiman's Matrix short story reflects this and was written during the planning stages of the movie, but does anyone know any other cited place for this information? Interviews, behind-the-scene books, official website, All There in the Manual (which manual), anything?
 * This is the troper that originally added that example to Executive Meddling. I first read about it in a wikipedia article on the themes of the Matrix. It said that the official novelization used the neural network idea, but I haven't been able to confirm that (I haven't even been able to find the novelization on Amazon.com). Other than that, there was some discussion on the internet about this (including the Wild Mass Guessing page). So, the only verifiable source is the Goliath story that you mentioned. Still, that story shows that they at least considered it at some point.
 * This troper never read the Goliath story nor the Wikipedia article, though I know about this. It might be in the movie "The Matrix Revisited".
 * There's an interview on one of the Uber-Ultra-Directors-Unabridged-Uncut-Cut DVDs where one of the brothers is asked about the whole "humans as power generators" thing and he answers something along the line of "We had a different idea originally, but it was easier to explain with Morpheus holding a Duracell battery", then going on about how it really didn't matter why the machines were reliant on living humans, but it fact that they were was the idea.
 * This is actually Fridge Brilliance Think about it, Why would that not work? Because of the laws of thermodynamic. Where did you learn them? In school. Where did you go to school? In the Matrix.
 * True, but if it weren't for the second law of thermodynamics, and energy could be completely conserved, then the machines probably wouldn't have needed humans in the first place; they could simply redesign themselves as perpetual motion machines, and more likely, that's how the humans would have designed them in the first place.
 * Because most humans ARE batteries, albeit economic sense rather than the electronic sense. They're plugged into this massive system in order to produce the labor which keeps it running, and once they cease to be able to produce more, they're discarded and replaced with a new fresh one.
 * Due to the human requirement to perform cellular aerobic respiration via oxidative phosphorylation, it is possible, once provided with the appropriate organic substrates, for humans to generate energy via catabolism of said substrates (i.e. in the form of ATP (adenosine tri-phosphate)). Usually this energy is used for bodily functions, and if not it is stored as fat or glycogen (anabolism), but according to the Second Renaissance, where machines experimented on humans ad nauseum, it is not out of the sphere of possibility that they found a way to "harvest" the energy before it is expended for cellular and organ function and use it as an energy source (yes, "harvest" isn't the right word, but I can't think of anything more appropriate at the moment and it gets the message across, right?). The only catch is that they would have to provide enough substrates that there was enough energy produced to keep cells and organs functioning at an acceptable level (to keep the human in question, y'know, alive) and enough that the machines could "harvest" excess energy (basically using humans as a conversion system for organic redox reactions). Yes, this does very much keep in with the application of the laws of thermodynamics and conservation of energy (and for anyone who doesn't understand the principle behind the idea of "breaking molecular bonds releases energy", please see any source on Glycolysis). Also, due to the fact that basal metabolism in humans is "downregulated" (again, not really the right word to use, but oh well) in comatose patients due to the diminished involvement of the CNS, it would actually be more efficient for the human consciousness to be active, thereby providing a form of cerebral stimulation to increase bodily function and hence increase energy conversion and expenditure. Considering that this all is occurring thousands of years in the future, it is not out of the realm of possibility that the machines - with very advanced technology, obviously - could use humans as a source of power (as long as they're providing the right nutrients, environment etc.).
 * That still doesn't explain why they don't USE A DYSON SATELLITE SYSTEM INSTEAD!! Or shit, they could just go to the moon! Machines don't need air, they could let the humans have Earth if they wanted to. Morons!
 * There's a nanite cloud over the planet that prevents machines from escaping Earth.
 * "Cows would generate more energy, they would never rebel, and the Matrix would just be one endless field of grass. They could call it the Mootrix!" Just recite Bellisario's Maxim and enjoy the movie.
 * It still doesn't obey the second law; any substrates they're supplying the humans with could more efficiently be burned. While on the aerobic respiration part, even plants and bacteria already trump humans (or should we say everything that belongs in the Animal Kingdom) at that. Also, if they have that kind of technology, it's not plausible that they couldn't simply make (nonsentient) machines to do the same energy conversion. Also, Morpheus specifically said that the human brain was an important part of this, though he could have been misinformed.
 * If humans are being bred and used solely for power, why allow them to have sentience? Surely the machines must realise that how they came to power. For that matter, why humans of all creatures?
 * They machines use humans instead of other animals for practical purposes. Animatrix shows that during the war they extensively studied the human body in order to understand how to destroy us better, and thus by the end of the war they already had the medical knowledge necessary to plug us in. They would need to start the experiments all over again in order to use other creatures. Plus, one could argue they they simply wanted to keep us alive, either as a sick form of vengeance or perhaps because they didn't want to completely lose their creators.
 * Indeed, machines might be creatively sterile. They may even keep humans around specifically to let them advance science in small ways before resetting the Matrix and making them forget. Meanwhile the Machines get little occasional upgrades out in the Real.

Where Do Matrix Babies Come From?

 * Where do the Machines get babies to plug into the Matrix?
 * In-vitro fertilization and artificial wombs. They've already got plenty of fertile humans. The first humans were captured survivors of the war.
 * Word of God says that Persephone's original function was to facilitate "donations" of genetic material from human men inside the Matrix.

The Matrix is for Porn

 * Why do the Zionites, excepting Mouse from the first movie, never think to use the Construct program for recreation? It would be more fun than any video game!
 * Only pod-borns would be able to do that, the people born in Zion don't have the implants necessary to access the Constructs. Some pod-borns do have personal Constructs. In the video game Enter the Matrix, Ghost has a personal Construct in Zion that he uses for meditation and practice. I imagine that the Zion culture would look down on people who spent too much time in Constructs. After all, that's almost exactly what they're trying to free the rest of humanity from.
 * One would think that the people in Zion would distinguish between people choosing to enter the Construct voluntarily, and for short periods of time, or being forced to live in the Matrix by the machines and not even knowing it.
 * Intellectually they may understand the difference. Emotionally they might not. Human nature.
 * Garry's Mod. 'Nuff said.
 * They actually do, in the Animatrix; it's the entire premise of "Program".
 * Not to mention the "activities" in "The Last Flight Of The Osiris.".

Residual Self-Image

 * Residual self-image. Doesn't work. Try to think of exactly what you look like. First of all, everyone should have been mirror image. Second, people should have had significantly less detail. Third, look up "homunculus" on Wikipedia or most anywhere else (not the alchemy one, the other one). Finally, just LOOK at Carrie-Anne Moss. Trinity is just screaming eating disorder. Therefore, I'd guess that her residual self-image would be some 300 lb.
 * The RSI isn't meant to be taken absolutely literally, as though the person has total control over what they appear as in the Matrix. Just accept that the information for what you "should" look like exists in inchoate, vague form in your brain, and the super-magic technology of the Matrix is able to read it and fill in the blanks, much as modern CG can generate a relatively detailed picture from relatively sparse input, thanks to being able to match it to common patterns.
 * And whether it came across clearly or not, I do think it's pretty obvious that one of the things about RSIs is that the Zion agents' RSIs make them look a lot more, well, generic than real people. The movie is shot such that everyone's faces look really smooth and expressionless in the Matrix, and only in "real life" do we see wrinkles, laugh and frown lines, nuances of facial twitches, etc.
 * Also, low, low blow about the eating disorder comment, man. Seriously, get off the high horse. Also, I totally fail to see how the homunculus fallacy has anything to do with this. No one is saying there really is a "little Neo" inside Neo's brain that the computer is able to find, just that in Neo's brain resides a pattern saying how Neo's body "should" look (just as there is for *everything else Neo knows or thinks*) and that the computer uses that as a template for Neo's appearance -- presumably because a body that didn't match how Neo "should" look would cause him psychological problems. (The origin of the term "residual self-image" is from the fact that people who have had some major alteration to their appearance in real life often constantly imagine themselves as their previous selves, and being forced to confront the change in their physical state often causes grave psychological distress. Amputees or people who've had radical reconstructive surgery or whatnot can't stand looking at themselves in the mirror, etc.)
 * I concur with the above. A couple years ago, I cut my hip length hair to about three inches and donated it. For weeks afterward, I couldn't recognize myself in mirrors, and kept reaching back to adjust a non existent ponytail. Now I've grown it back out a little, and continually treat it as shorter than it is. Your mental image of what you should look like is astonishingly iron-clad.
 * well if you think about it trin's appearance in the matrix changes a lot over the coarse of the three movies, in the first she is soft and shapely, round face, smooth skin, looking very nice in skin tight leather. by the 3rd movie she is looking really haggard, her face has lost a lot of flesh, check bones are showing through more and more. this may be a justification for the eating disorder comment.
 * Carrie-Anne Moss was pregnant during the filming of the sequels. This might explain any differences in her physical appearance over the course of the films.
 * It does, in fact, make sense. People have trouble imagining how exactly they look like because during waking time, the vividness of one's "generated visuals" is limited. Try to imagine another person you see often in detail, without a visual aid like a photo. When you're awake, it's very hard to do. In dreams, when your imagination flows more freely, you can see in much greater detail than via waking imagination -- sometimes including yourself. Some dreams where you see yourself are vivid and realistic enough to be mistaken for "out of body experiences". There is, generally speaking, enough information in your brain to reconstruct how you look like with high accuracy, it's just hard to access.
 * Moreover, the Matrix involves a bunch of machines with root level access to the human brain, and a lot of reason to make sure that human brain does not mimic anything outside of the reality of the Matrix. They're almost certainly quite capable of presenting much, much higher resolution concepts of 'self' than the modern day human provides.
 * In any case, the idea that it's "residual self-image" that makes people look like their real bodies in the Matrix is ridiculous: the pod-sleepers have never experienced life within their real bodies, hence would have nothing to base such a self-image on. Probably, the machines simply base a person's Matrix-bound appearance on the physical appearance of the body, using genotype to determine factors like hair color or baseline strength that aren't evident in the sleepers.
 * In one of the first concepts for Switch, her character was originally meant to have a screwed-up self image. In the matrix she was supposed to have been the opposite gender to what she actually was.
 * Does anyone have any source for the above? Last I heard, this was a fan rumor due to the fact that the character had an androgynous look and her name was "Switch".
 * And for that matter, when did transsexuals have a "Screwed up self image" Most of the ones I know are not screwed up, just different.
 * The basis of transsexuality, as this troper understands it, is that one's self-image is the opposite gender of one's physical body. "Screwed up" a poor choice of words. Although that raises the question of whether Switch's Matrix self--RSI--is her "real self", or "her" physical body is.
 * The entire premise of the Matrix was about the ability of humanity to accept a specific presented reality (the Architect even said this), and so RDI is about an already established digital image being accepted as a reality within the framework of the matrix (it's not about ACTUAL self-image, it's about a residual impression left behind by a previous self-image (which of course is dictated by the digital framework of the matrix). In the first movie Morpheus goes on to say how some people are so dependent on the Matrix because they are so invested/dependent on that version of reality. Or, if you're having problems with that idea, Mystery Science Theater 3000 mantra FTW!!!!!
 * It's still hilarious, of course, that all our heroes look way cooler in the Matrix than in reality. They must all have been pretty self-assured about their optics!
 * People lie about themselves on the internet.. wouldn't you be cooler in the matrix too?
 * I'd explain it like this: The Residual Self Image is something that applies to people who have been freed and are hacking their way in. When you're in a pod, your appearance in the Matrix is based on your actual phenotype. So once you're freed, you've already got a basis for what you really look like, and that sticks with you as your Residual Self Image.
 * Proprioception is a very accurate sense, even though it wasn't obvious enough to include in the "basic senses.". Doesn't seem too much of a stretch that, in the absence of a physical body, your brain would be able to create the sense of one (one would easily imagine that in a Matrix-type environment your mind's perception of your body's location would just be an array of pointers)
 * in my opinion RSI (for people still plugged into the Matrix) is not how we WANT to look (the resistance looks cooler than your average joe) but how we KNOW we look. People wish they were taller, thinner, blond, more endowed, etc ... but if these things happened without explanation we'd know something was wrong. Accepting that you are mundane gives you a mundane appearance; contrast Neo when he first enters the Construct, to Neo when he's saving Morpheus. He oozes badass in the second scene, but in the first he looks very normal.
 * I read somewhere that they did an experiment and showed newborn babies (who had never seen anyone) pictures of their mother or another woman. The babies responded differently to the pictures of their own mother -- they had some idea of how their parent (and therefore presumably themself) would/should look.

Where Did All the Prodigies Go?

 * In the first film, ability to manipulate the Matrix appears to exist on a spectrum, with "the other Potentials" in the Oracle's apartment openly violating the physics of the Matrix simulation while the more ordinary Zionites like Trinity and Morpheus can only change attributes of their own physical capabilities. Why don't we see any of these people in the latter two films? You'd think the Zionite military would have a special-forces unit or something for red-pills who can overly change the reality of the Matrix.
 * The video game "The Matrix: Path of Neo" touches on this. In the six months between the events of the first and second films, Neo has been saving potentials who can help in their fight. None of them are as capable as he overall, but they had some importance to Zion.
 * At least some of those are programs, and the "there is no spoon" kid features in a comic.
 * They can't be programs or it makes the Zionites really and truly stupid for not checking that every person they think is on their side inside the Matrix actually exists as a redpill outside the Matrix. I mean hell, why did they never check that with the Oracle?
 * But not everyone on their side is a real human redpill. The Oracle isn't, for instance.
 * And no Zionites (save Neo, who had the true sight of any entity in the Matrix) suspected this point until the last film, when the Oracle's "shell" changed. (A different actress, Mary Alice, was called in to replace Gloria Foster, the original actress, who died during production, but not before filming her scenes in "Reloaded." The Oracle was also limited in what she could tell the rebels. She could only puppet her version of the Prophecy without causing them to rebel against her, since she was as much part of the system in truth as any being in the Matrix. And remember--not all Zion operatives made contact with the Oracle: Only the very few that supported Morpheus's plan--to find the One and use him to end the war--chose that path.

Who Needs Humans?

 * JESUS CHRIST THEY HAVE FUSION WHY WOULD THEY FEED PEOPLE FOR ENERGY THE CENTRAL CONCEPT OF THE MOVIE MAKES NO SENSE! Where does the food for the IVs come from? If it's some k kind of fusion, why not just fusion somehow only makes food, why not just burn the food? And if you INSIST on using animals, why not something simpler? Hell, why not just vats of yeast? And if it has to be people, why not just take out the front 2 thirds of the brain and tie them down? They won't complain. Or if you need a full human brain, why not just keep them comatose? (That scene with the battery almost had me crying in the theater)
 * I read somewhere, could have been on this wiki, that the original idea was to have the machines use humans for computational power. A sort of role reversal. But due to Executive Meddling, Viewers are Morons etc. the plot was changed to the simpler humans used for energy idea.
 * Unless I misunderstood the premise of The Second Rennaisance, everyone here is missing the point. The human leaders willingly signed themselves up for slavery (as a power source or neural networking, take your pick) in exchange for not being wiped out entirely at the end of the war. One of the stipulations of the contract was that humans must always be given a choice - the capacity to opt out - even if they only feel it at a subconscious level. Thus the Matrix had to be created to fulfill the bargain. Of course, humans free from the Matrix aren't protected by the contract, so the machines hunt them relentlessly. (Addendum: this solution draws together evidence from at least two movies and the Animatrix, so correct me if I've got it wrong). But it boils down to a cross between "humans are the most powerful power source available" and "the machines are under contract".
 * The contract was forced on the humans as a humiliating symbol of slavery. It was never actually a "contract" in any form -- the human leaders were given no choice but to sign. This seemed very obvious from the framing of that scene. So no, the humans were not given the option to negotiate for potential freedom in that contract at all; the humans were only given a choice by the Architect out of necessity, because the Oracle told him he had to, and only after The Matrix: Revolutions was this choice made an explicit choice ("And everyone who wants to leave can").
 * (Also, this has nothing to do with the point -- the Machines wouldn't've bothered offering this "contract" at all in the first place if they weren't getting something significant out of it. The cartoon makes it clear they could easily have wiped out humanity if they wanted to -- but they *didn't* want to. Humanity was utterly defeated and when they had us at their total mercy, they decided to make the Matrix. Moreover, the assumption that because the Machines are Machines they must somehow be categorically incapable of violating contracts or agreements is really, really stupid. The whole point of the story of B1-66-ER is that the Machine War was only even possible because Machines learned to break the rules.)
 * The Architect said that the first two Matrixes failed because humans weren't given a choice, subconscious or otherwise. It was only after the Oracle investigated the problem that she came up with the idea to give the humans a choice, even if they weren't consciously aware of it. So this theory really doesn't fit.
 * Matrices, not matrixes. But yeah, fair point; I forgot that bit.
 * The point of the original comment seems to be that no, humans AREN'T the most powerful power source available. Human bodies are far too complex; far too little thermal energy is created by our bodies to justify the large amount necessary to fuel us. Animals evolved to be as energy-efficient as possible, that's why we get fat. It probably would've made more sense just to drop them into a furnace than to plug them in. The question is mostly, why did the machines agree to such a stupid idea in the first place?
 * I have a feeling that the Matrix was created to resolve a programming conflict, largely the conflict of hurting humans, which their base code doesn't really allow. Any actual harm to humans can be justified by 'that one has a firearm, and therefore poses a risk.' It's not that they didn't want to remove us, they just couldn't. I know, I know, 'Why'd they attack Zion, then?' It's not unreasonable to conceive that the Zionites, given the chance, would shut off the Matrix completely. Can you imagine the deaths just from the shock of the world turning off on you? Plus the starvation and lack of clean living space would kill countless more. Additionally, how many innocent people get killed by the Zionites when they're in the Matrix? In a warped way, they're still 'protecting' people, just to an extent not explored by Asimov's writings, and, in my opinion, a logical extension of the things Asimov posited.
 * The above is highly implied in The Matrix Online (if not outright stated in the storyline materials released by one of the game's developers as the game was ending). The Merovingian's investigations into the Machines' power source found that it was rather inefficient and could only power their civilization (which not only includes the Machines, but also their defenses, the battery towers, the fetus fields, and the Matrix itself) a few times over. The released storyline material says that the decision to use humans as a power source was not done entirely out of a need for efficiency and was influenced by the Machines' basic programming of being humanity's caretakers.
 * The Architect explicitly states that the Matrix had to have the apparent flaw of giving people the choice to leave or else there would be a much more catastrophic failure of "crops," thus necessitating the "One." However, there would eventually come an exponential growth of people not accepting the program would eventually endanger the Machines' farms and thereby the One fulfills their duty by hand selecting a group of individuals to restart Zion as it is annihilated and the Matrix program is reset.
 * Yeah. Why not use cows? Being methane-producing herbivores makes them quite efficient and they're a lot more passive than humans.
 * You said it yourself, herbivores. No sunlight means practically no plant life. Humans are fed the liquefied remains of themselves because they're omnivorous, something that would be more difficult with herbivores. As for the battery deal, Word of God says it was supposed to be them using our brains for processing power but Executive Meddling lead to the battery bit. Either one works. Hell, depending on how deeply you read into the philosophy of the film, you could draw all sorts of conclusions including "They're sapping off our chi" or whatever.
 * Er, all the nutrients for the vat-sleepers is delivered intravenously. Herbivore vs omnivore would make no difference, because nothing is actually being digested.
 * Unless the Humans Blew up the sun then Orbital or Lunar solar arrays transmitting power via microwave would still be an acceptable means of fueling oh I don't know lets say simulated deep sea geothermal vents with blind shrimp and tube worms if you still REALLY  need biomass that isn't extinct by now.
 * Not that this makes the plotline any less stupid, but anything that could totally block out the sun would probably block or severely weaken any microwave transmissions through it.
 * Or just move out into space where there is nothing to block the sun and leave the few human survivors to starve on the ruined husk of the Earth. Which of course brings up the point that humanity depends on the Sun to grow food far more then the Machines need it for energy. After all they can directly switch to fusion/fission/oil/coal/gas/geothermal/wind/whatever. Good luck trying to feed a few billion people on raw crude.
 * Yeah it is really stupid. Like he said, the Wachowskis wanted to have the humans used as a giant neural network computer, but executives didn't think the audience would understand it. I believe that the novelization still has this explanation. If anything, human brains use less energy and are more creative than bulky supercomputers made with conventional computer chips. It easily explains why the machines chose to use humans instead of say, cows (which have much less brainpower, consume more resources, and might have had large numbers killed in the war), and why they didn't just put the humans into comas or something. And honestly, do you find it any harder to understand?
 * When I first heard about the film's premise, I thought it was so silly that I'd try and think of a more thought provoking premise, and this was exactly what I thought of. When I actually saw the film, I just replaced any mention of the power source thing in my mind, the film was much better. Even if they did have a more plausible alternate explanation, having the machines literally require fully functioning humans to exist makes the conflict of the story far more believable (and would get its origin away from simply being a "robots go nuts" terminator ripoff and more like a malevolant version of the Puppet Master from Ghost in the Shell, especially if it had evolved naturally among human minds).
 * Omnivorous or not, you can't feed any system the liquefied remains of the dead members without an external energy source, you'll run out of chemical energy in the remains. Quickly. There's not much nutrition in excrement, and not enough in a fully grown human to feed a whole new human til it's fully grown.
 * So obviously feeding the pulped human remains to the living humans would just be a waste of perfectly good fuel.
 * Nobody ever said that liquified corpses were the only things being fed to the coppertops, just that that's what happens to them at the end of their life cycle. For all we know, the machines have converted all the non-human biomass on the planet into trillions of gallons of IV fluid, and simply haven't run out yet.
 * The best rationalization I've ever heard of is that the machines do it because they're a mite bitter after all these wars, and they like the thought of enslaving/tormenting humans. Also, Morpheus doesn't necessarily know everything he thinks he does.
 * Morpheus was shown in the sequels to have incomplete and erroneous information about the nature of the Matrix. Everything he and Zion know about the Matrix was told to them by The One from the previous iteration, who was being manipulated by the Architect. The "coppertop" thing could have been a Red Herring.
 * Yeah it doesn't make a single bit of physical sense, its basic science, all energy comes from the sun, without the sun you'll run out of energy, farming humans will just prolong the inevitable, breeding them will just waste more energy, its incredible the number of people who don't realise this.
 * Although your point is valid in context, just thought I'd point out that NOT all energy used by life on Earth comes from the sun. We USED to think this until we discovered life living around "black smokers" at the bottom of the ocean. They get their energy from geothermal sources originating in radioactive decay in the Earth's core. But yes, this is very much a minority of life and the sun is pretty damned important.
 * I just cover my ears and chalk it up to the Three Laws. Almost anything can be justified with a loose enough definition of "harm". After all, life in the Matrix is better than reality in many ways.
 * The only plausible interpretations of the idea that "humans are hooked up to the machines for their benefit" is that 1) human neural energy input and integration into the matrix is necessary (or preferable) for machine functions (otherwise why provide them with a neural interface at all?), 2) the machines are maintaining human life on the basis that humans provide a specific organic substrate in a now barren world that they can use and harvest for specific purposes, 3) recycling humans in such a manner IS actually a viable energy source (considering this is 20 thousand-something years into the future, geothermic energy is probably used up, solar is out of the question, they obviously haven't opted for a Dyson Sphere satellite network (WHY NOT?! *sob*), all organic matter on earth has been reduced to useless electron-dense deposits (most likely), water is probably a precious resource (by this time? yeah!), and generating radioactive isotopes to precede a nuclear-reactor-like energy source is probably either a stupid idea (considering the entire planet is already in a nuclear winter) or simply implausible (to mediate this kind of energy production and expenditure you're talking hydrogen fusion at an unprecedented scale) this isn't actually such a pathetic idea. If you'd tried to present a mobile phone to a caveman they would have told you it was impossible. I'm pretty sure by the year 20XXX they'll have found a way to redux the base laws of thermodynamics and structural engineering!), or 4) they're sadistic bastards who want to get back at humanity for all the problems they've made. MY biggest It Just Bugs Me is if these machines are advanced enough that they've managed to use human energy (or substrates) to maintain themselves, WHY DON'T THEY JUST USE EITHER APPLICABLE STRING THEORY, SOME FORM OF ADVANCED TERRAFORMING, OR USE A FUCKING DYSON SATELLITE SYSTEM INSTEAD!!!!!. Another explanation is that Morpheus is getting the wrong information, and that's just what the machines want the humans to believe (far more likely).
 * Addendum: I'd like to add to my previous statement by saying this - oxidative phosphorylation, people! ATP produced at expanded levels due to aerobic respiration from organic nutrients and substrates! The laws of thermodynamics, conservation of energy, STILL applies! Humans derive energy from the catabolism of organic substrates that the machines would not be able to do due to their lack of multicellular organs (which I presume they don't have). As long as they provide the necessary organic substrates they can actually use humans as a way to generate energy! However, as bodily human functions are regulated by CNS (Central Nervous System) activity, and if you left them in a comatose state, basal metabolism would be reduced to completely unproductive levels, keeping human consciousness active so a cerebral response mediates appropriate metabolic activity could by why the machines would require them to be hooked into a simulator like the matrix! And there's your explanation for why the matrix exists! ... Still doesn't explain why they don't use a freaking Dyson satellite system!!!
 * See the discussion under WMG: The Matrix on what they were really used for.
 * Whatever the reason for humanity's enslavement, it had nothing to do with a power source. No matter what, you will always get significantly less energy out of anything that belongs in the Animal Kingdom than you put in. If you want to produce organic energy, use the bottom of the food chain, aka plants.
 * The neural-net explanation is the best possible one by far. As far as "Why not keep them comatose"... um, they *are* comatose. What else do you call lying there motionless inside a tube, completely unaware of the outside world? But comatose people do have dreams and hallucinations, and the Matrix is basically one giant managed hallucination, designed to keep the human brains limber and active enough for the Machine consciousness to exist within them. (This has to be part of the explanation -- if the Machines could use dormant, inactive brain cells as components, then it becomes a lot harder to justify not using cows. It's actually pretty obvious, given *how the Matrix works in the first place*, that the Machines' existence must be as a shadow of conscious human thought processes -- otherwise conscious human thought processes couldn't affect it.)
 * Actually, a comatose patient is one with reduced and minimized brain function not conducive with either dreaming (which is precluded by a REM state which comatose patients are unable to have) or hallucinations (which is a sensory misconduction of information to the cognitive functioning areas of the brain when the patient is AWAKE).
 * The above is true. Hence they are not comatose. And they are obviously not dreaming, hence the machines have found a way to extend human consciousness into a platform construct. And considering how they experimented on humans ad nauseum in the Second Renaissance, I'm fairly sure they found a way.
 * I actually take it as the exact opposite. The machines are being merciful, trying to give their human creators an ordinary, pre-war world they can live in, without being a threat to the machines. Remember, their first attempts at the matrix were attempts to give humans Paradise. They only settled for a simulation of the modern world when that failed. The machines don't need humans at all, as the Architect all but said with his "we're prepared to accept different levels of survival" line. The Matrix runs at a net power less (and logically, it has to run at a net power loss, there's no way they're getting more power out than they're using to keep the humans alive) because the machines are running it for the benefit of humanity: drawing power from humans is just their way of trying to at least get a little bit of it back in the process. The point of the last two movies is that Neo, and the Oracle, are trying to prove to the machines that they don't need to keep humans in a comatose dream world to live in peace with them.
 * It's possible that Morpheus et al were misinformed/only knew part of the truth. If the neural net theory is correct, there's no reason not to use the waste energy humans are giving off, just as some data centers use the waste heat from their server racks to help heat other areas of their buildings. Inhabitants of Zion wouldn't necessarily know about everything about the multiple functions the machines were using people for. Alternatively, "powered by" can mean the sort of processors being used by a system (slightly less evil than being powered by Intel, for example), and over many years of fighting and destruction, the in-universe lore could have shifted the terminology to assume and transmit the wrong meaning of the term, making people thing "battery" instead of "CPU."
 * The "battery" story could be what the machines want the humans to believe, because it makes it seem like all the pods' occupants are equally replaceable. If the Zionites learned that the sleepers' brains are performing various processing functions, they might try to determine which are most crucial to the neural net's operation, and target such individuals to be awakened (or even killed), in an attempt to crash the system.
 * But why wouldn't some Zionites question it just like we're doing now?
 * Because we're looking at it from an external viewpoint as a piece of entertainment that we know is fictional and constructed by another person. For them it's just the world they live in, it's what they've been told and seen is actually going on. Some might question it, but it's sort of like questioning why the sun comes up... interesting, but unrelated to the fact that it will come up whether you understand or not. Ultimately the question of why the machines enslave humanity is irrelevant to the fact that machines have enslaved humanity.
 * Perhaps this thought is brought up later on this page, but maybe "real" physics are nothing like those of the Matrix. Why should they be? We only think the premise is horribly unscientific nonsense because it would be, inside the Matrix. Outside it, humans are (somehow) a highly efficient power source.
 * Because that would change all of human history, warfare, etc. to the point where the machines probably wouldn't have had a chance of taking over. It would essentially mean no conservation of energy in the real would which would imply limitless resources on earth. Essentially, Earth would be a utopia, but that's not what the Matrix of the past paints the world to be (it looks just like our real world circa 1999).
 * Because that would change all of human history, warfare, etc. to the point where the machines probably wouldn't have had a chance of taking over. It would essentially mean no conservation of energy in the real would which would imply limitless resources on earth. Essentially, Earth would be a utopia, but that's not what the Matrix of the past paints the world to be (it looks just like our real world circa 1999).

Zion's Stuck in the '80s?

 * In the scene where Neo gets "combat training" dumped into his brain (right before he tells Morpheus "I know Kung Fu"), Tank sees how well Neo takes to the procedure and says "Hey Mikey, I think he likes it!" Now, this would make more sense if Tank had been rescued from the Matrix as Neo had, but Tank was born in Zion--so how does he know enough pop culture to quote a TV commercial? They wouldn't have broadcast commercials in the Real World...
 * Possibly he picked it up from someone they rescued earlier.
 * Which would explain why he got the line wrong.
 * Or perhaps, by some coincidence, the phrase existed in Zion culture independent of the Matrix.
 * Perhaps it was injected into the Matrix through the brain of an advertising exec, who subconsciously remembered it from a data packet that had passed through his brain (assuming we go by the "humans are processors, not batteries" thing -- which I do, it makes so much more sense).
 * Or Operators, by virtue of 'watching' the Matrix all the time, tend to pick up the pop culture; note that in the second movie, Link makes reference to Neo 'doing his Superman thing.'
 * Or the first people who escaped realized they needed TV and immediately began working on a way to decode TV broadcasts from inside the Matrix.
 * Pre-Matrix television from the Zion archives, perhaps commercials were the only television survive the war.
 * Alternatively Tank just has an interest in pre-Matrix commercials, people in Zion have funny hobbies.
 * Zion has only existed as a real civilization for 100 years, remember? And the majority of its population are redpills; natural-born Zionites are a minority (and treasured and respected because of that quality). It shouldn't be surprising at all that Zion is saturated with real-world pop culture, or that they dance to real-world rave music.
 * Or maybe he's not quoting anything, and is just being weird and talking to some non-existant person named Mikey. But really, what question of motive couldn't be explained with "they just happened to think it was a good idea at the time"?

Symbolism

 * What is it with all the annoying 'religious' symbolism? I mean, a few little in-jokes is fine, and the actually important stuff-but they threw in everything from every religion they could get their hands on!!!
 * The dominant Christological and Buddhist symbolism was intended to show Neo's path, as his predecessors--enlightened, but locked in a world of samsara, a repetition of life, suffering and death than only the enlightened have a chance of breaking free to--something else. Neo is also a messianic superhero, which means his goal was to break everyone else out of the virtual samsara loop that the Matrix was, every 100 years. Without that "annoying religious symbolism", the movie series would be just another annoying kung-fu film, and adds a level of depth that some don't get, or care to. Your entertainment mileage may vary.
 * Don't worry that bugs everyone working theory, the W brothers just really like pointless symbolism.
 * It could be a nod to the concepts of the collective unconscious or racial memory. You know the idea that these things stick in our heads not because the Have Happened but because they Will Happen.
 * Wow, way to attack what's basically the point of the movie. It's like asking "What's with all the philosophical speeches in Fight Club? I want to see more fighting!"
 * The concept that there is a different plane of reality beyond the one we sense is a recurrent one throughout world religion, myth, and philosophy. The references serve as footnotes, showing that the W brothers have done their homework.
 * ...except that, as mentioned above, the symbolism and philosophical bent of the films doesn't really add anything to the experience (admittedly that's subjective, and this troper isn't a philsophy major). Compare to something like Ghost in the Shell, where the philosophical undercurrents are actually necessary to grasp the full extent of what's going on. It's a similar story for Fight Club - the philosophy and symoblism is inherently tied into the story. This is not so much the case in the Matrix films, where it seems to have been... well, smeared over the top of pre-existing themes.
 * Headscratchers is not for "the presence of this sort of content annoys me".

Atrophied Muscles

 * If Neo's muscles have atrophied from a life spent in the Matrix, why is he able to swim after being dumped out of his pod?
 * Swimming doesn't require superhuman strength.
 * But apparently vision does. "Why are my eyes so sore?" "Because you've never used them before."
 * Close your eyes for three years, then see how blurry your vision is. Try that for 20+ years.
 * Of course, if Neo never used his eyes before, the neural pathways for vision would not have developed, and his eyes wouldn't work at all.
 * Neuronal pathways are developmental insofar as they are controlled by maternal gene products and embryonic genetics; there is no usage requirement for their construction, although non-usage probably would result in some degree of atrophy.
 * Neural pathways for vision, as in the optic nerve, are developmental, formed from the embryological neural tube before a child is born. However, cognitive adjustment to vision takes a while, and the internal and external ocular muscles (ones that mediate pupil constriction, eye movement, and eyelid movement) would all be atrophied yes. Okay, not the internal ocular muscles because they're smooth muscle, but any skeletal muscle, yes.
 * For all we know, working out in the matrix works out your real muscles.
 * That's true. A bleed affect coulda taken place, just like when he hits the concrete in the jump program and his mouth bleeds. If he worked out inside theres no reason why it shouldn't happened outside.
 * There is no good reason. It would have been far better to have him sink like a stone, struggling like the weak kitten he should have been and almost drown except for the claw catching him. Even someone who had muscles once and didn't use them because they were in a coma for a few years and not exercised properly would not be able to struggle like that.
 * True. People here seem to be underestimating the effects of muscular atrophy. People who wake up from a coma will barely be able to stand up (if at all) and often need months of re-hab just to regain their previous performance. Heck, Victorian women couldn't even sit up without their corsets, not having used their back muscles since they were children!
 * Cross-ref: the "Awakening" scene in the first half of Kill Bill for a good visual depiction. Wiggle your big toe, anyone?
 * Am I missing something? It looked like, the body's own buoyancy aside, he was sinking, and his flailing attempts to tread water were just making things worse. (Aside: the human body can float pretty well if the lungs are full.)
 * Someone who hadn't moved for that long wouldn't be able to even try to swim as much as Neo did. His muscles wouldn't be developed enough to move his limbs.
 * Note that the real body can move in response to stuff happening in the Matrix-- for instance, when Neo's body twitches as the Agents are beating him up. It's possible that over time, this muscle activity is enough to make the body just weak instead of completely atrophied.
 * How do you know his muscles were atrophied? He didn't look like it, and presumably the AI's have good reason to keep their "batteries" muscles healthy, since muscle contractions generate signifigant bioelectrical pulses.
 * Because Morpheus downright says they've atrophied. It's the main reason they did the freaky acupuncture thing to him.
 * We've already established that the idea that the Machines run on "human power" in a literal, energy sense is idiotic enough that basically all the fans who care have just dropped it.
 * Simple, we discover in Reloaded that Zion and the human resistance are essential to the machines' plan, so it stands to reason that the machines would make it possible for humans to function once they had escaped. It would be fairly simple to give the plugged-in humans a small amount of exercise to ensure that they wouldn't all drown as soon as they were dropped into the water.
 * This Troper always thought that Neo's muscles had some sort of power as long as all the tubes were connected to him. Note that he doesn't collapse like a wet noodle until after the machine removes the headspike from him.
 * Genetics keeps a "minimum fat level" as long as they're decently nourished. With no development there wouldn't be much muscle mass to "weigh him down." (Simplified: muscles sink, fat floats).
 * If you haven't figured it out yet, the ejection and dunking are the W's symbolism for birth and baptism, or return to samsara, the cycle of life, death and suffering that is the real world of Zion.
 * Aren't we are missing the point here? It's not about whether or not should Neo's muscles be atrophied - it's about Morpheus downright saying they are atrophied when all the evidences were to the contrary.
 * Yes, but atrophied does not automatically mean "atrophied to the point where there is nothing there but a thin layer of tissue over the bone". He could mean "atrophied to the point that they are so weak you can't move around effectively on your own but there's still something for us to work with".

Bluepill-Killing Heroes?

 * Why do the characters have no qualms about killing the innocent civilians they're supposed to be saving.
 * Probably because they operate on the most extreme "Ends justify the means" philosophy that has ever been applied to someone who wasn't an outright antihero (or villain). To them, a person stuck in the Matrix isn't much better off than a person dead (whether or not you agree; I doubt you do), or at least the difference between trapped and freed is as big as trapped and dead, and more importantly if they don't do whatever is necessary to keep their operatives alive there's no hope of ever freeing more people. The agents have no concern for innocents or collatoral damage (heck, they can just undo that), and employ them directly to try to kill the rebels, so if they don't follow the same standards they're dead meat (as if just having three completely unstoppable unbeatable invincible entities who can teleport into any warm body and respawn isn't bad enough).
 * Now combine this philosophy with the abundant religious symbolism, and you get some frightening fanatical dogma, i.e. "If you're not with us, you're against us and deserve to die."
 * Let's not think too hard about this here. The people trapped in the Matrix can be converted into Agents whenever said Agents feel like. The Zionites have a very vested interest in killing them off completely when they oppose them, because leaving them for half-dead results in an Agent on their hands.
 * Yea they give this one a full scene of exposition. The Lady In A Red Dress simulation is supposed to teach them that anyone directly attached to the Matrix can, at any time, be taken over by an agent, who until Neo came along were considered invincible killing machines.
 * The precise quote: "The Matrix is a system, Neo; that system is our enemy. But look around you, what do you see? Teachers; lawyers; carpenters - the very minds of the people we are trying to save. Understand, Neo, that most of these people are not yet ready to be unplugged. And some of them are so inert, so helplessly dependent on the system, that they will die to protect it. ... It's another training program designed to teach you only one thing: if you are not one of us, you are one of them [agents] ... in the Matrix, they are everyone, and they are no one."
 * I'd say the characters are definite antiheroes. In the famous lobby scene, Neo chose the route that involved maximum civilian death, just because "no-one's ever tried it before". The security guards are clearly introduced as ordinary joes, reading the newspaper and drinking coffee, who are blown away without a twinge of conscience. Depending on your point of view, it's either to show that their world is so dark and desperate that they've been forced to abandon all their scruples to survive; or just to show how badass they are.
 * Remember that from their point of view, your entire life is a pointless sham and the reality of it is that you're already living in a terrible hell and existing to (literally!) feed and shelter the enemy. Unless you have potential to become a redpill, a bluepill is already a dead person, a corpse still twitching in a grotesque parody of life. And redpills treat bluepills as such.
 * Which is not too different to say that every "unbeliever", or "pawn of the decadent system" or whatever fanatical bullshit someone has brainwashed you to believe, is living a unworthy life and can be killed without remorse if it is for the good of the cause.
 * Exactly my point of view. They are not heroes, they are fanatics. Of course, like every fanatic, they think their cause is just and the collaterals acceptable for the greater good, but the viewer doesn't have to share this belief. I, personally don't think being "freed" from a reasonably confortable life (It isn't "real"? Who gives a damn? It keeps me alive!) to live in an uninhabitable hellhole is a "greater good" at all that justifies the trail of corpses.
 * Eeeeexcept that in this case, the people around them can actually turn into agents who will kill them at a moment's notice!! You'll remember that all the people that they kill are ones becoming agents are the ones who are going to become agents because they realise who they are. It's not fanatical when you're killing people who are actually trying to kill you. This isn't a case where someone is saying "You don't believe what I believe, so I'm going to shoot you know." It's a case of "You're going to turn into an agent of the system trying to destroy me and you will try to kill me." That's definitely Anti-Hero, but not that unreasonable.
 * Like it or not, they are at war. Killing the brainwashed slaves of an enemy that will not hesitate to hunt you down and messily kill you is not pretty, but it is also not the most illegitimate tactic. These aren't hapless bystanders; they are providing support to the Agents.
 * But how often did that really happen? Neo and Trinity storm the building, taking down every guard, and it's only when they make it to the helicopter pad that an agent intervenes. So much for being "the eyes and ears" of the machines.
 * The Agents didn't want to leave Morpheus unguarded -- Neo & Trinity might just have been a diversionary attack, after all. So they were letting the human troops try to handle it until they ran out of troops, and then sent one of their number to go kill them while the other two stayed with Morpheus. Didn't work out the way they'd hoped, but its not like its unprecedented for hidebound logical servants of an unimaginative machine to use unimaginative tactics.
 * I do beleive that Morpheus explains this one when running a training sim with Neo. He says something to the tune of "Our goal is to free humanity by taking down the Matrix. However, all these people are still part of that system we are trying to destroy. Until it is destroyed, they are part of the very enemy we are trying to defeat."
 * There's a story in the animatrix "the Detective Story" that looks at this.
 * I, Prime Evil, have it in my head that the "law enforcement"-type characters (e.g. security guards, cops, SWAT team guys, and such like) are how the Squiddies appear when they're in the Matrix. What do police officers represent? Law and order, in this case the "law and order" of the Matrix world. This is my frame of mind when I play Enter the Matrix and other games like it: the cops/mooks/whatever are AI and can be disposed of with a free conscience. It also explains why there seems to be so little ethnic/gender/cultural diversity within the Matrix's idea of law enforcement: just as one Squiddy looks just the same as any other Squiddy, so one cop looks just like any other cop.

NOW, I bet you're wondering where the Agents' overwriting ability comes into play. Here it is--the Machine world has a set-in-stone, top-down hierarchy. Even though they're all individuals ("I'm not!" came Squiddy Dave's voice from the back), they must all accept their basic functions as necessity. The same applies with law enforcement: the Agents are at the top of the heap, with the greatest responsibility but also the most flexibility. Therefore, among the Machines it's an accepted "given" that an Agent's going to do a little rewriting here and there, but it's usually restricted to one Agent per "avatar" (Yes, I know they're not avatars, but bear with me), and one at a time at that. This is also why "rewriting" is for the most part non-life-threatening, and only results in an easily brushed-aside moment of confusion ("How did I get *here*? Must have dropped off," etc.) It's only when Smith starts rewriting people left, right, and center that it becomes a problem.

Killing the Agents

 * Would it kill the rebels to get a little more creative in dealing with agents? Because the helicopter minigun taking out three agents proves they're not completely bulletproof. Sure, they can dodge any number of bullets and they'll always be stronger than you in any way, but the rebels have access to any weaponry that ever existed and possibly much that didn't in whatever quantities they want for free. My first step would be to see if they could dodge a bunch of bullets fired at the exact same time from a shotgun or just a stream of individual bullets of any length or rapidity (machinegun or pistol). Failing that, there's flamethrowers, grenades, and all sorts of other explosives and anything else which doesn't just kill by hitting you with a bullet. And that's assuming you can't, in fact, make weapons up (in which case lasers and homing-anythings spring to mind). The fact that it's not standard procedure to fight agents with explosives is just totally ridiculous to me.
 * In the video game Enter the Matrix, you can kill agents with explosives in a few levels. You aren't regularly given them, though.
 * You're probably forced to use existing definitions for tools when hacking the Matrix, the same way a Gameshark can only alter the flow of code rather than add anything new.
 * Once a simulated bullet leaves the gun, it's flight path is totally deterministic according to the simulated rules. So the agents, connected to the system, can predict the flight path with perfect accuracy. The problem for them arises when knowing that information isn't enough to save them. Presumably, any simulated weapon that relies on the system to work would be subject to the same rules as normal guns, and thus be mutable, while a bare hand or melee weapon is under the control of an unpredictable human brain with free will. That, plus perhaps the Zionites can only duplicate gear that they can bring back from the Matrix, and anything they make up is not going to have the appropriate "drivers" to be compatible.
 * Anyone remember fighting Psycho Mantis in Metal Gear Solid?
 * We've seen that they have access to working man-portable miniguns. Mouse dual-wields the damn things. I can only assume that the agents can detect the wave of panic that would occur as bluepills observed a bunch of people in trenchcoats walking around with artillery, thus bringing them along for most missions would be impractical.
 * Those aren't "man-portable miniguns". Those are automatic shotguns.
 * I would guess that since the Machines are monitoring humanity to prevent the discovery of the Matrix, see Mr. Anderson's little talk with Mr.Smith. Then they would also be guiding technology and as such anything that is created in the Matrix beyond a certain level of sophistication would be flagged and checked out post haste.
 * Uh, I'm pretty sure agents couldn't actually die at all until Neo showed up. When Smith got hit by the train during the subway battle, he just occupied another body inside the train and kept on going. i'm pretty sure killing their human host achieves nothing at all.
 * Similarly, the 'Dodge This' agent, Agent Jones, didn't die, he took over another nearby body.
 * Even Neo couldn't kill an agent; the only reason Smith was no longer an agent was because the system had the three Agent v2s released to confront Neo-level capabilities. That's the same thing that killed previous versions of Agents, such as the werewolves or tengu. Killing an agent only slows them down, so carrying really big guns kinda defeats the purpose.
 * Half of this doesn't make sense and the other half is applying things that happened in the sequel to the original film.
 * A flame thrower is a short ranged, mostly one shot weapon, which, along with the fact that flame throwers tend to EXPLODE, killing the user and maiming everyone near him, is why they aren't used by most modern military forces. and as i recall Neo did try to throw tons of bullets at an agent and that got him no where.
 * Excuse me, flamethrowers are decidedly not short-range (at least, relative to human reach; compared to most ballistic firearms, yes they're shorter range), "one-shot" weapons; and the perception of them being such is due to inaccurate portrayals in video games (not that most video games are accurate portrayals of anything, much less weaponry). A flamethrower is specifically supposed to be able to project fire at a long range. The M2 flamethrower, deployed by the USA in World War II, The Korean War, and The Vietnam War, has an effective range of 65 feet (20m) and a maximum range of 132 feet (40m), which is well within the in-Matrix fighting distances seen in the films. Further, the USA isn't the only country to have ever deployed a flamethrower into combat.
 * The minigun didn't kill the three Agents, it killed the bodies they were using. Since they can just switch to new ones and come right back, there's no point in making the effort to carry around shotguns and flamethrowers just to blast holes in people. The best strategy is to run, and hope you get to an exit soon. It's not because they don't know that Agents can't dodge every bullet, it's just that there's no point trying to fight a battle you cannot possibly win. Neo was the first one (no pun intended) to come along and actually kill an Agent -- but not for long.

Matrix Powers in the Real World

 * Even if I make the gigantic leap of accepting that, on the grounds that (it sounded better in my head), why on earth do
 * That last one is a case of YourMindMakesItReal, I think; he got infected with The Virus in the Matrix and the effects carried over.
 * Yeah, that power doesn't need to work in the real world, because your mind is the same in both worlds.
 * They specifically said that Bane appeared to have suffered massive brain damage from electricity frying his neurons through his implants, thus causing the "delusion" that he was Agent Smith. (Software stored in meat isn't any less rewritable than software stored in disks, it just takes more brutal methods.)
 * Speaking of which, Neo's powers do not work in the real world. He can't exactly fly or do kung fu there. The only powers are the ability to disable sentinels and the golden sight, and even they only work on something that is connected to the Machines somehow (like the Sentinels or the Smith-possessed Bane).
 * Why can't Neo do kung fu? I thought that stuff was just downloading straight into his brain, why must he be in the Matrix to use it?
 * Because he's only downloading the Matrix rules and subroutines for performing kung fu whilst inside the Matrix -- not the physical abilities or attributes necessary to perform it in the real world. Although he says "I know kung fu", it's because he still doesn't fully comprehend the difference between the Matrix and the real world. This is why Morpheus replies "Show me," instead of some line like "So do I" -- because he is trying to show Neo how the Matrix is divorced from reality, and how Neo can bypass its rules.
 * Maybe they can still do real-world kung fu too, obviously without all the Matrix slow-motion stuff, because when Bane is attacking Trinity, she still manages to fight back pretty well.
 * This still doesn't make any sense, however. Given that your "residual self image" or "digital mental self" or whatever is based on your own body, anything you learn to do with said digitial self should be able to be carried over into the real world. Characters still wouldn't be able to do the kinds of physically impossible things they do in the matrix, but real martial arts techniques should still carry over. When Trinity learns how to fly a helicopter in the Matrix, she should be able to fly same said helicopter in the real world. The only explanation that makes any sense is that the characters become so used to having their reality-stretching abilities that they can't function without them. In other words, the training wheels come off the bike, and they haven't learned to ride without them. Come to think of it, gamers who play with cheat codes all the time tend to suck without them. Question answered.
 * Not trying to beat the issue to death, but I would cavil with the suggestion that intellectually knowing how to do something directly translates into the unflawed physical capability to do that thing. If that were the case, all martial arts classes would be a single session, two hours tops, during which you are taken through the physical movements required to perform the technique, after which you are a black belt. Muscle memory is different from brain memory -- you literally have to train the techniques into you so they become second nature, so much that you react unconsciously to an attack rather than think about it. This is the prime difference between Matrix martial arts and real-world martial arts: in the Matrix you aren't physically using your arms and legs, so no muscle memory is required -- it's all subroutine and program manipulation.
 * Hey guys? Muscle memory isn't stored in the muscles but in the various motor centers of the brain, AFAIK. If you download the muscle memories of doing "kung fu" in a simulated body that responds identically to your real one until you learn to bend the simulation's rules, you've downloaded the muscle memories necessary to actually do kung fu in your real body. The lack of Fremen-style combat practice by Zionites in the real world was simply the mistake of training to play with cheat codes rather than training to the maximum of real ability before adding cheat codes.
 * Well how about the fact that while the "residual self image" Neo is in prime physical shape, the "real world" Neo still needs what seems like weeks of physical therapy before even being able to walk? Ditto, while his mind knows kung fu, his body does not, no matter how much of YourMindMakesItReal is involved.
 * That's because Neo's Matrix image isn't that of his physical-world body, which he didn't even know existed until it was dumped from its pod. It's that of the healthy, physically-fit simulated body he'd been occupying for nearly all his life. Note that the Neo we see in the Matrix and Construct doesn't have plug-holes all over his limbs and spine.
 * Also remember that all the people who can plug into the Matrix are effectively cyborgs, with their neural network manipulated so that they can be connected to the system. Who says that there isn't a bit more than that, especially in the One's body, considering that the One is consciously created by the Machines for specific purposes.

Cops as Good as Agents?

 * In the beginning of the first film, why can ordinary cops run as fast as an Agent? Or, for that matter, a Zionite?
 * Masquerade? The machines have a vested interest in not rousing human curiosity too much. The Zionites... not so much, yet having news about a woman running at breakneck speeds all over the place could cause undue pressure on them too.
 * So what about strange happenings like "Wasn't there a door here instead of a brick wall until just now?" or "Great Scott, did that woman just turn into a guy with a black suit and a gun?"
 * The Agents have clearly been shown to have magic technology (i.e. utility programs) capable of modifying memories and whatnot. (Remember Neo's weird "dream" about the "bug"?) Also that they're in prime position for government cover-ups.
 * Seriously, the Matrix is clearly in the tradition of several other movies all about some giant government conspiracy all around you that most people are too blind to connect the dots and see. Presumably pointing these things out is part of how Morpheus' band recruits redpills.
 * The real answer is, they can't and they aren't. Hell, the entire point of the first chase scene is to show the cops getting winded, stumbling, failing to jump across the gaps that Trinity and the Agent are leaping, etc. The chase may only be one or two rooftops, and the cops are already being left behind.

Tank's For Being "The One"

 * How come at the end of the helicopter sequence, Tank is awestruck and says "He's the one!"? If he'd said that right after Neo had dodged the bullets, fine. But what Neo had just done was not get pulled off a building by an awkward weight...tricky, yes, but far from mind-boggling.
 * Because otherwise they'd just be breaking the action scene for no reason. He didn't say "He's the one!" to that particular incident, but to the entire string of awesome stunts he'd pulled in that mission.
 * He also stopped the helicopter from exploding until Trinity was outside the blast radius. The wobbly building windows weren't just a random special effect.
 * All the previous effects had been done by Neo on his own body. Normal humans inside the Matrix have very little problem doing that, and all the dodge-the-bullets effect did was show he was really good at that level. If you take the neural networking metaphor, all redpills have little problem tweaking a few bits that are running their software. The potentials, however, can change the bits of an item that they're touching; it's within their brain's part of the neural network. Neo morphing the explosion of the helicopter he was no longer touching and glass that he had never touched, in a dramatic manner, was well beyond the range any potential showed.
 * The bending glass had nothing to do with Neo, In a situation like that in real life glass would react much the same way, and the matrixes physics are based on reality, thus the bending glass. NO NEO INVOLVED.

Agent Aiming Skills

 * How were the Agents capable of shooting Morpheus precisely in the leg through a solid wall, but unable to hit Neo when he was a stationary target in a helicopter?
 * Shooting Morpheus in the leg might have just been an accident. They just shot at the wall where they thought Morpheus was and one bullet happened to hit Morpheus in the leg. As for Neo, their accuracy probably suffered because they were a bit distracted trying to dodge all of the bullets from Neo's minigun. And who knows, maybe Neo was unconsciously using a bit of his latent One abilities to deflect some of the bullets.
 * Do agents get distracted?
 * Maybe they just run out of RAM.
 * There's a thread on the Discussion page for Real Time Strategy about why AI is (or seems to be) always bad in that genre, and why the game can't simply assign an AI routine to each soldier on the field. The short answer was, "Because your computer still can only think about one thing at a time, and eventually the queue would get so long that it would lag out." While Agents presumably have much more raw computing power at their disposal, it stands to reason that this is still true. (So in other words, More Dakka was always the answer to dealing with Agents: fill the air with so much lead salad that they don't have time to think about anything but dodging.)
 * Smith did fire, like, four bullets at ankle level along Morpheus' approximate running path, most of which missed. He's good, but he can't see through walls.
 * Why not? Have the A.I. Overlords never heard of a patch?
 * The "A.I. Overlords" (presumably the Architect) want the Agents to be reasonably capable of "reality enforcement", while not giving them too much power -- Smith has demonstrated what a rogue Agent is capable of.
 * Also, like Morpheus explained, Agents are incredibly powerful, but their abilities are built on the rules of the Matrix. Making them able to blatantly violate the laws of physics like Neo and some of the rogue programs can would lead to instability in the Matrix program and probably create all sorts of bugs.
 * But why can't they be _aware_ of things beyond their own bodies, even if their _actions_ can't extend beyond what is possible? Like ignoring the fog of war.
 * If you accept the neural network metaphor, their capabilities have to fit within a normal human brain (presumably that of their host). Like the average redpill, they can alter the abilities of the host body within the Matrix, but their abilities are limited to the part of the code running in that human host. Getting further information requires communication, which is a little... slow.
 * Basically, the Agents are working at either the human maximum (Captain America) or biological maximum (Spider-Man) potential of someone with their body types. While they're superhuman in comparison to average people, they can't be given literal superpowers (like X-Ray vision) without breaking the system. The One is specifically special because he can break the system.

The One is Overrated

 * Why is that being the One apparently comes down to flying and poking somebody's heart? You can see the fricken' code man, you've proved that the rules of this system mean nothing to you? Why aren't you pulling crazy crap like standing on ceilings, phasing through stuff, sticking your first through people!? You shouldn't even have to stop bullets, you should be able to reverse their flight plan entirely using them to kill people!
 * Four reasons, two pragmatic, two in-universe. Reason A: The Matrix 1 movie was only intended as one movie. QED Neo's transformation is basically meant to be complete at the end of it; he can fly and is therefore completely unbound by the rules of the system. Reason B: (Following off Reason A.) There ain't much story in "Neo became the One, broke the rules, crashed the Matrix. The End." Certainly not enough to do two more films. Reason C: I don't think being the One means that the rules of the system mean nothing to him. It just means he's able to bend the rules much more effectively than even an Agent can. The flying trick ultimately is changing gravity in a localised way around Neo; he doesn't move in a frictionless way. The bullet trick is manipulating spacetime in a very localised area around him. Doing stuff that really upsets the rules is a lot harder. And no, Morpheus's story that there was a man born inside who could "remake the Matrix as he saw fit" doesn't contradict it; that was a story, a control mechanism, seeded into humanity by the machines. Reason D: "Most of these people are not yet ready to be unplugged." At no point does Morpheus go public with the truth of the Matrix; the Zionites are always fighting a war by way of resistance. Possibly that means Neo can't risk the more flagrant breaches of Matrix physics because it either attracts the attention of agents or really screws with the heads of those still imprisoned.
 * To be a bit more concise: Being The One doesn't mean that he can stop a river, just that he can swim upstream.
 * Well put.
 * For that matter, Agents can't bend the rules of the system; only Neo (and, to a limited extent, other redpills) can do that. True, an Agent can have the maximum number of HP allowed by the system, but they can't do what Neo does, which is play by other rules entirely. Agents are Min Maxers. Neo cheats.
 * I don't see a problem with Neo cheating, given the entire film is basically an aesop of the fact The Computer Is a Cheating Bastard.
 * It's not so much "cheating" as it is Munchkining the living hell out of the system. To use the HP explanation, the max value for that slot is 999. That's what the Agents have. Neo can add another digit to the value. NEO cheats. The Agents are simply NPC's that are unbalanced and WAY too hard to kill.
 * In all honesty, it seems less like a budget or rules case, but more a case of Neo himself not being able to completely accept his status as a physical god. Think of this: in the first film, Morpheus states that Neo was removed from the system far later than nearly all redpills in existence at that time, something that is incredibly dangerous due to (pay attention here) the fact that after a certain age, humans are not able to accept the "real world." Morpheus is, however, willing to risk it because he believes (correctly) that Neo is the One.
 * In the context of my guess here, this information means that Neo, despite freeing himself from the Matrix, still has subconscious ties to "real world" physics, and therefore only does things that are an upgrade to what normal redpills can do (flight relates to redpills' jumping; super speed and "bullet stopping" relates to redpills' uncanny dodging abilities; hyper-combat relates to redpills' super-combat, etc). We should note here that "ghosting," walking on ceilings and walls, direct matrix code manipulation, and copying are all things that others have been seen doing, but conspicuously not Neo himself.
 * Moreover, Neo may simply not be imaginative enough to come up with that many freaky ways to screw around with physics. He didn't get picked randomly for the job of One, he was singled out by the machines to play an engineered role. It's possible that they deliberately selected him for the part because he's not got much imagination, thus ensuring his in-Matrix stunts wouldn't be too crazy for the rest of its systems to process and adapt to.
 * Neo may also be wary of breaking the rules too bad lest he actually crash the Matrix. They do want to bring down the system, but that would result in far more human death than they really want... the idea is to tear the system down bit by bit, not just smash it and send a few million people down the tubes and into the drink. If I recall correctly it's implied that the amount of alteration Neo did towards the end of the second movie in his desperate rush to save Trinity actually damaged the Matrix in ways besides smashing up some of the construct buildings.

The Machines Need to Get a Life

 * What do the machines do when they aren't collecting energy from humans? They have a city obviously, do they have jobs? Do they have individual lives? Or are they part of some sort of... collective entity that exists only to keep itself existing?
 * The machines in Matriculated have some individuality, but likely there's a central hivemind they can tap into as well. As for what they do besides enslaving humans, Goliath has them exploring other worlds (how they got a "Seed Pod" out past Darkstorm is left unclear, as is how they got the main character's ship out).
 * I'd think for the most part yeah, their purpose is simply to keep existing. It's a pretty large feat to even have a machine that does that. But I suppose, over the years, they could have evolved other goals.
 * The movies seem to imply that the machines have individual personalities, politics, goals and dreams very similar to humans. Though we never see the machine city, we did see the train station, which included a machine family who had cut a deal with the Merovingian in order to move over to the Matrix to make a better life for themselves and their children. That doesn't seem very hive mindish to me.
 * Just their child, Sati. Rama-Kandra and his wife are never seen again.
 * The Second Renaissance also shows 01 up close, with traffic and pedestrians wandering about, although the pedestrians are squiddies flying on different paths than larger vehicles. It's probably safe to assume that the Machines are a species, with individuality, hopes, goals, dreams, and desires, but it's a mistake to call them "similar to humans." They're a species of machines, and as such, these words have different meanings to them. This is basically the entire point of Rama-Kandra's monologue; the Machine society is based on entirely different rules and values that seem foreign to humans, but it is no less deserving of being called a civilization. Rama-Kandra also proves that the Machines are capable of dissent; individuals can disagree with governing policy (Smith may prove this already, but he also doesn't see anything worth preserving about civilization; Rama-Kandra is clearly not at odds with who or what he is, or his purpose, he just disagrees with an aspect of an otherwise satisfactory government.)

Putting a Robot on Trial?

 * If the robot from Animatrix: Second Renaissance was put on trial for murder, doesn't that mean it was granted or assumed to have more or less the rights of a human being, which could be taken away upon its conviction? And if it is assumed to have such rights, wouldn't that make its actions basically self-defense?
 * I got the impression that the robot wasn't itself put on trial, but that they were debating the right of the robot to have a trial in the first place. The robot itself was called to speak so it could rationalise its emotional response to the events and prove its humanity. In the end however the council voted to deny machines due process and dispose of the him as a simple defective product (For pragmatic, economic reasons most probably). This injustice is what caused the pro machine riots.
 * Possibly not. Strictly speaking, self-defense works only as long as you are actually in danger (or at least a reasonably convinced you are) and has to be somewhat proportional. The robot is shown killing everything in the house (including the dog), and crushing a human's head with its bare hands.
 * I got the impression that the whole story was Machine propaganda. "You see, you humans tried to destroy us for no good reason, so we just started doing your jobs better than you, so you tried to kill us all again, so you screwed the whole planet trying to destroy us all. See? We're justified in putting you all in jars!" Something like that.
 * Why would a butler robot need to have full-blown AI and enough strength to crush a human head with its bare hands? For that matter, couldn't the machines have been programmed to ENJOY their work?
 * Well, there's a long tradition of ludicrously overpowered SF robots, but maybe it's not a robot 'butler' but a universal robot worker that just gets told/programmed to do a given job. If it was used as a manual laborer or a soldier superhuman strength would be very useful. As regards the robot being able to rebel, perhaps there is a loophole or error in the program, or maybe it just wasn't designed very well (cheap model with lax safety standards?) Maybe true AI is impossible without making free-willed A Is.
 * The robot doesn't rebel because he hates his job. The robot rebels because he's about to be deactivated and destroyed -- and, in fact, insofar as he's devoted to his job, this matters doubly because he, in his own judgment, *has done a good job* and therefore cannot process his owner's whim to have him junked as a logical requirement of his job. In a situation like this, the nascent seed of self-preservation that seems intrinsic to becoming sentient is able to trump duty, when duty is being so clearly callously tossed aside.
 * And obediently accepting it when your owner tells you that your service is done isn't part of the duty a robot would be programmed with? What, did the appliance industry give up on the ol' "planned obsolesence" schtick, somewhere along the future timeline?
 * AI Is a Crapshoot. Humans gave it some decision-making programming, which overrode its order-following programming.
 * it makes some sense to have a helper that is very, very strong. if, for instance a person bought a t.v. that was very large and heavy, wouldn't it be a goodsend to have someone who could carry that TV all the way up, and put it down right where you want it? or a child looses something under the fridge, robot comes in and moves the fridge to get to it.
 * "Why make the robots ridiculously strong" is also covered in the "I, Robot" movie headscratchers. If we assume the same logic was at work there, robots were probably engineered to effectively have superstrength not only to serve but to protect humans. If something heavy falls on a human, it would be expected for the nearest robot to run over, lift the heavy thing off, and if necessary carry the human quickly and untiringly to medical care.

Infinite-Ammo Code?

 * How come it took them until the very last movie (its remake of the Lobby shootout) to discover an Infinite-Ammo hack?? Heck, why doesn't Neo create a whole bunch of Ones by turning whatever code or expanded understanding he has of The Matrix into a training program and downloading it into everybody's heads? Smith proved you can overwrite wetware with software; I was waiting for Neo to do the same.
 * Because expanded understanding is not perfect understanding. He's still learning his powers.

Why Don't Ya Just EMP 'Em?

 * Here's what's bugged me about the final attack on Zion. So, in the first movie, the EMP is depicted as the only weapon against the machines. In the final battle, everyone has robot walkers and rocket launchers, etc. This isn't what bugs me, what gets to me is: why the hell didn't they mount an EMP device in Zion? They could have just set it to repeated blasts to repel the assault. I know, "machines run into EMP blasts" makes for a bad story, but just ignoring EMP? I remember the flight of the hovercraft to bring the EMP to the city, but...not mounting it in the city itself doesn't make any sense.
 * EMP in the middle of the defenses is a really bad idea, hence why that commander got so pissed off at Morpheus for bringing his ship there and setting it off. Sure, it kills all the sentinels, but it also knocks out your own defenses, and then the next wave comes to kick your ass. For some reason, EM Ps seem to only work once, hence why the ships got slaughtered when Smith/Bane activated one early, and why they couldn't just activate it again. As for building one way up and out of range from the defenses, well they really didn't plan on the sentinels coming down from above. By the time they found out about that, it was too late and they had no time to build specialized EM Ps to attatch to the ceiling, not to mention no way of telling precisely where they'll burst through.
 * In 'The Matrix Online' when humanity moves to 'New Zion' they take this into account, EMP mines are stuck throughout the tunnels leading towards zion, the only way in is directly down (Mineral deposits and magma and stuff stop the other ways) and the only way down is by going into a 'dead drop', purposely deactivating your electronics so that you don't get fried, which pisses the machines off something fierce and causes the truce to finally break.
 * In addition, using the EMP would probably ruin all of the machines in Zion that make it livable.
 * "For some reason" is actually a decent reason -- in real life, most EMP generators powerful enough to do something like that generate the sudden pulse of energy required by setting off some kind of explosive. Obviously it's not easy to rig such a thing up again after it's already been blown.
 * The reason the EMP "only works once", is because when you set off that one EMP, it destroys/shuts down all the other EMP generators, along with any other tech in its radius. An EMP is a weapon of last resort, since using it shuts down the rest of your ship. Bane activating it early shut down any other ships close to it.
 * EM Ps only destroy electronics that have current in them. Thats why you shut down your hovership thingy when you are about to blow the EMP. Therefore, any number of EMP Generators could be set up around Zion and the only problems would be charge time between connecting the power and detonating.

Open Cockpits On the Mechas?

 * What bugs me more than this is the Robot Walkers in general. I mean why bother building mechs without any COCKPIT PROTECTION?!!? That's like building a fish tank without using any glass. Absolutely pointless.
 * Why would they need any cockpit protection? Did any of the machines actually shoot at them? No. They just relied on their sentinel claws to rip up the mech pilots. The only defense against that would be some sort of heavily armored "shell" enclosing the pilot that the sentinels couldn't break through easily. Assuming the legs of the mech could even carry this extra armor, this would dramatically increase the weight of the mech and decrease its mobility. The pilot can no longer aim each mech arm independently because he's crammed into an armored metal coffin cockpit. Oh, and you can't put a window in the cockpit because sentinel claws would break through it easily, so the pilot would have to rely on a video screen connected to an external camera (which, if broken, would leave him completely blind). You've turned a light, agile combat mech into an overly complex, overly heavy block of armor that probably couldn't even support its own weight. Congratulations.
 * Why would they need any cockpit protection? How about because each mech is standing shoulder to shoulder with other mechs each holding two massive guns over their heads ejecting thousands of red hot shell casings that are raining down randomly on anything in the general area. After a minute of firing those guns in such close proximity you would be lucky if one pilot out of a hundred wasn't completely incapacitated by thrid degree burns over most of his body! Obviously it wouldn't do much against a sentinel but even a 28g expanded steel mesh or a piece of plexi glass would at least save mechs from being disabled by shell casings. How effective would a modern combat soldier be if a shell casing was to slip into the colar of his vest or perhaps slip behind the back of a seated soldier and fall between his ass and his chair?
 * This troper was under the impression that the mechs were descended from the mechs used in Second Renaissance, were we see the machines cutting through the cockpit protection to rip a man out of it. Cockpit protection was NO GOOD.
 * Just because it is possible to overcome armor does not make it useless. After all there are a lot of weapons that can take out a tank but their armor is still very important and useful. Not to mention an enclosed cockpit with "life support" would provide protection from all of the biological and chemical weapons the Machines should be using.
 * I disagree. The mechs were neither light nor agile. They stuck to static firing positions most of the time. Moreover, window glass is far from the only solution for cockpits, so nobody can say what can or cannot be effective. Even metal grating would be better - at least it would give some time for nearby mechs to give some assistance. Instead of mechs, they should have just built embedded .50 cals pointing at the sky. There was a sentinel in any possible direction, after all. (further, just because armor can be compromised doesn't mean it's worthless)
 * None of the tactics or technology used by either side in the fight for Zion make any sense. After the machines tunneled in they could have easily dropped in any number of chemical/biological/nuclear weapons (being miles underground there is no danger of a EMP pulse reaching the machines) instead of swarms of drones. And if they were sending in machines to attack why not arm them with ranged weapons of some kind? The human battle suits having no protection is ridiculous and if bullets etc work perfectly well on the machines why were Zion's ships not armed with those chain guns too? Of course because the machines have apparently built numerous Zions for humans and then destroyed them (which also makes less then no sense) why no just hide some kill switched and back doors into the machines that maintain the place to begin with?
 * 1. They've destroyed Zion before. I'd say they have a pretty good idea of what works. 2. Ranged weapons would take ammo, and they pretty clearly don't need them. 3. The artists admitted that if the suits had enclosed cockpits, you wouldn't be able to see the pilots. And the ships did have chainguns. 4. Because then the humans could find them and figure out something was up. And who said the machines build the various Zions?
 * Oh god. 1. Honestly? Your argument is "they should know how to do it, so the way it is in the movie therefore makes sense"? 2. They "clearly didn't need them"? They had to use swarm tactics just to get past the machine guns. This is not an effective use of resources. 3. Do you know how flimsy that reasoning is? The various Gundam series, Top Gun and other fighter plane movies, and hell, even Star Wars have shown how to make the audience identify with piloted machines without actually removing the cockpit. A paint job for the hero machines could have worked, with closeups on the actors for whenever we need to see the pilots screaming.
 * 1. That they did it before just makes the tactics used that much more unbelievably dumb. There is no way they defeated the combined armed forces of humanity by throwing a swarm of drones at us. So what happened to all the know how and weapons they would have had to develop the first time? 2. There is no way sending 20 drones to die so the 21st can reach your target is more efficient or effective then having one or two stand off and fire bullets/missiles/etc and resupplying them as needed. 3. That just about proves my point. The tactics and technology used were nonsensical because someone thought it would look better that way. 4. Who else besides the machines could possibly be rebuilding Zion after they destroyed it time and time again? The first human refugees from each reboot of the Matrix need a place they can survive to already be prepared for them or they would simply starve in a sunless world incapable of supporting organic life. Not to mention the technology used is clearly above the late 20th century technology that even the best educated people just coming out of the Matrix would know how to create.
 * Zion makes precious little sense in any aspect. Even if you assume Neo hits the reset button - they're "restarting" the human race with 23 people. We know you can implant memories in people but it still makes no sense! Just... EVERYTHING. It's a true Voodoo Shark - the explanation behind Zion becomes an increasing mire of implausible justifications. OK, assume 23 people with memories relevant to context are put in Zion, with their hovercrafts, production facility, life support and manual on how to save people from the Matrix... oh... that's already crazy... and then we're supposed to believe that the apparently energy hungry machines want to attack Zion regularly (given what Morpheus says)... and then that the One will manage to survive - unless the Machines were trying to kill him pretty hard... and magically only develop weapons that evade EMP in the last week of the "war". It just goes ON and ON. Regardless of whether there people predicting the Matrix, so many events in the real world transpire EXACTLY as is needed - it really would have made more sense for the "real world" to simply be another level of the Matrix construct.
 * No one in the future(in most fiction not just the Matrix) knows how to use nuclear weapons properly. 1)Swarming tactics should not exist in the future because tactical nukes will always trump a zerg rush. 2)When the humans are originally defeated they don't just say "screw it" and fire off hydrogen bombs into the upper atmosphere creating a lot a electromagnetic pulses that would ruin any unsheilded circuitry on the planet. That would kill all the robots and leave the humans able to rebuild their own machines. 3)No one uses faraday cages to protect their equipment from EM Ps. 4)Enhanced radiation warheads(neutron bombs) would produce free neutrons that can pass through feet of solid steel, depleted uranium, and lead. Neutron fluxes destroy both organic cells and solid state circuitry. Neutron bombs should be the weapon of choice against both machines and men. Basically we get a nuclear weapons taboo because lauching missles and cannon shells with nukes in them as your primary means of attack wouldn't be very cinematic.
 * Before a perfectly good point gets lost, I'd like to reiterate it: why would they need mechas at all and why would they need them manually controlled in particular? They had a hundred years to prepair - they could just set the whole perimeter of the bay with AA-guns! No need for complex, cumbersome and fragile hydraulic robots, no need to deliver ammunition by hand, no threat to soldiers - just a small enforced pillbox with a stash of ammo beneath it and a battery of barrels pointing to the ceiling. And gunners could seat in the HQ, sip cocoa and play Incoming with the squids! As for the Rule of Cool, the whole encirclement of the bay simulteniously bristling with Big Fully Functional Guns (think of the Autobot city shifting into war mode in the Transformers animated movie), wouldn't exactly yield to a bunch of pistol-wielding robot-loaders. I even recall them having a turret in Zion, so I don't get why not place dozens of them.
 * This only works if they know years in advance that the machines are going to attack the dock and that they are going to attack it with swarming tactics. Otherwise, their weapons need to be flexible enough to respond to wherever the machines are attacking in whichever manner they are attacking. And the machines would likely just avoid attacking any place where such extensive defenses had been built into place. To quote Patton "Fixed fortifications are a monument to the stupidity of man".
 * Unlike the situations Patton probably refered to, a) the machines most likely had no way of knowing what kind of defences humans had, and b) little to no choice in the attack direction. How are you supposed to attack an underground city if not by burrowing directly down to it? Especially if you're a hard-logical machine. As for flexibility, a battlefield as cramped as the dock didn't allow for much maneuvering anyway, so mechas in fact acted as turrets, only unstable, fragile and with both gunners and loaders exposed. BTW, the absence of bigger guns is another thing that bothers me.
 * Has anyone ever heard of Metal Storm? Their guns can fire up to 1,620,000 rounds per minute. You can, basically, flood the entire dock with bullet fire for a few seconds, and no machine will be left flying. And this is just technology we have now.
 * Their "1.62 million RPM" gun is a 36-barreled prototype that preloads all of the bullets into the barrels and discharges the round electronically (this is, in fact, how a bunch of the more notable Metal Storm weapons work); this is how they can even achieve such a ridiculous rate of fire in the first place - there are no mechanical or moving parts. The short of all this is that, while they have a prototype that can unleash 1.62 million rounds per minute (technically, 45,000 rounds per minute per barrel), the weapon system has total capacity of 180 rounds - or 5 bullets per barrel. Want more bullets in your clip/magazine/barrel? You have to either make the barrel longer, or add more barrels, and reloading is going to be a bitch.
 * Also, "flood the entire dock with bullet fire for a few seconds"? At 1.62 million rounds per minute, that's 27,000 rounds per second. Once again - the 36-barrel prototype has 180 rounds, total.
 * Leaving aside that the scrappy human resistance living in deep underground tunnels using cobbled-together technology basically made out of scraps in a cave doesn't necessarily have access to experimental railgun technology.
 * Designers have said that closed cockpits would make more sense, but they wanted audience to be to recognize characters. Also, in The Second Renaissance UN controlled mechas have closed cockpits.
 * The key to a mobile gun platform is that it is mobile. There were fixed AA guns in the dock, but if they are taken out, that's it. That sector it's covering is lost. Whereas with AP Us, you can move them about to areas as needed. As for the cockpit issue, I think the philosophy behind their design was simplicity and economics: resources are limited in Zion and you want to make a weapon that can be produced with as little material as possible. Too much material and its too heavy/slow. Too many electronics and it might be susceptible to all sorts of electronic haywire (They are fighting machines after all).
 * Except that all the room they had was one rather narrow platform, where they could hardly move at all, so it wouldn't have made any difference really. As for the cockpit, surely they weren't THAT short that they couldn't wield a couple steel slabs on them, were they? Hell, just take off some metal doors and use them as makeshift shields, it would've been better than nothing (not to mention, it would've looked hillariously)! And in their conditions heavier would actually be better, since the machines used ramming tactics, and dodging them was not an option in any case.

Why Don't Ya Just Possess Him?

 * In the first film, the Agents are coming to arrest Neo at work and Morpheus leads him through the office by cell phone, helping him avoid their gaze. Fine, neat scene. But then it's revealed that Agents can take over any software (read: human mind) still hardwired to the Matrix, which at this point Neo is. So if the Agents wanted him that badly, why go to the trouble of arresting him at work? Why not just take him over and bring him to wherever they need him?
 * Because their original plan was to use Neo's willing cooperation to bring 'the terrorist' Morpheus to them, while pretending to be ordinary Federal agents arresting him for an ordinary crime. When Neo refused to take the deal in the "phone call" scene, they then went to plan b) stick a bug in him. But since the Zion Resistance can remove bugs, it can be seen why they didn't choose the bug as plan A.
 * The real reason is that it would break the dramatic pacing of the big reveal. But for an in-universe explanation: I don't recall any people that were taken over by agents being released from that state without dying (or the Agent dying). It's possible that it's a one-way process.
 * Nah, in the games it's revealed an agent can leave a human without killing them.
 * As far as the agents knew, Neo was just another potential resistance member. They had no idea that he'd become a god-like being that'd bring their demise, that is, until the end of the first film. Killing him doesn't solve anything, as freedom or death both eliminate him as an energy source. As stated, they only wanted to capture him so he could provide information about Morpheus. Unlikely to happen if he suddenly gets possessed and transported to a compound.
 * Speaking of that, why don't they try to make a program to just transfer the memory files to the central computer or such?
 * Also, there's a simpler in-universe explanation: operators watching the Matrix code can detect agents just by the code visible on the screen. When Smith shows up to confront Neo in Reloaded, Link says "Whoever he is, he's not reading like an agent." If an agent had taken Neo over, Tank (in the first film) would have recognised it a mile off and the Resistance would have broken contact. Indeed it's possible that's how the Resistance knew Neo was bugged - because of something a bit "off" about the way his code appeared on the screens.

Machines Dissecting People?

 * In the Second Renaissance, why did the machines need to dissect and generally screw with human bodies to study them? Presumably humans would have created medical robots that should know all of this stuff already.
 * Maybe they were studying humans further? I don't think there was mention of humans already owning the "machine/human interface"-tech, and it would have been sort of important if there had been half-human cyborgs in the war.
 * Human-made medical robots would be programmed with ethical limitations. 01's bots have no such qualms.
 * Not only human made robots, a huge part of all medical/anatomical/biological/psychological research on living beings this side of WWII has been ham-stringed by ethical considerations in real life. The machines would be able to do all sort of research that hasn't been touched for that reason and which might prove useful to the war.

Backup Copy Agents

 * Why don't the machines keep backups of their useful software, like agents and such? Why don't agents just respawn after they're "killed?" (Jumping bodies doesn't count; that's not proper respawning.)
 * And why not? Agents are not regular programs, they don't have "physical" avatars. Possessing bodies and jumping to another when the former is killed is their default mode of operation. As for the other programs shown, all except the Oracle and the Architect are exiles, they were scheduled to be erased anyway. The machines wouldn't bother to actually respawn them.

The Matrix Has Lousy Programmers

 * Why is the Matrix written as the worst possible way to run a simulated world, ever? The 'programs' you see running around should merely be avatars of the programs, not the programs themselves. Just to make a real-life analogy, have you ever actually seen an MMORPG where killing a monster destroyed its programming code?
 * Because that's the way the program works. Remember, we don't have any sentient, photo-realistic world simulation programs, so we have nothing to compare it to. Complaining about how the program is built when we can't even program something anywhere near that in the real world is equivalent to someone from the middle ages complaining about airplanes not being able to hover in mid-air or fly sideways. The reason it doesn't is because it can't.
 * Some (military) planes can hover in mid-air and fly sideways.
 * It's actually exactly what you're saying. This is how the Agents function; their code is never in danger. Exiles, on the other hand, are in the Matrix illegally, and they have no safe haven to store their code while they live on the inside; they have to be totally in the simulation in order to have a chance at evading detection.
 * Because in the Matrix, you're not attacking graphics with graphics, you're attacking the program itself, and the stuff you see is just how the brain interprets the electrical signals. Agents are just special.
 * Exactly. The Matrix is not a graphical simulation of a computer program, it is the program. The Agents, and other programs, don't see a world made up of buildings and cars and people, they see the code directly. Humans see the world as they do because that's the way human brains interpret the information they're being given. The entire point of the first movie was Neo learning to see the Matrix as it actually was, rather than as his human perceptions were telling him it was.
 * I agree Dwarf Fortress is better coded than the Matrix
 * Tell ya what, you code a simulation that can completely convince a single human brain that it's reality and I'll accept that you're knowledgeable enough to determine that one that does it for at least a few million human brains is written badly.

No EMP's When They Nuked 01?

 * Okay, so we know that electromagnetic pulses stop the machines dead in their tracks. And we know that in the Animatrix, it talks about how the humans A-bombed the living daylights out of the machine home city. But the Animatrix talks about how the bombing was entirely ineffective since radiation doesn't effect the machines in the same way it does humanity. Okay... but what about the EMP that the a-bombs put off? Shouldn't that have been even more devastating to the machines than anything else?
 * Chalk it up to the Animatrix creators not doing the research.
 * No, they did do the research in this case. Nuclear bombs only cause noticeable EMP's when they're detonated in the upper atmosphere. Near-surface explosions wouldn't have any. As for why the human military didn't think to EMP the machine empire to begin with, or exactly how the machines could survive thermonuclear temperatures and yet be vulnerable to some fast-moving electrons... that's another question.
 * Even if the radiation and EMP were both ineffective, a nuke is still a big freakin' bomb. It should've accomplished something.
 * Also, even primitive 20th-century human technology had developed the capability to shield some aircraft flight systems from EMP attacks. Presumably the machines also developed this capability thus rendering syuch a tactic ineffective. Although, again, why exactly said machines chose to abandon said shielding technology in subsequent machine models (or indeed didn't retrofit their squiddies with anti-EMP technology after it was used against them even once ... is another question.
 * Probably the same reason not all soldiers deployed into war zones today are outfitted with full body armor: 1) cost, 2) sacrificed mobility, and 3) individual preference (some solders don't want to wear body armor in certain situations because of the added weight and the loss of maneuverability).
 * Except: (1) Cost is not an issue if you control the planet and all its resources, and the machines have "all the energy they need". (2) The squiddies have some kind of anti-gravity or hovercraft system; they almost move frictionlessly. Mobility seems a minor consideration. (3) Individual preference from a machine?
 * Don't forget that the machines actually want to give the humans the impression that they have a small fighting chance.
 * Even if the Machines survived the EMP and radiation caused by the bombs (which is rather plausible), how did they survive the explosion itself? Everything near Ground Zero of a nuclear explosion is practically vaporised, and the resulting shockwave causes extensive damage several kilometers away (depending on the yield of the bomb). Considering the amount of nuclear weapons launched at 01 it seems impossible that the Machines were not wiped out. Even if the initial bombardment was not an all-out attack (to minimize environmental damage), there should have been no similar concerns after Operation Dark Storm, since Humanity was on the losing side. In fact, they did use nuclear weapons against the Machine army, but strangely accomplished nothing. How is it possible that nuclear weapons (especially if used in large numbers; even today we have thousands of them available) were so utterly ineffective against the Machines?
 * The writers probably just wanted to point out that even our most powerful weapons were completely useless against the machine onslaught. There's no real reason why they shouldn't have worked. Only because the writers chose them not to.
 * The narration itself answers this, it mentions that unlike humans, "the machines had little to fear of the bombs' radiation and heat". They clearly found ways to counter the effects of nuclear weapons.
 * Ionizing radiation actually accounts for relatively little of the total energy released by a nuclear explosion; most of the energy is from thermal radiation (heat) and the actual blast (pressure). So... the Machines must've had some crazy good structural supports/integrity to be able to survive a nuclear blast (or several).

Does Dodging Bullets Look Impressive?

 * What was so impressive about Neo dodging the bullets in the first film? OK, it looks cool on the surface, but that's only because of special effects, which Trinity didn't see. In "reality" all that happened was he did the limbo and fall on his ass, most shots by that agent would've missed anyway.
 * When the Agent dodges bullets it has that crazy blur effect to show he's moving super-fast. Trinity said "You moved like [the Agents] do. I've never seen anyone move that fast." implying that, from Trinity's perspective, Neo moved fast enough to create that crazy blur effect.
 * Before then, when you stood your ground and an Agent shot at you, you died. The end, Do Not Pass Go. You survive only by running and running fast. By contrast, Morpheus said he's seen men empty entire clips at Agents and hit nothing but air. Neo's probably the first person anyone has seen be shot at by an agent like that and survive.
 * True that all he did was "limbo and fall on his ass," but it becomes impressive when you realize that he started his limbo after the agent's first bullet left his gun.
 * Exactly. Though we only saw it from Neo's perspective, going by Trinity's line ("you move like they do") it's safe to say that, as said, he was actually doing the same blurred, 8-way twisting effect the agents do when they dodge bullets.
 * An Agent fires a buttload of bullets at a guy. Next thing you know, this guy's on his back like everyone else Agents have shot at -- except he only has a graze on his thigh. Pretty damn impressive.

Cypher's Secret Operator?

 * How did Cypher plug back into the Matrix to talk to the Agents without an operator?
 * He likely made the excuse of using the construct for some reason (lady in the red dress, maybe?) to get plugged, and simply shunted over to and from the matrix from inside.
 * He set it up to jack him in automatically. That's what he's doing when Neo surprises him. I think I got this from Art of the Matrix, but I'm not sure.
 * Still doesn't wash for pragmatic reasons. In order to connect to the Matrix, the Nebuchanezzar has to be at "broadcast depth", which is something only Morpheus as captain seems able to order. And the implication is that the Zionites only stay around at that depth for as short a time as possible because the longer they stay the more chance the Machines will pinpoint their location. So Cypher doesn't realistically have a chance to contact an Agent on his own; missions are too short, and operators seem able to pinpoint a person's location without too much difficulty; Tank pinpoints Morpheus's location even though he's in a building with massive security around it and three agents.
 * Remember that Cypher can reach the Agents from anywhere in the Matrix simply by making an unsecured cell phone call.
 * But he can't have dinner with one of them over the phone.
 * You need to be at broadcast depth to hack into the Matrix. If you're entering the Matrix with the willing cooperation of the machines, it would presumably be easier. Hell, if nothing else they could send down a Sentinel with a relay antenna and order it to loiter just outside the Nebuchadnezzar's sensor range. So, on an earlier mission into the Matrix, Cypher gets a moment alone and makes a phone call to the Agents, saying that he's willing to sell out the Resistance and asking them to set up a meet. The System then makes arrangements to set up a discreet radio relay to the Nebuchadnezzar and calls Cypher back later on his phone with a time and place. Since Cypher is the guy who takes the night shift as operator, he has lots of time left alone with the system to plug himself in without anyone noticing.
 * However, this raises the question of how he got back OUT.
 * Maybe he had Tank or Mouse helping him, under the pretense that he wanted to do some solo training, or wanted to pay a late-night visit to the "lady in the red dress". He could then change the readouts so that, while he's secretly talking to the Agents, it looks to them like he's just doing whatever he claimed he was plugging in to do.
 * If you're entering the Matrix with the System's willing cooperation, then logging off should be a piece of cake. Remember, the Operators are just hacking into functions already in the Matrix's code -- the Matrix itself could use those capabilities as well, if it chose to.
 * Confirmed by the sequels; if the System agrees to let you jack out, you don't need an exit.
 * Who says he'd been in the Matrix when he talked to the Agents? Maybe he was in a Construct and had phoned in the codes so the Agents could hack into it for their meeting.

Lock Hates EMP's?
"Lock: The council awaits your report. You'll forgive me for not attending, but I need to find a way to salvage this debacle. Roland: Did I miss something here, Commander? I thought we just saved the dock. Lock: That's the problem with you people. You can't think more than five minutes in front of your faces. That EMP knocked out every piece of hardware, and every APU. If I were the machines, I'd send every sentinel I had over here right now. "Saved the dock" Captain?, you just handed it to them on a silver platter!"
 * Why was Lock so pissed that they fired an EMP late in Revolutions? They were already losing the battle anyway.
 * The EMP was fired off early and devastated their entire defensive line.
 * No, that was the EMP fired late in Reloaded when they still had a bunch of ships, which was indeed fired before the other ships could get out of range and wrecked the defensive line. As for the EMP fired late in Revolutions, I don't know... the only hint we have is this conversation:


 * Probably ol' Deadbolt had smaller reserve weaponry in place (even on film it wasn't only AP Us being used in the defence; there were handheld missile launchers as well, for example.) It wouldn't have been prudent militarily to commit everything just to defend the first assault. However, if his reserves needed electronics in any way to function, the EMP would've rendered them useless, not to mention that any meaningful way to communicate and/or coordinate a defence was similarly zapped. Which basically reduced the defence options for Zion down to handguns, rifles, knives, sharp sticks, and conducting said defence by yelling to one another or using smoke signals and mirrors.
 * Ockham's Razor suggests two other answers: 1) bad writing, and 2) Lock just continuing his role as The Scrappy. (Srsly, this troper was glad to see Harry Lennix play a likeable character in Dollhouse, because he wasn't sure the man could actually do it.)
 * The answer is quite simple. Commander Lock is a colossal jackass. Bear in mind that earlier on in Revolutions he discusses the arrival of a ship with an EMP with a man who is presumably his 2IC. Lock says that if the EMP was fired they'd lose the dock, and is told in response that the dock has already been lost. He blows his stack because he's an arse, as both Reloaded and Revolutions make entirely clear. And he doesn't count as The Scrappy because you're not supposed to like him.

Machines in the Middle East?

 * In the Second Renaissance we see that the machines have founded their city in the Middle East (presumably Saudi Arabia). But what nation would voluntarily cede its territory to allow for the creation of such a city?! I'd imagine the Wahhabi monarchy of Saudi Arabia would consider the machines to be abominations to boot, making it all the less likely a place to build 01.
 * Metagaming it, it's because that whole area is rife with religious significance. In-universe ... who said it was ceded without something in return? Could be the Sauds traded the territory off. 01 seems to be formed right in the middle of the Quarter of Emptiness; if human beings can't live there, and the machines offered some sort of technology in payment, why wouldn't they give it to them?
 * The question is based on an unwarranted presumption: that there has been no geopolitical change between now and the time of The Second Rennaissance. We don't know what the situation was when 01 was founded. It could be that the land was UN owned for all we know.
 * Considering that people had developed fusion and AI, the Saudi's oil wealth may have dried up. There would definitely be some significant change there, we just don't know what form it would take.
 * The phrase "Cradle of Mankind's civilisation" (not the exact wording, but pretty much what was said) suggests they went for Mesopotamia, which is in what we now know as Iraq. Again, the lack of any mention of quite how they came into possession of this land opens up all kinda of Unfortunate Implications, more so given the geopolitical climate of the region at the time the Animatrix was released.

Too Much Matrix Makes Smith Go Crazy?

 * Why does Smith say that sensation in the Matrix is driving him mad? How can and why should a machine feel anything in the Matrix?
 * He's not going mad; he's getting angry. His hate is the product of a kind of machine evolution -- where other programs have developed to feel love (Rama Kandra) or greed (the Merovingian) Smith developed the capacity for hatred, probably as a consequence of his revelation that humans are like a virus.
 * Short, boring answer: There are humans with him in the Matrix, and he really hates humans.
 * More complicated (but cooler) answer: The machines are advanced intelligences, able to inhabit digital realms of staggering complexity. By contrast, the Matrix is a construct that -- per its intended use -- must be comprehensible to humans and their biologically limited ability to process reality. To a machine of sufficient intelligence, such a place would be astoundingly mundane, perhaps even scatological. ("It's the smell...")
 * Then again, Smith seems to be the only machine that has a problem with this, and he's not even that advanced compared to some of the others...
 * The purpose of the Smith program is to capture and kill the One / the resistance. The Architect makes clear in Reloaded that Smith cannot actually be allowed to succeed. Smith knows that he can never succeed, and that he's doomed to fail over and over again every time the Matrix is reloaded. That knowledge drove him over the edge.

Agents Afraid to Die?
"10 DETECT ANOMALY OR EXILE 20 TELEPORT TO ANOMALY OR EXILE 30 ELIMINATE ANOMALY OR EXILE 40 GOTO 10"
 * During the freeway chase in Reloaded, Morpheus fights an Agent on top of a trailer and at one point nearly falls off but grabs the Agent's tie. But the Agent will just respawn if he dies, so why exactly doesn't he simply let himself be pulled down along with Morpheus, leaving the Keymaker alone and defenceless atop a rig that can easily be taken over? By the very same Agent, even?
 * First, agents struck me as very direct programs with a simple command program:


 * Second, taking over the rig doesn't help, because someone has to be driving it for the agent to be able to get onto the roof and eliminate the Keymaker. He can't just crash the rig, because the agent's host would likely die in such a crash and there wouldn't be a concrete assurance that the Keymaker expires also. The agent has to take out the Keymaker personally, therefore he can't just let himself die.
 * Only crashing the rig (into another rig) was precisely what they decided on later. And judging from the resulting explosion it would suffice if it wasn't for Neo. And anyway separating Morpheus from the Keymaker would make their work much easier.
 * Keep in mind, the Agents can be Ridiculously-Human Robots too. Just look at Smith even before he's 'freed'. He probably just wanted to personally kill Morpheus in a fair(ish) fight. If you think about it, he could have easily just whipped out his gun and blown the both of them away.
 * In the first film, Smith also had no problem with holding himself and Neo in front of the incoming subway train. My guess is that during the highway fight, Agent Johnson was optimally placed and didn't want to sacrifice himself at that moment.
 * Agents probably just have innate, reflexive self-preservation protocols programmed into them, for a variety of reasons. The guy didn't just let himself be pulled over because his programming's reaction to almost being pulled over was to try and save himself. The only time Agents are shown just letting themselves be "killed", they make a conscious decision to do so ahead of time.

Morpheus's Invisibility Cap?

 * I have a small Just Bugs Me, though ... in the first movie, when the first squiddies are prowling around the hovercraft. In response, the team shuts down their power sources and goes really quiet. Morpheus then puts on a black cap or hood. The only logical reason to do this in context is because the machines can see with enough accuracy to tell the difference between shadows and a black man's bald head. Two problems with that: (1) the squiddie looks straight at the hovercraft without detecting anybody and (2) Morpheus doesn't tell all the whiteboys in the house his crew to conceal themselves or, y'know, hide. So why the hat? Tinfoil radiation blocker? Any thoughts?
 * This troper always thought it was because Morpheus was cold. They shut down all the power to the ship, which would include the heaters.
 * This troper simpoly believes it was Morpheus' lucky cap. So he wore it so as not getting detected by the sentinel.
 * This troper thinks it makes him look bad ass. Isn't that what all ship commanders go for?
 * It's to keep down any glare coming off of his shiny bald head.

Who Needs Codes When You've Got Drills?

 * So many....For one, in the first movie we hear all this stuff about needing "codes" to access Zion. So how do the machines invade? THEY BURROW IN. WHAT WAS THE POINT OF ALL THAT CRAP IN THE FIRST MOVIE. GAHHHHHHH!!!!!
 * First, you're assuming that Agents have the same information as the Architect does. I don't think that's a safe assumption. Moreover, the different programs' purposes are different: Agent Smith's function is to ensure the stability of the Matrix, take out redpills where possible, and ensure Zion is eventually destroyed - once he completes the latter function, he no longer has to be in the Matrix at all. I'd argue he doesn't even know the significance of the One's path until he's accidentally reloaded into the Matrix. The Architect, on the other hand, has a vested interest in pushing Neo into becoming the One -- since it's only by Neo returning to the Source that the Matrix can be successfully reloaded and a new cycle begin. The Machines attacking Zion was part of that cycle, and just as importantly a "cue" for Neo to be pushed further down the Path of the One.
 * This neglects something really simple. The codes they were asking for were, to quote, "the access codes to the Zion mainframe." (iirc, anyways) Mainframe. Like, computer mainframe. You know...the one that we see in the third movie. This may even include the OS on their hovercraft. This Troper is inclined to assume that the idea would've been to then break into one of the hovercraft, and from there into Zion, from there to all the rest of the hovercraft...bad things happen. Assuming the machines actually mind the sentinals and such getting blown up, that'd have been a lot simpler, quicker, and safer. Tunnelling into Zion may originally have been a backup plan, or even a diversion.
 * The original script had the oracle's apartment be inside the Zion mainframe. There was an entrance into it from within the matrix, that you needed the codes to use. Getting the codes would have meant that they could get in and just shut down Zion (presumably air, heat, water, food, etc), without having to invade.

The Sun's Right Up There!

 * In the third movie, as Trinity and Neo fly one of the ships, after they get thru the Electo-Magnetic field of death what do we see?....THE SUN!!! What the hell,why bother with humans, couldnt the machines have built like huge solar-panel towers to funnel the needed power?WHAT NEED WAS THERE TO BOTHER WIT HUMANS AT ALL!!?!?!? GAHHHHHHHHH!!!!!
 * That's the fundamental plot device on which the entire movie is built, but you're asking the wrong question; it should be, "Why use humans as a power source when nuclear energy is about two million times as productive as that many humans locked in together?" As it is, solar power's knocked out as an option because the Machines can't penetrate the scorching of the sky to access solar power.
 * The scorching of the sky that is at such a low level that running your hovercraft up a hill of sentinals and "jumping" off the peak will put you above it? While I agree the fundemental plot device requires you to believe they need people farms instead of power plants, this scene is so totally unnecessary and shows such a massive flaw that it really should have been cut. It's like being trapped on the ground floor of a building because the elevator is broken and moaning about it while sitting on the stairs.
 * I seem to remember from some supplemental material somewhere that the Dark Storm Effect is made up of nanomachines, or was instigated by nanomachines. The machines are still functional inside the Effect, and attack and deactivate any mechanical presence that goes into the Storm. Might also explain why the hovercraft seemed to conk out after its swan dive, too.
 * The nanomachines that make up the Dark Storm are mentioned in Mahiro Maeda's commentary for the two Second Renaissance episodes of The Animatrix. Maeda worked closely with the Wachowskis on those episodes. They're also mentioned in the script for The Matrix Revolutions, during the scene where the Logos enters the clouds. Quote, "The molecular replicators immediately drain the life from the Sentinels and they fall dead--".
 * So why not tunnel vertically into every mountain that reaches up above the Dark Storm, then convert each one's peak into a massive solar collector?
 * I thought that the idea was that the sky was just available (but only recently), but that the machines had been using humans for so long that they didn't realise that after all this time project Dark Storm would have faded. I mean it's pretty ironic that if they just looked a couple of kilometres up, they would be able to find the sun. I really thought that entire sequence was just saying "the machines with all their logic and perfection cannot even conceive of the idea to look up now when it didn't work thousands of years ago." I really thought it was saying something about the human concept for imagination. ... I may have been wrong though.
 * Did anyone notice how they were crashing into the ground until Trinity restarted the ship? I just thought that with all the lightning going on in that cloud, and machine that attempted to get up there would shut off.
 * That is exactly the reason they flew into the clouds in the first place! There were too many Sentinels for Neo to destroy so they flew up into the clouds. How come nobody noticed that all the sentinels that followed immediately got zapped and plummeted back down? The hovercraft itself shut down as well, it's why they friggin' crashed!

What Happened to the Twins?

 * Where did The Twins go? I mean, they disappeared with no explanation, not even in the supplementary material. What gives?
 * They were probably supposed to have been destroyed by the freeway explosion: it engulfed them while they were trying to phase their way out of the fireball, and then we never saw them again.
 * No explanation in the supplementary material? It's explained in The Matrix Online. The Twins' code was spread out into the simulation's stratosphere after the explosion. The Merovingian was able to artificially create copies of illegal reality warping codes that were originally used by Agents in an old test version of the Matrix (these codes were sealed away because they were too overt and caused rejection and/or death in the bluepills that witnessed them). He used these codes to bring the Twins' code back together. From Chapter 6.1 onwards, the Twins appeared in several of the game's live events and critical missions.

Getting Medieval On This Matrix

 * If the humans are using telephones/modems to hack into the matrix, WHY THE FUCK ARE THERE TELEPHONES AND MODEMS IN THE MATRIX??? Set the scene: Medieval matrix, all the excitement, none of the security risks.
 * Those aren't real telephones and modems, they just represent communication ports and nodes in the grid. They'd still exist in some form no matter what the Matrix looks like to the redpills. In a medieval setting, they'd just appear as something native to that period, like a parchment and quill that the heroes use to "write" themselves in and out of the Matrix. Apart from that, the machines were aiming for the next best thing to a perfect world, and the closest match their non-human minds could figure out was the modern world.
 * There's also the fact that Zion (especially those who help the One fulfill the "prophecy") are unknowingly helping the Matrix to continue to exist. The Machines (or at least the Architect) aren't pleased with it, but they're a necessary part of a flawed solution that makes the thing function.
 * This troper suspected that the Human-Machine war may have destroyed a huge chunk of the historical record, so the Machines might not have even known enough about the medieval world to accurately replicate it. Consider also that the real world is already significantly more advanced than the world the Matrix simulates, so the machines were already trying to limit the human's access to technology.
 * Even if historical records from earlier periods survived, their simulation-designers probably needed lots of audio, video and photographic records to work with. They wouldn't be able to create a very credible medieval simulation, because all they'd have to illustrate what they were building would be paintings and woodcuts.

Hey Trinity, the Phone's Right There

 * At the beginning of the movie, Trinity is at a hotel, a bunch of cops and some agents show up and chase her, she runs, and gets out. Then at the end, Neo leaves the Matrix through a phone in the same hotel. Why the fuck didn't Trinity use this phone to exit instead of running far away to reach an exit?
 * Not all the phones work all the time. Mission Control has to establish an exit point on their side, and tell the heroes where to go to find it. For whatever reason, Tank couldn't connect to the hotel that time around.
 * When was it ever said they were the same phone, or the same location? And Neo doesn't exit in a Hotel, he exits in an apartment building.
 * The building seen at the beginning and end of the movie is the Heart O' The City Hotel. You can see Smith look up at the hotel's sign right before the movie cuts to Neo running through an alley to climb the building's fire escape. Smith managed to cut Neo off and shoot him before he reached the hardline because he'd been there before and knew where the hardline was before Neo did.
 * It is the same hotel, even the same room: 303 (An allusion to Trinity's name: Same is found on Neo's apartment: 101). At the start of the movie, the hardline was cut, forcing Trinity to find another exit. At the end of the movie, we realize that the things that the Agents change in the Matrix aren't persistent--hardlines will return to normal because that was their original inherent design programming before the Agents twisted it.
 * I have one question for the first scene and one for the last one. First, when the agents arrived to the motel, why didn't they immediately posses the cops who were arresting Trinity? It's not as if possessing people in public was a complete taboo - they did it a lot when they chased Neo in the end, and they probably could just rewrite cops' memories or just kill them all and write it off on Trinity. Second. Why didn't Smith blast the phone in the room while he waited for Neo just to be on the safe side? He's a program, he's supposed to be meticulous.
 * As to why they didn't possess the cops immediately: I believe the intent is that the scenes of Trinity in the room and the Agents arriving are not in strict chronological order. When Smith arrives, he says, "Lieutenant, you were given specific orders ... those orders were for your protection ... no, Lieutenant, your men are already dead." I take this to mean that by the time the Agents arrive, Trinity has in fact already killed the cops in the room - we just see it slightly out of order for dramatic effect.
 * The phone trinity was using was tapped at the time IIRC. They mention something to that effect during the credits sequence. Perhaps you can't use tapped phones to exit, or it would have led the machines to the ship.
 * Yeah, the simplest answer is that the Machines just shut down that hardline temporarily while they knew Trinity was there. It could be that the machines also have some use of those hardlines (they must exist for some reason), so once she was out of the area they stopped blocking it.
 * The agents don't know where Neo's going. There might be a hardline around that doesn't have people nearby - remember that while they can pick up on people's shock and surprise and teleport to that location, they can't do it if nobody's around. They don't have the same "overmonitoring" system that Operators do to watch Neo as he runs, so they don't have any choice but to pursue him on foot and break cover, as it were. As for why Smith didn't blast the phone - it's unclear, but he may not have had time; he might have just arrived when Neo opened the door. Remember Smith cannot have possessed a person to get to that location -- otherwise Neo taking him over and exploding him also should have insta-gibbed Smith's host as well. Also, Smith's getting a bit wonky even by this stage -- he's suffered a defeat at Neo's hands, he's carrying a grudge for him and he wants to kill him himself.
 * The reason Smith doesn't blast the phone is simple: The operator would know if the hardline went down. The moment it gets cut, Tank would tell Neo to go to another hardline elsewhere. So Smith needed that hardline fully operational if he wanted to ambush Neo.

Pulp Fiction Homage?

 * Did the scene in the first movie, where Neo gets picked up by car after he had that... bug implanted remind anyone of Pulp Fiction ? When Switch (I think she was sitting in front of Neo) turns around, gun in her hand, I (and a few of the people I watched the movie with) immediately thought of I Just Shot Marvin in the Face. Trigger safety is not a big thing in the Matrix, is it?
 * It may very well have been an Homage to Pulp fiction, which is pretty funny when considering that Pulp Fiction was an homage to... pulp fiction. For an in-universe explanation it was a tense moment and Switch either forgot to use trigger safety, or simply does not know/care about using it. A second explanation could be simply because Neo refused to listen to Morpheus and chose to meet with the Agents. So she was pointing the gun at him in order to fire if he suddenly became hostile.
 * Neo didn't "refuse to listen to Morpheus and chose to meet with the agents". He lost the phone, and unless he was going to suddenly figure out how to get down from the outside ledge of a 20 story office building on the fly, he didn't have any choice but to be captured by the Agents.
 * IIRC, Morpheus had already told Neo to use the paint-scaffolding to get to the top then hung up the phone. Neo was holding the phone because...well...he was distracted. There was no conversation going on. Neo tried to get around teh support beam and chickened out.

Is Morpheus Bad With Dates?

 * OK, in The Matrix, Morpheus says this to Neo after his rebirth: "You think it is the year 1999, when in fact it's closer to the year 2199." Now it is established that we're 200 years into the future. Yet in Reloaded, Morpheus tells the crowd that, "I remember for one-hundred years we've fought these machines!" Bwuh? So it's now 2099? By that calculation, the war began in 1999. A lot can change in 100-200 years, so which is which, Morphy? Are we in the year 2099 or 2199?
 * I may have answered my own question by remembering that Morpheus also said, "I can't tell you exactly what year it is, because we honestly don't know." and it's possible tha the war began in 2099 thereabout. Still, just irks me a bit.
 * I think Morpheus is talking about Zion's war with the machines, not humanity versus machines as a whole. The 21st century was the first war and the Matrix's creation, and Zion's war began around the start of the 22nd century, which is what Morpheus meant by "for one hundred years we've fought these machines". He's way off since Zion's gone through five cycles already, but from his perspective, the year's roughly 2199.
 * Here's the noodle-baking answer. In "Reloaded," yes, Morpheus notes that Zion has fought the Machines for nearly 100 years. Neo learns that 5 Ones have existed before he, and that the Machines have destroyed Zion that many times (per the Architect), with each One accepting the option that Neo did not. In addition, the Architect notes that there were two unstable versions of the Matrix before that (of which the Merovingian first arrived in, bringing in his little minions). That means that the Matrix program eventually decays (like Windows 9x) every 100 years--and that the Matrix, if not just the war--has been fought for at least 600 years, if not older. The year in the real world is closer to 2600 to 2800.
 * Morpheus only said it was closer to 2199 that to 1999, which implies that the former was the minimum date he considered plausible. He has no way of knowing what the maximum plausible date might be, only that it's something a lot higher than 1999.
 * In fact, Morpheus specifically says, "We can't tell you exactly what year it is, because we don't know." The dialog actually makes it quite clear that 2199 is basically just a guess. So, the answer to your headscratcher, OP, is "You didn't pay attention to the movie."

Scientists In the Matrix?

 * Are there ANY scientists inside the Matrix? If our world were a simulation, however crafty, sooner or later people would figure out stuff doesn't add up. There are people out there who built a piece of scientific equipment the size of a city just to see what happens when large hadrons crash into each other. With this in mind, recall the episode Beyond in the Animatrix that showed there are actually blatant bugs in the Matrix physics engine.
 * If the machines are the ones writing the code for any experiment an in-Matrix scientist might undertake, then they can certainly ensure that the test appears to generate results consistent with that scientist's environment being real and not a simulation.
 * Since the Matrix's layout mostly seems to be a single giant city, it's possible that there really aren't any scientists, for exactly that reason. Each person in the Matrix probably assumes that there are scientists that they've just never met, and hears about them and sees them on television and such. If anyone gets too scientifically inclined and starts noticing all the weirdness (as Trinity's dialogue in the club implied happens to lots of people), they either stumble upon the Resistance and become a "red pill", or the agents notice them making too much noise and handle the situation.
 * They probably chalk up their results to machine or user error. Occam's Razor suggests that as a highly-preferable alternative to "Reality is a complete sham brought about by Machine overlords." Those that persist probably Go Mad From the Revelation and get themselves discredited.
 * The oracle dropped a line about ghosts and other supernatural beings that were in fact errors in the matrix... and few people really buy ghost and vampires stories. And even when they do, going from "I saw a ghost" to "Our world is a computer program" will look like a major case of Epileptic Tree. Plus, the agents can just wipe out memory like they want, so if a scientific or otherwise influent person encounter a bug, they just reset him. There, problem fixed.
 * There are other locations inside the Matrix besides the Mega City. In Reloaded, we see the mountains where Neo is teleported from the Chateau. The first movie mentions the Heathrow airport and the fact that Morpheus is hunted by the governments of many countries. Enter the Matrix shows a post office and an airport. The Animatrix shows what is obviously Japan, and the USA and France are mentioned. I guess the Zionists just prefer to operate in that one city for some reason. As for scientists, I presume the glitches are random and rare enough and not reproducible, so they get chalked up as hallucinations, equipment malfunctions, and the like.
 * No, The Animatrix showed a training program that was based on Japan, not the Matrix. And just because the bluepills think there's more to the Matrix than the city doesn't mean there actually is. When Neo asks for his location, Link replies "you're not going to believe this, but you're all the way up in the mountains," but he doesn't say which mountains or anything more specific: the way he says it suggests that there's only the one range beyond the city. If we're only shown the megacity and all the action takes place within it, conversation of detail suggests that, like The Truman Show and Dark City, the city is all that really exists. Post offices and talk about airports and other countries could just be Insurmountable Waist High Fences, virtual props created to maintain the illusion that the Matrix is bigger than it really is. (For what it's worth, the Matrix Wiki says "the Matrix simulation covers approximately a vast swath of landscape, some 1000 miles in diameter from the Downtown center of the Megacity at the center to remote terrain such as "the Mountains" surrounding it".)
 * Oh, wow. A 1000-mile diameter circle yields a surface area of 785,000 square miles. Smith refers to "billions of people" living in it. With just 1 billion residents, that yields a population density (1273 ppl/sq mi)equivalent to South Korea, carpeting an area the size of Texas and Alaska combined. 2 or 3 billion people puts it up into the equivalent of Bangladesh. If there's mountains, bodies of water, and other large areas effectively devoid of human inhabitants, it starts creeping towards city-states like Hong Kong or Singapore. Under those circumstances, there really can't be more than just the one big Megacity. I'm trying to imagine an entire continent looking like this, and it quite boggles the mind.
 * Not a training program, actual Japan (in "Beyond"). A character in "World Record" refers to her aunt in France. Neo's birth data, as displayed by the Agents, claims he was born in Capitol City, and if there is a Capitol City, then logically there are other cities. People actually use the airport to fly somewhere -- where? Finally, Path of Neo shows the United States Congress being overtaken by Smith. Conservation of detail is a law about fictional narrative and has nothing to do with the design of virtual realities. Sorry, but Occam's Razor points to a large geography inside the Matrix. Saying there are no other cities in the Matrix because all the movies take place in Mega City has no more basis in fact than claiming that the Moon is a cardboard disc glued to the solid sky because you personally never visited the Moon.
 * There's nothing to say that "Beyond" is set anywhere except an outlying neighborhood of the same city. If it was really set in Japan, why would the agents, who are treated as local authority figures, still be caucasian and look and act exactly like the movie agents, instead of something more geographically relevant? That would make sense if Yoko lives in a Japanese district of the city, not so much if she's supposed to be in another country thousands of miles away. Also, a character referring to "her aunt in France" means little. Did we see the aunt? Does the aunt really even exist? The Matrix is a false reality. It's a lie. That's the whole point. You can't trust anything inside it. The television shows what the machines want it to show, the newspapers have whatever headlines the machines want them to have, the maps look like whatever the machines like. The whole point is that none of it's real. So the only thing to be trusted is what we actually see, which is a gigantic city with lots of districts and the surrounding mountains. As for the Capitol building and Capitol City, for all we know the city itself is called Capitol City and thought of as a national capitol by the bluepills. The Matrix isn't just time travel into the 1990s like some people seem to treat it. It's a virtual ant farm, an MMORPG that mimics daily modern life. Given the choice between an entire, unseen virtual planet and what the movies actually showed us, which is the megacity and its surroundings, I prefer going with the megacity and its surroundings as the Matrix, especially since that fits with the theme of the Matrix as a mental prison, a bottle-world that drives some people mad. The Other Wiki presents both explanations side by side, and the Matrix wikia goes with the City in a Bottle one, so it's up to the viewer to decide which answer they personally prefer.
 * The Japanese Agents would still be caucasian because they are the classic MIB, part of the usual image (MIB page image and popularish movies not withstanding) of which is "they're all white guys"
 * That's not in-story, that's a meta inspiration for the Agents: that's like saying Neo can shut down Sentinels because he's Jesus, or Morpheus has powers in the Matrix because he's the god of dreams. There's an Asian district in the megacity, and the presence and recognized authority of the agents as we've seen them in the movies can be taken as evidence of "Beyond" taking place within it. From the Matrix wiki: "The International District is a district of the Mega City. It is essentially a conglomerate of Asian cultures, and mainly consists of small shops. Despite the presence of several powerful gangs of exiles, no single interest really dominates in this district."

Stupid Caretaker Robots?

 * Also, one of the most obvious flaw: when Neo wake up in the real world, he is welcomed by a "caretaker" robot, who stare at him for some seconds and then... just flush it down a drain, where he is safely recovered by his allies (who somehow managed to get that close to the farm without being attacked by sentinels), instead of, you know.... just killing him outright and recycling him. Because no matter what the redpills do before and after the matrix, they have to escape the farm at one point, and it seems like the perfect moment to attack, seeing as how they are stranded on a huge tower with their muscles atrophied and their body still connected to the system via a bunch of pipes...
 * This troper assumed that the bot had been reprogrammed by Morpheus and co. I mean, it pretty much releases Neo from his restraints. It's hard to interpret as anything but helping.
 * This Troper saw it as a "dumb" AI. It got the signal that Neo's pod was showing no life signs or whatever, and went to disconnect the corpse and flush it down the drain. It's not designed to know the difference between the living or dead. In hindsight it's not a great explanation (the machines know red-pills have to come out somehow and should know this is when they're at their weakest), but it's better than nothing.
 * The One is vital to the matrix, and the rest of Zion is by extension. The caretaker robot left Neo alone because it was supposed to.
 * Or maybe flushing a vat-human down the drain is simply standard procedure for whenever something goes wrong with one of them. If they're dead, they get dissolved into nutrient soup; if they're alive, and awake due to a glitch, they drown and then dissolve. Either way, there's no need for it to kill him once it's confirmed that he's awake and therefore no longer a quiescent little coppertop: drowning in the pipeline will do the job just fine.

Cypher's "For" the Confusion?

 * Does it bother anyone how badly Cypher (or Joe Pantoliano) mis-emphasized the sentence when he explains to Neo why they always have to view the Matrix in code? Quote: "The image processors work for the construct, but there's way too much information to decode the Matrix." It took this troper ages to try to understand just what the hell Cypher meant before realizing he should have emphasized the word "construct".
 * This troper was also thrown somewhat by this strange emphasis on the "h".
 * Things like this happen. Either things kept screwing up the take and that was the best one they got, or it was late in the day and everyone was tired and didn't notice the wrong emPHASis until later when they didn't have time or money to go back and reshoot, or whatever. Or, theoretically, it's deliberate, to indicate that there's something "not right" about Cypher... that he just doesn't seem to be functioning properly.

Mental Projection or Mental Self?

 * Does anybody else have a problem with the line "It is the mental projection of your digital self"? To me, it just seems the wrong way round. Maybe it's just personal preference but "the digital projection of your mental self" sounds much more logical, given that it is the computer projecting what you think you should look like.
 * It sounds unintuitive, but it all depends on which way you look at it. Your "digital self" is the block of interactive code that's racing through the Matrix and interacting with other bits of code. The "mental projection" is what makes that code look like a guy wearing a trenchcoat and sunglasses.
 * The funny this is, in Path Of Neo, when you encounter Larry and Andy before the final battle, they introduce themselves before adding: "Or rather, these are the digital projections of our mental selves." My theory is that both versions are technically correct: the RSI is a mental projection into a digital world of a mental image rendered digitally. Signs point to the theory that the RSI is more than just the plugged-in mind creating an image of itself; that it is in fact a fully formed digital "body" that the minds inhabits.

Why Don't Ya Just Nuke 'Em?

 * In Revolutions, why didn't the Sentinels just drop a bunch of nukes into the city once they finished drilling through?
 * Same reason they didn't do it the first six times. They want to save the city so they can re-populate it later. No sense in throwing away a perfectly good city.
 * Well, then why don't you just use tons of deadly nerve gas? Or napalm. Lots and lots of napalm. They seem determined to use the strategy that will waste the maximum amount of machinery as possible.
 * I'm presuming the reason has something to do with why they keep re-populating and encouraging the rebellion of survival in the first place - (could just be that the first time round they said "hey, this works, we'll just keep on doing things the exact same way...")
 * Also; machines have hive-mind tendencies were individual consciousness is integrated with the whole, so I'm guessing the individual destruction of a few hundred thousand sentinels doesn't really bother them (Values Dissonance people!)
 * Also, at the end of Revolutions, all humans still part of the Matrix would be given a choice of staying or leaving. How would they really react? "I got some good news and bad news. Let me start with the bad news: your life's a total sham. The good news is, you can get out of the sham and live the rest of your days in an Absurdly Spacious Sewer, eating goop! So, whaddya say?" I mean, in the first movie, Neo almost had a heart attack after being told the true nature of the Matrix!
 * For me that was about the only intelligent part of the sequels. We're told that people who are connected to The Matrix will only accept the program if they are given a choice, even if they're only subconsciously aware of it. With peace between humans and machines there's no need to lie anymore, so people can be free to accept the relative peace and safety of The Matrix, or the filthy sewer of Reality. Most people, when faced with that decision would willingly choose to live in The Matrix, and the status quo is maintained, but without crazy trenchcoated saboteurs running around.

Matrices All the Way Down?

 * How do the Zionites know their level of reality isn't just another virtual world? Isn't that the kind of faith they're fighting to get people out of? Alright, they see the machine empire and the people-pods, but really, if the machines can design a fully believable reality, why stop at one?
 * I think they sorta have to believe their world is the real one, or else where does it stop? If our reality is a Matrix, is the next 'highest' one a Matrix too? Is it Matrices all the way down? At some point, you just have to take it as fact that the world you're fighting for is the real one, or else you'd just fall into despair and inaction.
 * If you accept that they need humans as batteries, then you will have to accept what this means: that the machines can't let any single human go. Seeing as how they prefer functionality over epic, it makes sense that the next layer up is another simulation. Doesn't stop anyone from believing it is real because it has more limitations placed on it - the Zion level is, by all means, a near-perfect copy of "the real world", which means you would fully believe it was not the sim. Further, take this: if you were to claim in Zion that this is all a dream, all a sim, you'd probably be treated for some sort of "Matrix madness." (they had a term for that in the films)
 * Given the nature of the first film, the matricies all the way down theory seems a plausible way for the W brothers to have included the Socratean theory of nature into their myriad of borrowed concepts.
 * BRAHHHMMMMMMMMMM!!!
 * Doesn't Neo gain the ability to manipulate "reality" as well as the Matrix at the end of Reloaded? I don't recall if it ever really fully explains that, but that would be some pretty good evidence that the "real world" is just another Matrix and he learned how to apply what worked in the simplest one to the more complex one.
 * Neo only gains a limited ability to see and influence things built on the same code as the Matrix. He is only ever shown exercising any power over things that originate from the Machines, such as Squiddies or Agent Smith's meat puppet. The second is probably justifiable because Smith is partially living in the neural network installed in all Coppertops. He never gains the ability to fly, stop bullets, or anything like that in the Real, meaning it's almost certainly, well, real.
 * It would mesh well with the Architect's plan for Neo to deliberately repopulate Zion after the war. That would work a lot better if the machines controlled Zion and could just wipe it clean, clear out all the bodies and sentinels etc., instantly, as well as help Neo and the others to "find" adequate sources of food and somehow-still-working ancient technology. However, it would destroy the premise that the redpills are out of the (main) Matrix preciesly because they couldn't accept it; why then would they accept the Zion part of it?

Trinity's a Bad Negotiator

 * In Revolutions while Neo is stuck in limbo at the train station, when Trinity, Morpheus, and Seraph go to deal with the Merovingian at Club Hel. He asks for the Oracles eyes in exchange for Neo which obviously he wasn't going to get, Trinity eventually gets her gun on him and he surrenders Neo. The problem with this is two reasons first off in Enter The Matrix its implied that the Merovingian is a vampire so a shot to the head would do very little, secondly they had another bargaining chip in the fact that Neo could stop the Smith virus something the Merovingian should have feared.
 * When was it implied that the Merovingian is a Vampire? This troper doesn't even recall him *appearing* at all in Enter the Matrix.
 * I don't recall him appearing in Enter the Matrix, either. He has a fuck ton of vampire and werewolf programs in his employ (why, I have no idea), but it never gives an indication that he's a vampire.
 * They're closer to his version of the Matrix, thus they're easier for him to control.
 * It's more implied in the movie (per Persephone) that the Merovingian was more like Neo. He was likely this in beta 2 of the Matrix (where the Architect says that a second version was redesigned "...based on your history to more accurately reflect the varying grotesqueries of your nature." Beta 1 was an unacceptable utopia. The second was more like a haunted house where things went "boo" and tried to eat you--no choice, only cause and effect. Given the Merovingian's minions and his complete distaste for choice, preferring cause and effect, he was likely similar to Neo in his role to stabilize beta 2. It may also be why he holds so much influence, even enough to attempt to kill the Oracle to attain her power.

Where Do The Redpills Go?

 * What do the families of the people they free think of their disappearance? Especially since, aside from Neo, most of the minds they free are kids, what about their parents? Is everyone they free an orphan? What happens if a potential "One" happens to have a big family who loves them very much and would kick up a fuss if they were to suddenly disappear? And along this line of thought, does anyone actually *have* parents? If people are no longer born, but grown, how does anybody have children?
 * I would guess that whenever someone jacks out of the Matrix preemptively it runs a program that maintains the escapeds digitial image and properly prepares a death(most likely accident or suicide). Now as for the issue of parents the machines probably collect samples for the creation of fetuses to feed humans and whenever an impregnation occurs in the Matrix the machines use the two correct samples to create a child so as to not have a faulty digital self. Say for example inside the Matrix you were born to a white family but outside the Matrix you were in fact an asian child, this could lead to a rejection of the Matrix. So as measure to prevent this the machines match accordingly.
 * I got the impression from watching "The Kid" on the Animatrix that red pills who chose to leave the Matrix left behind a body. Admittedly, the kid's a unique case, but we don't see what happens to the Neo's body after the red pill program is done with it. When he jacks back in, he probably has a new avatar.
 * Actually, I would think most redpills are single, pale, wan, isolated hermit hacker types. Ie, people who long ago stopped having much contact with families and the real world. Neo's most ubiquitous human contact before being dragged out to the club seems to be with clients/customers and his boss.
 * I think that's Fridge Brilliance. People who don't accept "the program" are probably going to be antisocial, too, since all their lives they have felt something's wrong with the world, and thus are trying to remove themselves from it, if only unconsciously.
 * There doesn't really have to be an excuse. In real life a truly astonishing number of people go inexplicably missing every year and many of them are never heard from again.

Fabric in Zion?

 * Where do the Zionites get the fabric for the clothes they wear outside of the Matrix?
 * Probably scrounging deserted cloth shops and likes, and/or stripping people killed in the war.
 * Most of their clothing seemed of natural fibers. Ever heard of hemp? A persistent little weed that grows quite well in artificial light, makes strong fibers--and smokes good, too.
 * Or, when preparing Zion, the machines might have seen that need and compensated them with it.

Hell is Other Bluepills?

 * Would the definition of hell be existing inside the Matrix, but having a boring life?
 * Isn't that why people chose the red pill in the first place?
 * What, and living in a Crapsack World taken up to eleven doesn't suck balls? The Crapsack World I'm referring to is the real one, by the way.
 * From an internet post I saw after Reloaded came out: "So, I take the redpill only to spend the rest of my life in a cave with a bunch of techno ravers. I totally get Cypher's character now." Although the implication I took from the red pill/blue pill thing was that the blue pill would just erase the memory of Morpheus et. al. but it wouldn't deal with the feeling of displacement that a redpill has. That is ... a blue pill is a death sentence, because eventually the Matrix will drive the guy mad since he can't get out but can't accept the program, either.

Is the Architect Sexist?

 * In Reloaded, the Architect tells Neo that after he visits The Source he'll have to select 23 people to restart Zion: "sixteen female, seven male". What's up with that? Why not make it 12 female and 11 male (including Neo that would be 12 of each)?
 * Presumably because women can only have one baby at a time, so having more women to fewer men can let you get more babies if you only have a limited number to start with.
 * But why would the Architect care about the Zionites breeding? Looking at the rave scene, most of Zion's inhabitants had plugs, and were therefore redpills from the Matrix. If all the women were getting pregnant, who would be going into the Matrix to free more minds?
 * They would still be going in to free people because freeing people is the whole point of the resistance. But you still need a viable population on the outside, and until Zion can rebuild the resources to go into the Matrix, they're going to have to be self-sustaining.
 * His perfect machine mind has calculated that two females for every male is the optimal rate.
 * Then all that AI research wasn't for nothing after all!
 * The Architect obviously thinks of humans as just animals. He has no concept of culture. As such, monogamy would be an alien concept to him. Humans by nature aren't monogamous. It was simply impressed on us by thousands of years of cultural evolution. Once you get rid of that, it's just mathematics. Feelings are irrelevant when survival is at stake. He figures one man may impregnate and support two women for the first generation. Then the ratio would stabilize.
 * Also don't forget that they mostly unplug children, who still need nurturing. Women tend to be more nurturing then men.
 * Only in specific cultural contexts. Not necessarily in a biological sense.
 * It's a cultural context that's influenced by biology. The mother spends more time with the child instead of hunting, gathering, or doing other important work. Not only is she recovering from giving birth, she also needs to feed the child for some time after it's born. In a sufficiently small population, where every life counts (in the survival sense, not the ethical sense), it's simply not pragmatic for the mother to do anything beyond caring and nurturing the child for the first few months of its life.

Turning into Sati?
So… Was some poor Indian girl suddenly possessed by the spirit of Sati? Or was some dude’s residual self-image changed to that of a child, just like he would have become agent Thompson? Could she possibly run in the Matrix without hijacking a blue pill, because she is considerate and completely unlike those mean agents? Thinking about it, none of the Exiled displayed the ability to jump hosts, except when real life wrote the plot for the Oracle.
 * The way I understood it, the Matrix is a network of human brains, while the Machine World is a network of computers. Sati, a sentient program, was conceived in the Machine World. She then exiled herself into the Matrix.
 * I imagine there's a difference between "jumping" hosts and a program having its own body.
 * My guess is that programs like The Oracle and The Merovingian can't possess humans, only Agents can do that. As The Oracle said, the Machines apparently allow certain programs to move into The Matrix as a form of exile if they face deletion due to obsolescence. It wouldn't be too hard for The Matrix to simply construct a digital avatar for them. If a program's avatar is "killed", the system will construct a similar replacement.
 * The Oracle does apparently have a human host, and was forced to jump to another one between the second and third movie, but it'd make sense for her to be a special exception like the agents. She's meant to be a unique program who can understand humans, who can work with them and figure out where the Architect's going wrong with the Matrix. She probably co-exists permanantly and peacefully with a single host's mind, and relies on them to help her relate to other humans. As for the exiled programs like Sati and the Merovingian, yeah, they seem to be pure avatars with no human hosts at all.
 * That was not a human host. In the words of the Merovingian, that was a shell. In the computer sense. The Oracle's "body" was just a GUI: the part of the program that defines what it looks like. That was what was deleted: when the Oracle switched from looking like Gloria Foster to looking like Mary Alice, that was like switching from Gnome to KDE, nothing more.

No one can be told what the matrix is?

 * This pivotal line has always bugged me. Of course you can be told what the matrix is; that's how they were able to make a movie about it. Was Morpheus just being secretive to get Neo to join his cause without full disclosure, or is there some other reason for this that I missed?
 * I think the idea is more along the lines of, "Well, we could tell you, but you're not going to fucking believe it if we do."
 * Seconded, and in particular that belief is the key thing. Redpills know there's something wrong with the world, but even they (with a couple of very notable exceptions) can't will themselves out of the Matrix as such, it takes a disruption of the I/O carrier wave and then disengaging him from the system - i.e. hacking his brain. Besides, Morpheus's line is a QED: by the point he says that line, he's told Neo where the Matrix is, and that it's all around them, and that it's a prison for his mind. Net result on Neo's perceptions? Nil.
 * Also recall that this is after Neo's already seen some Serious Shit™. A lot of it he simply tried to rationalize away and convince himself there was some logical explanation for it still rooted in the worldview he knew... heck, he was clearly even trying to do that about the tracker robot stuck in his stomach. Sitting him down and explaining the whole thing in excruciating detail would have done precisely nothing. Anyone who expected the truth to be pleasant after Morpheus' speech would be kidding themselves anyway.
 * Agreed: This is the same reason many cannot contemplate the nature of faith. You can't explain it--it must be experienced in some way for it to be real. Unfortunately we can't unplug people as easily as Neo was to see the nature of faith as he sees the nature of the Matrix.

Communication in the Matrix

 * The Architect's main role in the continuation of the Matrix is to meet the One when they return to the source and persuade them to reset it, allowing the system to continue. Neo's one is different (no pun intended) because Trinity is in danger. The Architect realises this and comments on how it will break the cycle, possibly dooming them all. Two problems I see with this; Why did the Architect tell Neo about Trinity's peril, seeing as he was the only source of info on the Matrix in that room? Secondly, the danger was that an Agent is attacking her. The Architect is presumably the Head Honcho of the Matrix, so why didn't he tell said Agent to back off?
 * The Architect has to tell Neo because Neo, being an expression of humanity's fundamental desire live free (the systemic anomaly), has to make an informed choice. Basically, the One is the avatar of humanity, chosing in every cycle to reject the system or preserve its existence. It has to be an informed choice, or else it's worthless. Besides, the Architect built the matrix, but he doesn't run it.
 * Your first point makes sense. However, even if the Architect didn't control the Matrix, would it have been so hard to send a message to whoever does control it (or directly to the agents) that their target had to remain safe?
 * It wouldn't have really made any difference. The choice was for Neo to either let the Matrix crash, or to reboot both it and Zion, which meant every living redpill had to die. Even if the agent hadn't been there, Trinity's death was still a necessary sacrifice in order to continue the cycle. Her being in danger at that moment just presented Neo with the decision in its most painful, direct form: in order to save the Matrix, Neo has to let everyone in Zion, including Trinity, die instead.
 * Good answer. Just one last thing; the Architect warned Neo that reentering the Matrix would cause a crash and kill all the bluepills, yet the only consequence we see is an explosion in one building (the one he leaves). The Matrix continued as normal. If Neo's choice had to be informed, how could the Architect lie about the crash and not the other stuff?
 * I think the Architect meant that the Matrix would begin to crash if he made that decision. Going by the Oracle's dialogue later, the One's existence always triggers an instability that threatens to crash the Matrix. Smith was the instability this time around. Normally, the One makes the choice to reboot the system, which dodges the problem: had Neo done that, Smith would have been wiped out right then (that's probably happened each time before too, with each viral enemy getting destroyed by the reset before it became a threat). Because Neo chose to keep his humanity and save Trinity, Smith just kept getting stronger, until Neo had to find another way to stop him from destroying everything.
 * Cool. That answers all my questions. Thanks.

The Internal Clock Broke

 * Time in the Matrix must be one hell of a Mind Screw. The problems I see with it are:
 * Why haven't any bluepills noticed that it's always 1999? //
 * If time can't progress forward or backward, then how does in-universe history stay on a consistent timeline? For instance, if Columbine happened in the Matrix, would it suddenly have happened in 1998 once that date comes around in the Matrix again?
 * No, it's not always 1999 in the Matrix. At the very start of the first film, it's 1998 (the first text on the screen reads "Call trans opt: received. 2-19-98 13:24:18 REC:Log>."). We know that the One has rebooted the matrix five times before, so it's roughly 30 years between reboots (assuming Morpheus' guess that the real year is 2199 is anywhere near accurate). Maybe the Matrix goes through the years 1970-2000 each time.
 * The way I read it was that the one hundred years that Morpheus refers to in 'Reloaded' is the near-complete cycle of Matrix 6.0. When Morpheus explained to Neo in the first movie that it was "Closer to the year 2199" he was Guesstimating from his personal knowledge of history, which did not include knowledge of the other iterations of the Matrix. Therefore, it's probably closer to 2699 when the movie takes place, but each one hundred years the internal clock in the Matrix resets to 1900 (roughly the time when hardwired telephones started becoming household items). I could be wrong though, that's just how I figured it in my head.
 * I had originally assumed the same thing: that the Matrix would reboot in 100 year cycles with the resetting of Zion. However; this presents some continuity problems. How does the matrix account for history? Historical events like war, famine, epidemic are fundamental to technological progression and we can easily trace back the history of the telephone, the television, etc. Lack of historical record leads to myth and speculation, which would weaken the "reality" of the Matrix. If the Matrix is repopulated with brand new "souls" each rollover, how could the machines assure a coherent progression to the 1999 we see in the first film? This assumes that some element of free will is present for the human batteries. It is possible that the Matrix has pre-fabricated personalities that act as vehicles in Matrix for the batteries while fulfilling their function in vitro. The reboot cycle must be long enough for at least the oldest person to have experienced a life cycle, unless they are preloaded. 30 years would not allow for any older extras/characters in Matrix.
 * I always thought the matrix time was in a loop so every new years on 1999 would loop back to an earlier year and altered minds accordingly.
 * But that doesn't work. Time isn't something as consistent that can be rewound back a year and just change everyone's memory. What about all the researchers and scientists who make big breakthroughs or discoveries in 1999? Do they just forget all their work at New Year's and go back? People are making progress and that is what years are marking. Is all the progress of 1999 undone every year? How could that not be incredibly jarring to the people's minds?
 * Uh... You just answered your own question. You said that "time is rewound back an year and [they] just change everyone's memory". Then you complain that it is impossible for people to "forget all their [scientific] work at New Year's". What? Doesn't the definition of "change everyone's memory" state that they would forget their work?
 * Erasing memories wouldn't necessarily erase all the deeper neurological changes imposed by having lived through those experiences, though. If I start off 1999 liking dogs, then get attacked and mauled by a dog in the summer of that year, and finish off 1999 terrified of them, then that's going to have caused my neurons to establish new "dogs = bad stimulus!" pathways by the time the clock resets. Even if I don't remember the attack, I'd be left with a sudden and inexplicable fear of dogs that's hardwired itself into my brain, for no apparent reason.
 * Why would you assume such an experience-based fear would be "hard-wired" into you? I'm not sure there's any scientific basis for that.
 * You're forgetting the Matrix reboots every time a One emerges and then reaches the Source. Presumably that takes roughly 100 years or so. That's where the restart on the clock happens each time.

Rebel With a Stupid Cause

 * Why the hell are the Zionites causing so much death and destruction in the first place? This problem is similar to the above folder Bluepill-Killing Heroes, but while that question is easily answered by saying that they have no choice but to deal harshly with all potential enemies, this question is why are they fighting in the first place? Yeah, the Matrix is terrible, blah blah blah. Um, actually what's so bad about it? People live normal lives, they go to school, get a job, get married and so on and so forth. It's almost exactly like real life was before the machines took over, except that every once in a while a person can't accept the false reality. This is not a Crapsack World, it's actually very much like the real world, possibly better. While freedom fighters in most stories, like the rebels in Star Wars, are resisting a brutal dictatorship that commits atrocities with or without provocation, all of the machines except for corrupt ones like the Merovingian seem pretty content to let people live their lives. If people didn't rebel, all of the nasty things you see in the movies wouldn't be happening: the Agents would have no purpose for existence so they wouldn't be body snatching people and throwing them into harm's way, the unknowing cops and soldiers and whatnot wouldn't be slaughtered for being in the way, and life would pretty much continue as normal. When you look at it like that, the Zionites seem like extremely selfish assholes.
 * That's one way to see it. The other way to see it is that the entire human race sans the Redpills are being bred as slaves, live in an elaborate prison, have their very bodies taken over by the guards of that prison whenever they want and sacrificed if they see fit, are forcefed their own dead, are murdered or have their memories altered when necessary, and all this is done to sustain the machines that enslave them. Even if you assume that some people would prefer that setup, they don't have a choice until the end of the series.
 * Its kind of like the book Brave New World, everyone is genuinly and honestly content with life and dont question the fact that it has been engineered somewhere outside their control. Its meant to bring up a moral dilema in the viewer of which is better, happiness or truth. The Zionists are simply those who believe it is better to live in a crapsack world because a truthful existence is the only "real" existence.

Smith is actually a Machine "Redpill" and the Machine equivalent of "The One"

 * In the first when you compare the other Agents to Smith, he's acting in a very abberant manner, having apparently been active apparently rather a long time and has killed many Zion rebels. When you watch the behaviour of the other two Agents, they seem to wait for conformation of orders or for information from the system when dealing with rebels, whereas Smith seems to act intuitively and actually gives them orders on how to proceed. This is noticable at the end where he figures out how to beat Neo to the phone, whereas the other two travel together through the building seemingly in a logical manner.
 * Evidence for him being a "Redpill" is that he orders the other Agents to "Leave" him along with Morpheus, they seem to be slightly perplexed by as it wasn't something they were ordered to do. He removed his earpiece so that the system couldn't hear him tell Morpheus how he feels about the Matrix and uses the word "ME" when he talks about escaping and considers himself a prisoner just as much as the humans are. In effect... he Unplugged.
 * Then when the other two Agents come in, they realise "He doesn't know!". They even share a look that that isn't how Agents behave.
 * Evidence for him being a Machine "One" is that he is destroyed and killed, but decided to come back, mirroring Neo's death and ressurection. He also at the end desplays the ability to manipulate the Matrix itself.
 * In essence then... the question "Why do you continue to fight, why do you persist?" "Because I choose too" could also apply to him.
 * It does fit with the symbolism of the series, if Neo is The Messiah, then Smith is his Anti-Christ. Though if Neo becoming the One is part of the architect's plan, this begs the question, did he plan for Smith too.
 * Smith was always meant to be the anomoly that threatened the system if Neo didn't reload the matrix.

Why Didn't Cypher Just Resign?

 * At the end of the second act, Cypher repeatedly asserts how sick he is of military life: "I'm tired of fighting, I'm tired of this ship...", "all I do is what [Morpheus] tells me to do. If I have to choose between that and the Matrix--" Wait, those are his only two options? The Zion military/government isn't a dictatorship (the third movie flat-out states that Kid was only in the corps because he volunteered) and it doesn't look like Morpheus is in the habit of drafting people, either. So if their military leaders don't work by conscription and Cypher is that dissatisfied with service on the Nebuchadnezzar, why can't the Zion authorities put him through for a transfer or something? Zion is a city of thousands; surely, there are jobs that need doing beyond defending it from machines.
 * Cypher might have just been bitching about Crapsack life outside of the Matrix in general, not just in the military.
 * ...Yet all of his most vocal complaints are specifically about life and service under Morpheus. Except for the less-than-palatable "goop" that the rebels subsist on, but if all he wants is to taste something different...well, isn't that sort of thing what the Construct is for?
 * 1) If you're a free human, you have to work so that you and the community can survive. You can either work in Zion, or you can work on a ship. Cypher probably figured working on a ship was easier because there's lots of free time, leering at the Matrix, and using the Construct... but he's still an entitled brat, so he whines about the less-than-great aspects of his life. If he wasn't on the ship he'd be whining about having to tend gardens, or whining about having to maintain railings, or whatever. 2) Cypher says when he's having his treason dinner with Smith that "Ignorance is bliss." He basically says that while he could have a steak in the construct, the knowledge that it's fake ruins it for him. Thus why he stresses that he wants to not remember anything about his time as a Redpill... he wants to go back to being a happy, unthinking piece of livestock.
 * If you go back and watch the first movie again, it does kind of feel like the hovercraft crews have this implicit "mind-freeing = conscription" sort of thing going on. Maybe that was changed for the sequels?
 * Er...fine. But then that raises the question of how the conscription practice could hold when the resistance is likely to be freeing far more minds than there are jobs available.
 * I don't think you really understand just how much work there would be to do in a settlement like that.
 * While he hates the real world overall, he's been on Morpheus' ship for a long time so that's why he complained mostly about that. Plus he's likely too impatient to wait even if his problem was with the ship.
 * There's also the implied concern that the humans might lose the war and he'd get his guts ripped out by a sentinel. By contrast, he could go back into the Matrix and be a rich and famous movie star. Plus there's his weird pervy scene with Trinity after he betrays the crew that suggests he had a thing for her. He had a lot of reasons.
 * Also, he probably didn't plan on the definition of freedom being "you get to help us fight a century-long war against machines in a post-apocalyptic world where we live underground in caves." Morpheus, in a sense, lied to them all. Obviously, if he told them what they were really getting themselves into, most would likely walk away. Cypher was just one of those who got pissed and snapped.
 * Morpheus does explain. Cypher just didn't pay very good attention, and blamed his own assumptions on Morpheus. No one else feels lied to, even though they're clearly not exactly enjoying life in the Real. Cypher's just entitled and pampered, and likes to blame others for his own mistakes and problems, to the point that he was willing to help murder hundreds or thousands of people so he could have a steak.

The machines and programs are different groups?

 * Are all the programs in the Matrix just programs, or are they robots that have into the Matrix? Do any of the programs we see have robot bodies waiting in the real world? Can the robots even get into the Matrix?
 * All artificial intelligences are part of the Machine Empire regardless of if they posses their own bodies. Machines can get into the Matrix, and this sort of happens in the Animatrix, but they don't have any reason to unless they're refugees or criminals from the empire.

Let's call them purple pills.

 * What happens if you take both pills simultaneously?
 * Xkcd thought of this.
 * Actually the red pill is said to contain some sort of tracer to find the person within the machine mainframe in the real world. The blue pill is likely just some sort of sedative and mind-eraser so the person can go on with their life in the Matrix unaware of anything else. So taking both together would likely knock them out, but they would still be able to find them in the Matrix mainframe and unplug them.
 * Assuming competent programming practices, taking both simultaneously should result in nothing. If you have two utilities that will cause a crash if both run at the same time, and you wrote them both, its a good idea to put 'IF other utility is already running THEN end' as the opening subroutine of both files.

Why was Morpheus so sure about Neo?
""Hi, are you the One?" "No." "Okay, thanks.""
 * This one has been bugging me since the first movie. How exactly did Morpheus Know that Neo was The One? What indication was there that made it plain to Morpheus and no one else? Nobody, including Neo himself, ever seemed to wonder just what tipped Morpheus off that Neo was the one (no pun intended) he's been looking for his whole life.
 * The Oracle told him he would find The One, and Morpheus believed he did. He didn't Know, he Believed. Significant difference between the two terms.
 * Okaaaay, so then what made Morpheus believe he'd found The One?
 * Considering how many people Morpheus apparently liberated before Neo, I would actually not discount the possibility that he was just going on random hunches.


 * Less stupid possibility, Morpheus probably put in a lot of off-screen work to pinpoint Neo as a candidate for One-ship. There's also the question of how the Agents were so sure Morpheus would go after Neo that they planted a bug in him -- the machines obviously knew something, and Morpheus was able to play off that.
 * Morpheus never says how long ago he spoke to the Oracle. Maybe she told him years ago that he would find the One, but that she told him last month that the next one he freed would be the One.
 * Maybe he just looked for hackers with a handle that was an anagram of "One".
 * Fun Theory: the Oracle told him he'd fall in love with the One just like she did Trinity. There was a lot of Ho Yay from Morpheus's side ...
 * Probably just another of the aspects of the whole "You have to have faith" message that runs through the whole movie. Neo felt "right" to Morpheus as being the One, so Morpheus trusted in that feeling. The Oracle probably told him "When you finally find the One, you'll know it." Morpheus took a close look at Neo, and whatever it was that made him think "This is the One", he went with his faith in that.

What was Neo's job?

 * Neo appears to work in a cube doing...something. If the One is designed to love humanity to ensure he picks the right door when it's time to reload, shouldn't he have been working for a charity or something?
 * As someone else said above, the kind of person who'd be suspicious of the Matrix's reality and would choose to take the red pill when the time comes probably means being detatched from the people around you and being considered a little weird, an outsider. In a sense, Neo (and the Ones before him) had to be something of an antisocial geek, or he'd never have been in a position or mindset to get recruited by Zion. But apart from that, the One is, despite all the code and hardware the machines invest in him, still basically human, and his free will plays a pivotal part in the process. The machines might have given Neo a family and upbringing intended to make him as messianic as possible, but this particular time around, he grew up to become a cubicle-worker and insomniac hacker.
 * The first movie shows that Neo is a programmer working for a respectable software company although he also blacklights as a hacker creating illegal programs as a side business. Although he is naturally anti-social as seen with the fact that he lives in a small apartment with no pets and seemingly few friends, he still is a kind person who helps his landlady take out the trash. Neo does love humanity but he is also somewhat of a loner, someone who feels outside the system.

What made Neo so special to the Machine God?
As far as I understand, the MG used it's connection to Neo to delete Smith after he assimilated Neo. But how was that connection any different from its connections to all other Matricians? And even if it required a dedicated line for the "troyan horse", couldn't it establish it to any of the non-assimilated ones and then let Smith assimilate them? You can't tell me it actually didn't know about the mess in the Matrix untill Neo came and told it, can you?
 * Neo is The One. Simple as that.
 * O-o-o-okey, any answers that will not make me want to type "thank you, Captain Obvious" or something immature like that?
 * It's explained in the movies that The One is an anomaly--something that the Machines can't control or directly replicate, and that includes special properties that other normal people in the Matrix simply do not have. Ergo, whatever those properties are were probably necessary to fix whatever the hell Smith had done. You asked how the connection was different? There's your answer, that everyone else isn't The One, and doesn't have those properties.
 * Smith mentions that some part of Neo imprinted onto him, which freed Smith from the matrix, by bringing them back together, the MG was then able to delete the now non-invincable Smith.

Persephone is acting crazy

 * In Reloaded at Merovingen's place Persephone kills a "vampire" guard and then tells the other to...either go and tell Merovingen about what happened or stay and die. I'm totally confused with that scene. Why would she want her husband to know what was going on if it was clear he'd try and stop them? Why were the heroes OK with that? Why exactly did she kill the first guard? What was with that strange choice she gave the second guard - she sounded like she was forcing him to go tell his boss what was going on, but why wouldn't he want to do it anyway?
 * She assumed that the Merovingian would come personally to address this betrayal (which he did) and Neo would kill him for her. The Merovingian hasn't exactly been faithful to her (probably a part of their borderline codependent relationship) and as evidenced by Agent Smith, programs who spend too much time in the Matrix get a little insane in the mainframe.
 * Fair enough. That leaves the question of heroes' inecplicable connivance. Seeing how they didn't try to impose their will on Merovingen after he refused them, apparently they didn't seek confrontation. And now they just allow it to happen. Why? Ok, Persephone was kind of in charge there, but would it hurt to just ask: "lady, just what do you think you're doing?" After all, killing her cheating husband wasn't part of the deal.

Sniper Minigun?

 * In the first movie, when Neo attacked the roomб where the agents held Morpheus, with a minigun, how did he manage not to kill Morpheus at that? Miniguns are not exactly precise and Neo made quite a generous swing, hitting all the agents surround Morpheus but not the man himself. Hell, the first trail of hits led directly to Morpheus!
 * No, it doesn't. Pay closer attention. The trail of bullets sweeps downward and moves along the floor in front of Morpheus... because Neo is shown angling the gun downward as he brings it towards Morpheus. Neo is very obviously not just going in a straight line, he's using superior Redpill reflexes and hand-eye coordination to angle his line of fire away from Morpheus.

Dodging bullets But Not Fists?

 * The Agents (and later Neo) have the ability to move so fast that they can dodge bullets, and the effort doesn't really seem to drain them. Why don't they just use this ability to dodge much slower punches and kicks? Does the ability only apply to bullets?
 * Probably something to do with the way punches and kicks move, and how it would be much easier for someone at that range to set you up into a bad position by forcing you to dodge. It's probably just easier for them to block.

Copying a Program? Get Right Outta Town!

 * Smith's ability to copy himself is viewed as a bizarre new power. But it just serves to highlight the fact that, even with 1980s technology, copying programs, and having the copies run simultaneously, is one of the most basic things in computing you can do.
 * He's transferring an entire consciousness, not uploading an mp3. There's sort of a difference of scale, if nothing else.