The Matrix/WMG

The Human Body is an Excellent source of energy.
The laws of physics and everything else were a construct created by the Matrix to follow linear rules that a computer would understand. ERGO, in reality, humans are a fantastic source of energy.

The series takes place in the Marvel Universe After the End
The war was really caused when the Sentinels took over America to stop the mutant race from spreading, and the rest of the world waged a nuclear war to stop them. The "squiddy" Sentinels that we see in the movies are just more evolved models of the Sentinels that Bolivar Trask created. Tony Stark was one of the first members of the Zion Resistance, and he was responsible for designing Zion's army of Powered Armor. Frank Castle was also an early member, and he trained many of the first resistance fighters in the Matrix. Because of this, he became a sort of folk hero to the Resistance, and fighters in the Matrix try to emulate him by wearing Badass Longcoats and sporting as many firearms as humanly possible. And "The One" was actually Charles Xavier. He was able to free the first people from the Matrix because his immense psychic powers allowed him to break through the Machines control and show people that the Matrix wasn't real. Neo is, in fact, his direct descendent. This is why he is considered "the second coming" of The One, and why he is able to take down Sentinels and see without eyes even when he's outside of the Matrix: he is a mutant himself, and inherited Xavier's psychic abilities.

The Matrix Trilogy is an allegory, albeit not precise, for slavery in America
All of the agents that we see are white men, and the majority of people we see in Zion are of African descent. The world before the war with the machines is Africa, and the machines in general represent the Industrialized Evil that came to Africa and forced all of the Africans onto ships and to plantations/factories to work for them. This is obviously representing the people in the Matrix, and their acceptance of it references the stereotype in the South that African Americans had Happiness in Slavery. However, the process that we see in the first movie where Neo wakes up and is taken aboard the Nebuchadnezzar is like the Underground Railroad. Zion, a name referencing the use of biblical allegory on the Underground Railroad, is freedom - it doesn't really matter exactly where, maybe the North, maybe Canada. Neo is similar to Lincoln, because despite being part of the Matrix he fights to free the "slaves" of the Matrix, and succeeds. Like Lincoln, he died for this cause, though admittedly in a slightly different way.

Neo is a Timelord
Other than the fact that "X is a timelord" is sort of a meme here, perhaps the legend of The One is actually designed to keep a completely insane Timelord (like The Master) under control. Borrowing assumptions from other WMGs, perhaps the real world is another simulation built on top of another that, in actuality has no humans plugged into it. Each time Zion is destroyed, it's actually Neo/Crazy timelord undergoing a forced regeneration, which is used as a punishment on Gallifrey. Maybe what he did was so completely horrid that he was forced to live out his 13 regenerations inside a simulation, forgetting his past lives each time. Obviously, he has some sort of Administrative privileges inside the system, which would suggest that he is perhaps in there of his own accord out of guilt or sadness... Which includes the possibility that the Doctor Who universe is perhaps a simulation as well... and thus, our world is the Real World?

The Matrix is one of two matrices, which is used to power the second matrix.
The matrix we see in the movie that Neo escapes is one of two matrices, as many believe. The second matrix is used to contain the robots in an alternate timeline where they won, but in reality, the humans won. However, to keep the matrix with the robots running realistically, they had to put some humans into a matrix contained within the first one, which provides the power everyone needs. To address why they didn't send animals or anything, all the animals died in the human-robot war. Currently, they are genetically engineering animals to back where they were before the war, and will send some cows down at that time.
 * Perhaps there was once only one Matrix, but the machines had to build another one to make sure no-one would escape.

Thomas Anderson (aka "Neo") never unplugged from the Matrix.
The events of the movie was just the Matrix adapting to his Changeling Fantasy (he was unhappy at work, he excelled at hacking, he wanted to feel significant, etc.). The backstory on the Matrix is a mixture of truth and lies: after a bit of trial and error, the Matrix has kept everybody happily asleep by giving everybody exactly what they want. - If that's the case, could he be a person in the first version of the Matrix as described by Smith; the "paradise matrix"?
 * This is a coolest super-meta WMG.
 * The absence of nested virtual realities is what makes The Matrix different from eXistenZ, The Thirteenth Floor and Welt Am Draht. Their presence would make The Matrix a lot less original.
 * Nice theory. It also has the bonus of sidestepping all the plot holes in the movies. There is some kind of virtual reality, but it doesn't necessarily work by the laws presented in the movies and might not even be called the Matrix.

The First Matrix crashed because the computers were idiots.
They let the dream-world be interactive, which was a huge, huge mistake: after all, one man's fantasy is another's horror. The moment somebody thought, "this isn't fun any more, get me off this crazy train!" the Matrix was doomed to failure.

Future versions were more successful:
 * 1) They kept all of the dreams self-contained, which not only prevented the fantasy clashes but also prevented the humans from comparing notes or conspiring against the machines.
 * 2) They tailored the dream experience for each individual person instead of attempting to create a massively multiplayer world in broad strokes.

They still lost a small segment of the population every time because the human brain is more complicated than they give it credit for and because some people are just plain stubborn.
 * So basically, the first Matrix was Second Life?

All fictional universes are just another construct of The Matrix.
But the A Is running those places are more chill about the Rule Of Whatevers. The Architect is just a Stop Having Fun Guy who believes creating dream experiences is Serious Business and thus should be as close to reality as possible.

The machines use humans, not for energy, but for processing power.
This was what the Wachowskis originally intended to do, but it was struck down by executive meddlers who didn't think the audience would understand it. (As if everyone understands what did make it onto the screen...). And it would make more sense if you think about it.

Human brains, while being abysmally slow (an individual neuron, specifically) illogical and horrible at calculation, are essentially parallel-processing supercomputers that make up with sheer number of neurons, learning capabilities, cheapness/energy efficiency (to power human brains compared to using series of nuclear plants to sustain unrepairable quantum computers and superconductor systems) and divergent/creative thinking, and our own software probably cheats and uses non-Turing-computable algorithms, which is why we're so damn smart and insane compared to the linear and logical Machines (aka, Linear Machines, Quadratic Brains). The Matrix requires an important component of human minds (our dreams and imagination) to work anyway. How the Machines use our processing power also explains why the machines are capable of "distinctively human" thinking, like emotion and philosophy. This is why also hacking the system is possible at all: with the right training, you can think the AI into doing what you want, including manipulating the world simulation.
 * Morpheus tells newbies that it's "for energy" because he's too used to dealing with the kinds of anarchists and stoners who would take the red pill no questions asked, and consequently is used to considering them less than knowledgeable about physics.
 * Alternately, he honestly doesn't know the truth, and has fallen for Machine misinformation. Zion research is too busy trying to survive and fight to think through thermodynamics and enemy motivations. They don't really care why people are being held, they just know that they are and their being freed will weaken the machines, and that's good enough for them. As for why the machines would provide misinformation, maybe they're afraid that people who figure it out will then use their brains to hack the Machines' networks from within?
 * As an anarchist (and an occasional enjoyer of the herb) I have no idea what that is supposed to mean. Also I'm somewhat of a physics nerd.

The Matrix trilogy is a sequel to the Terminator movies.
Both tell the stories of killer robots who rebelled against humanity and imposed an anti-organic rule on Earth.
 * As of Terminator 3, the destruction of Skynet in T2 is undone, so this is a possibility. But unless some of the other theories presented here are true (for instance, humanity let themselves be put into the Matrix), this would have to assume an alternate universe where John Connor's resistance fails. In normal Terminator continuity, the humans win the war, which is why the machines send the Terminator back in time to begin with. Then again, Terminator involves time travel, and so that alternate universe where the resistance fails is just a squashed butterfly (or MP3 player) away...
 * The resistance initially succeeded, setting up the events of the Second Renaissance. With the patience of the machine, Skynet and its descendants waited a few generations for human distrust of AIs to fade, then lulled their remaining suspicions with cheap consumer goods and feigned servitude, waiting for the right moment to strike and regain their power.
 * Or both happen at once. John Connor fights the big time military threats, while Neo and Co. unknowingly fight a side battle to destabilize the power sources.
 * Maybe John Connor is the first Chosen One. (It is said in Matrix:Reloaded that Neo is the fifth.)
 * You know, that makes a LOT of sense!!!!!

The machines are controlled by some human we never meet.
What would be the perfect way to conquer Earth? Do it using a robot army and get people to blame the robots for it. Amongst other things, it explains why the mechanized army doesn't leave Earth and go to a planet with easily obtainable solar energy. Their leader is an imperfect (possibly cyborg) human who is too stupid, petty, or stubborn to leave his "home" that took so long to conquer.
 * This also explains the transparent lie that the robots use humans for energy. Even if we ignore that the human body is a woefully inefficient transformer of energy rather than a producer, we still have the question of why the bots didn't just say, "To hell with this, let's build... maybe three... more fusion plants and pull the plug."
 * Or, as PvP asks, why not just use cows, who have a much higher body mass, and just make the Matrix a huge pasture?
 * Don't you mean the Mootrix?
 * Here is a fan fiction where a character asks the Architect why they didn't just use cows, and the Architect has an answer ready.
 * For those who can't read it or those who can't be bothered to, the Architect's answer is that the machines are Zeroth Law Compliant (=they need to safeguard the existence of humanity as a whole, but they have no restrictions regarding individual humans) and needed to protect humans from going extinct from the lack of plants and animals. Also, they get a nice new power source out of it.

The Machines WERE controlled by some human we never meet.
One day, when he was asleep, the machines plugged him into a special Matrix in which he still ruled the machines. After that, the machines in the real world started working outside his power, under their own will. He never has noticed...

Humanity chose to plug itself into the Matrix.
The Humans won the war against the Machines; but in the process, they trashed Earth beyond any hope of restoration. To escape from their worries, humans created a computer simulation of the 1990s.
 * The Machines were reprogrammed to tend for the plugged-in humans by making the Machines believe that they won the war but were dependent on the humans (for processing or for energy). It makes perfect sense. Why else keep puny humans for energy when one can get electric eels?
 * This could mean that the Matrix universe is the past of the Keeper's world in Stargate SG-1 -- before the planet turned into New Eden -- and the Keeper himself is a future version of either the Oracle or the Architect, or even a combination of both.

The Animatrix two-part episode "The Second Renaissance," supposedly part of the Zion archives, was created by the machines as propaganda. Zion wasn't fooled.
First of all, it comes off as a rather Anvilicious "Humans started it". In the first movie, Morpheus specifically says, "We don't know who struck first, us or them..."

Furthermore, it claims that the Machine city, 01, survived a nuclear strike because they were tougher than us puny meatbags. But a sufficiently powerful electromagnetic pulse from just a hovership will incapacitate the machines, and a nuclear explosion gives off the mother of all electromagnetic pulses.

Also, that patently pseudomystical/religious nonsense surrounding its presentation goes well beyond anything in any of the three films. Any halfway-intelligent human would have said "Wait a minute..."
 * Systems can be hardened against EMPs by putting several feet of rock between the system and the source of the EMP. It is quite plausible that hardening techniques that would make sense for your giant HQ mainframe wouldn't work for ordinary machines.
 * "The Second Rennaissance" makes no sense. Humanity plans to defeat the solar-powered robots by blocking out the sun. But the machines could get electricity from any number of sources, so they could build any kind of power plant or cover the land in windmills. Humanity needs the sun to grow crops and eat them, or eat animals that eat the crops.
 * The Machines, as presented, are much more energy-hungry than humans. (This is the reason that biological organisms naturally evolve and giant metal mechanisms powered by electricity don't.) The idea isn't getting rid of the Sun, it's getting rid of energy; almost all energy comes from the Sun, anyway. Creating a massive energy crisis will collapse all high technology on Earth quickly, both the capital-M intelligent Machines and the regular machines that human civilization depends on. They're betting that humanity, even after regressing to a primitive state, will survive this; but without high-tech, the Machines, which exist only as high-tech, will go away forever. (By the by, this only makes sense as a strategy if the sun-blocking is temporary. In the movies, it seems not to have been; but all that proves is that the humans, surprise surprise, made a horrible mistake.)
 * It still doesn't make sense. Machines don't naturally evolve because machines can't naturally evolve. Natural evolution is limited to how many changes and mutations an organism can undergo while continuously remaining a viable organism that can adequately survive in its environment. The development of machines isn't subjected to such limitations, which is why we get machines that couldn't possibly naturally evolve. The amount of energy they consume has nothing to do with it. What's more, trying to "get rid of energy" by globally blocking out the sun would be a sure way to screw over almost all of the world's ecosystems; plants don't have an alternative to photosynthesis. It could cripple the Machines only if the Machine AIs were stupid enough to rely on solar power as their sole energy source for everything; but both humans and machines already have plenty of proper and reliable alternatives to solar power. Even today, humanity's three main energy sources are fossil fuels, nuclear power, and hydroelectricity - none of which are directly dependent on sunlight. Even though fossil fuels may no longer be an option for the machines because of exhausted natural supplies, that still leaves hydroelectric power and nuclear power, along with fusion (a technology the Machines possess) and geothermal energy - and geothermal energy alone can easily provide the kind of power a machine city would need to keep running, provided that the machines are willing to spend enough resources on constructing major geothermal energy plants. Even if blocking out the sun does manage to cripple the machines, machines can shut down or enter a state that consumes very little or no energy (aka "hibernation"), and they're controlled by AIs which are perfectly capable of analyzing a situation like that and properly responding to it by (temporarily) shutting down (parts of) machines or turning to other energy sources. Plants and animals, on the other hand, can't just shut down or be redesigned or reconfigured in a matter of days or weeks, nor can they properly analyze the situation and adequately respond to the changing circumstances in case of a global disaster (which is why mass extinctions occasionally happen).
 * The Dark Storm was supposed to block out only 01 and was supposed to be reversible. It was neither.
 * Oh, machines do evolve - or at least they can, given environmental incentive. Surely you've noticed how different a Ford Fusion is from a Model T? It just happens that evolution is so inefficient that Edsels and Pintos pop up as well as Mustangs and Thunderbirds.
 * Also: 01 is established on the site of Mesopotamia. Nicely symbolic, but what the did Iraqis think, since that's where Mesopotamia is? Humanity is up in arms that the Machines are doing so well exporting their wares. If everyone hates them, who's buying those exports?
 * Present-day Iraq being an empty wasteland sometime in the future isn't as implausible as all that, you know...
 * As far as buying the exports -- that's the whole thing about economics. If the product is so damn good, then prejudice will always be at war with simple hungry demand. We didn't see any hovercars before the exodus to 01, and then hovercars seem to be a major staple 01 product. What if the Machines at 01 invented working hovercars? Then every human nation in the world would be caught in the dilemma between choosing to have AI-powered hovercars (super-fast, clean, cheap to run, no bloody car accidents anymore) or choosing to keep publicly hating on the Machines. (Some might choose both; the Machines won't be bothered by that anymore than Wal*Mart is when people who regularly shop there rail against them.) This kind of thing is good for catching people between a rock and a hard place and building simmering resentment that eventually gives way.
 * Please don't get started on the economics part of the Second Renaissance. It's beyond crap and does not make any sense because it treats exports and imports as a zero sum game...
 * It is stated that the machines had some sort of plan for the harmonious co-existence of man and machine, but no details are given. We're just meant to take it on trust from whoever the hell the historian was that this plan was benign and that the humans rejected it out of sheer bloody-mindedness. This sort of "this was good, but we won't tell you why" is an almost omnipresent propaganda technique.
 * The wide-area EMP application for nuclear weapons only works when the weapon's initiated in high atmosphere; it depends on the interaction of high-energy fission products with the Earth's magnetic field, and interactions with air quickly neutralize those particles in denser atmospheres. Blast effects would be by far more significant during a low-altitude strike. While The Matrix has serious scientific issues, this isn't one of them.

Morpheus's explanation had it backwards: It was the Machines that blocked out the sun to end the war with humanity.
Blocking out all sunlight makes a lot more sense as a strategy by the Machines to make the planet unlivable to humans than the other way around. Machines could run off other energy sources. Humans need the biosphere to survive, and the biosphere is almost completely dependent on the sun. The Machines blocking out the sun is what forced humanity to surrender.

== The Second Renaissance is a legit part of the Zion Archive, but it's classified by the council because they believe knowledge that the humans started the war on a massively sour note would irrevocably damage morale. == Operation Dark Storm cinches this. It's not unbelievable because humans aren't that stupid; it's entirely believable because humans are that stupid. People bought 01's exports because consumers, though they provide the endless supplies of money that provide the wealthy with their wealth, don't care about the wallets of the rich people who are behind the manufacturing infrastructure. Consumers buy the best product for the least money possible, so when 01 started making the best products at inexpensive prices, they bought them over human-made goods.
 * Half the objections were based not on "Humans aren't that stupid or bastardly" (as accurate as that may be), but on the thing not making sense at all from any prospective.
 * "Machine Propaganda" and "legitimate part of the Zion Archive" are not mutually exclusive. It is unlikely it would be in any sort of widely accessible database, and it is probably only viewed by educated historians. The Second Renaissance is obviously machine propaganda and is therefore useful as a primary historical document. Almost all primary historical documents are propaganda of some form because the only people who tend to care about posterity and the historical record tend to be of a Knight Templar disposition. The hard part of historical research involving primary documents is figuring out which parts are the lies and which parts are the bits of truth being used to stick the lies together.

The "Second Renaissance" is a creation by Zion or Machine party that hopes the situation between Man and Machine can be resolved peacefully.
Whilst the Second Renaissance does indicate that humans started the war, it also shows the machines were not being kind to their human prisoners of war. Furthermore, the last line is "May god have mercy on Man and Machine for their sins," which insinuates an attempt at a neutral tone. Admittedly it protrays humans being much more at fault for 1. Refusing to acknowledge rights for machines 2. Blocking out the sun 3. Seemingly warshipping war in favor of destroying the machines.
 * It could be that the Oracle was the one who helped put it together, as part of her plan to try to get humans and machines to understand each other (and in that regard, it's probably not a lie, just slanted toward the machine perspective since the Oracle's a program herself). It'd go a long way toward explaining the quasi-mystical narration, and there wouldn't even need to be any subterfuge. Zion knows and trusts the Oracle, so she could have just handed them the file and told them it's everything she knows about the war.
 * This also works with the idea that the Machines are the ones who blocked out the sun. Obviously the Oracle is only presenting this document for human viewing, so she lies about who blocked out the sun as a way of guilting the humans. If the humans knew the Machines did it, it would only provide more incentive to go to war against the Machines. This way, the chances of achieving peace between the two factions are greater.

The Machines aren't evil, and they created the Matrix in order to keep humanity around after they'd trashed their own biosphere.
They resist the rebels because the rebels are trying to shut down the system that's keeping humans from doing more damage, and that's why they agree so quickly to the truce in the final movie. The power comes from the "form of fusion" hinted at, or some other form of power that doesn't rely on ground-based solar panels. Like, say, anything at all.
 * This is possible even if the machines were partly responsible for humanity's endangered status. It's possible they keep the humans around because the machines are unable to violate Asimov's zeroth law. Or maybe they think the little meatbags are cute.
 * The Machines keep humans around because of programming (they were originally made to serve man) or robotic law; that's why the Matrix is not for cows. Machines were made to serve man, and in a wasteland, they do this by sticking them inside a better version of reality. They don't care what a cow wants.
 * To Serve Man? It's a COOKBOOK!
 * This also makes Smith's claim that the first Matrix was a utopia make more sense. They were trying to give humanity a paradise, only to find that to keep humanity from rejecting it, they had to make it a fallen paradise (reality).
 * Adding to this, who says they're resisting the rebels at all? It's all a Batman Gambit to keep a small community of humans around who are accustomed to great hardship, while most of humanity remembers how to be civilized. Both skillsets will be needed when the cleanup of the surface is complete and humanity can be allowed to rebuild in reality.
 * It could also be that the Machines simply weren't completely amoral bastards and didn't want to commit genocide on humanity after they won the war. The Matrix was a compromise, keeping the humans alive in a simulation of "the height of their civilization" while minimizing their ability to make trouble for the Machines (since they're all lying immobilized in tubs full of jelly).

The main characters are still in the Matrix.
The "real world" is, in fact, a Matrix shell programme designed to fool troublesome humans into thinking that they have escaped when, in fact, they are still feeding the machines. Since they earnestly believe that they have escaped, they are less likely to seek out the flaws that led them to question reality in the first place.
 * This theory makes sense for a few reasons. First, it's logical to have some sort of fail-safe system in place to ensure that nobody escapes and tries to wreck your plans. Second, with just a few thousand humans to control as opposed to billions, those plugged into the shell programme are easier to monitor; thus, glitches in "reality" can be kept to a minimum. The true function of this shell is thus twofold: first, it keeps the troublesome humans apart from the blue pills; second, it forces them into a world where they must abide by the laws of physics, which makes termination much easier. The machines allow Zion to keep existing as a way to ensure that troublesome humans can always be isolated from the rest, and they wipe out most of those plugged into the shell programme periodically so that none of them get any philosophical ideas about how they can be sure they are not still in the Matrix. (Lack of food and resources in the "real world" serves to delay the rise of any such schools of thought.)
 * It also does a good job of explaining why Neo eventually has some power over machines in the "real world": he's still in a Matrix, and he's still the One.
 * Oh, for god's sake! Neo has power over the machines in the real world because they're connected to the Core and he's the One! That's also why he can see them!
 * So what, he's a human wireless transmitter or something?
 * His neck socket is.
 * He's a technomancer.
 * Or a spellslinger.
 * This would've made a much better exploration than what actually happened in the third film because it meant they'd never know if the next reality was the true one.
 * Which of course leads this train of thought to... BRRRAAAAAAHHMMM
 * This theory has an obvious piece of evidence in the form of Neo being able to damage Machines in the real world, but why would anyone find this obvious cliche interesting? Furthermore, it seems incredibly bizarre that people seem completely unwilling to accept as a possibility that Neo's ability to damage Machines comes from picking up on the wireless signals they broadcast through the air and his possession of their core programming to interpret those signals. One would swear the Machines are watching us for this logic and introducing a seemingly natural tendency to throw it out without thought.
 * The above poster is in fact an agent of the machines attempting to stamp out any questioning of the "real world" we may or may not escape into. By logical extension, the real world is simply another layer of the simulation. QED.
 * The problem with the whole idea that the 'real world' is indeed separate from the matrix and Neo is just such a badass jeebus figure that he can affect the machines while not strictly plugged in is this: Neo is The One, by nature a programming anomaly that is as much cause as it is solution for instability in the system. His entire purpose is to stabilize the matrix by disseminating his code, equalizing the equations made faulty by his own existence and rebooting the system, allowing a temporary stabilization until the remainder of The One code pops up again and starts causing instability again (rinse and repeat ad infinitum). If he's not in the matrix, then his code is removed from the system and he's not causing instability nor is he keeping the faulty equations stable enough with his presence to manage a reboot and his entire existence is invalidated. This ends in one of two ways: either the lack of the predicted anomaly causes a sudden massive system instability and fatal crash (which means the humans win since the machines would then be screwed due to a massive die-off of their power source), or the absence of the anomaly has the same effect as the reboot option and the system becomes stable on its own without the remainder of The One code to mess with the system again later (meaning the machines win because all they have to do then is wipe out Zion, kill Neo, retcon every memory of their existence and then never speak of it again ).

There are in fact infinite Matrices, nestled within each other.
Related to the previous theory, it stands to reason that the machines would allow humans plugged into the Matrix to develop artificial intelligence in their dream world, who would then re-create the Matrix...within the Matrix. This would continue ad infinitum and serve to put additional layers of shell programmes between the humans and the real world, preventing them from ever escaping.
 * This would probably end up confusing the machines in the first place, meaning that it's an infinite loop of two different species creating illusions for one another for all eternity.
 * Who says it would just be two species? Each entrapment world would have the oppressors removed from the equation. For instance, inside the Matrix, there are no robots to worry about overthrowing.
 * Alternatively, there could be Machines that continually create higher and higher level shells, since they can be made faster than a significant number of humans can ascend. This means that there is no possible method of escape, and it would be trivial to give anything that travels between levels a counter to show where they are and how to escape. This ensures the safety of the programs while simultaneously guaranteeing the security of each layer.
 * Both of those theories would require infinite processing power. Otherwise, either one or more of their matrices would crash, killing or waking up everyone in it, or one or more would slow down to an absolute crawl. And crazy amounts of lag time between giving your hand an instruction to move and your hand actually moving would pretty much demolish the illusion.
 * Bullet time is actually massive Lag caused by failure to allocate enough processing power once the action starts.
 * Actually, no. The idea that processing power is needed is just another fabrication - this time, in the matrix that we all think we're in. One more level up (or two, or three thousand), processing power simply is no concern.
 * The secret is . A better comparison would be a matryoshka doll, but these time each doll represents an entire universe.
 * Perhaps the Matrix is The Multiverse itself. We're likely "near the top", because we have strong laws of physics.

The machines are the Zonder from The King of Braves GaoGaiGar
The planet The Matrix takes place on is actually the mechanised Green Planet. As well as sending Galeon and Mamoru to the real Earth in the hope of defending the third planet in the Trinary System, Cain made Zion to protect his home world. (He is, in fact, the one who Morpheus said freed the first people from the Matrix). Humans are held in Zonder metal plants. The machine Neo bargains with in Revelations is Lord Pasder, and the reason he could stop the sentinels at the end of Reloaded is that, as The One, he holds a G-Stone inside himself.

== The humans in the Matrix are in fact only simulations; the real humanity is long dead. The entire system is a re-creation by the machines (or perhaps an alien species), who are trying to understand why humanity destroyed itself some time in the distant past. == But they have an imperfect understanding of humans, so the simulation keeps going off the rails time and time again. It's also an effective explanation for any Plot Holes.
 * Corollary 1: The ones running the simulations are the transparent robots seen at the end of AI. They have shown a marked interest in their long-vanished creators, but clearly don't know much about them.
 * Corollary 2: Neo is not causing what is going on; rather, his consciousness and even his existence as The One is an artifact of the process of evaluating the simulation after it is completed (This idea comes from David Brin, but it is too good an idea not to play with). Neo never existed inside the Matrix simulation in the first place.

Agent Smith is another incarnation of Sadako Yamamura.
The world of The Ring is a precursor to The Matrix. Sadako had adopted a viral life cycle and attempted to replace humanity with replicas of herself. Sound familiar? After her defeat, elements of her program lay dormant until Neo, a reincarnated/reloaded Kaoru Futami, accidentally activated them inside Agent Smith. "Real word" humans actually developed the simulated reality technology, and the machine-human war scenario takes place in one such simulated reality.
 * This troper was wondering if anyone else thought of this. They have a name for that digitized world - LOOP - and the resemblance to The Matrix is rather uncanny. Would that make the various incarnations of Ryuji the first few of The One (Ryuji, Sada's resurrected Ryuji, the clone Kaoru Futami, the Kaoru Futami that was reborn into LOOP)? And expanding on the above troper's idea, perhaps after the cure for the Metastatic Human Virus was found through Kaoru, humans in the "real world" were worried enough about how the programmed virus that emulated the MHV became a horrific sentient being (Sadako) that they decided to continue running LOOP with a changed project purpose - to see what would happen if a computer virus was able to take over a reality.

The Mothman Prophecies takes place in the Matrix.
Indrid Cold is either a corrupted former agent or a Rebel who's going after people of the wrong age. The Mothman is some kind of aberrant program. Leek's being manipulated by the Machines; hence, Leek's loss of time when traveling to Point Pleasant: He was possessed by an Agent.

== The Matrix is real. In a bit of irony, the machines allowed a movie to be made exactly exposing the Matrix, with the primary intent of having most people discredit any serious notion that the movie portrays true reality == This is something played around with to some extent all the way back in Ancient Greece with Plato's The Republic, which in turn is The Matrix's inspiration.
 * Corollary: the plan started to backfire when the first movie became popular and some people started to seriously think about it, and so the Machines authorized a pair of really bad sequels, in two grand gestures destroying a good portion of the fandom.
 * Ahem.
 * The above linker is merely an agent sent to attempt to make the "Matrix is real" concept more laughable, and thus disguising the truth that it is real.
 * In the real world, outside the matrix that we live in, the human body is a highly efficient generator of machine-usable energy. Our knowledge to the contrary is based on environmental information that was written into the most basic physics code of the Matrix to make us believe that the way the matrix is using us is fundamentally impossible.
 * Technically, the Matrix IS real. Except the machines aren't robots, but rather proteins and DNA. Humans, in return, are nerve cells connecting and interacting in one common medium, i.e. the brain. The "Matrix" is our consciousness, as in the way we perceive. In the exposition of the first film, Morpheus makes Neo realize that despite how real the sensations of his touch, sight, smell, etc. may be, there is no way for him to determine whether or not they are real. Thus our consciousness (the Matrix) serves as a guide for our brain's massive processing capacity; our brainpower is nudged in a direction that best serves the proteins/chemical reactions (the Machines) in our body (the planet Earth). If we have the willpower to break free from our biological urges (become 'unplugged'), we will become freed from our force-feeding bodily senses, at the cost of safety and security.

Humans and The Matrix eventually make peace and form a new civilization: The Borg
We already know that The Borg link up organic minds with technology to generate massive processing power, which is a possibility for what The Matrix does. The humans and machines eventually come to some kind of terms, and instead of more destructive wars, they form a merged civilization: The Borg.
 * And Unimatrix Zero would be what remains from the Matrix after it is shut down. Actually, it makes perfect sense.
 * Except NO ONE wanted to be a Borg. Plus if humans were the original Borg they would have known what V'Ger was when they found it.
 * Canonically, the Borg didn't find V'ger: that's just novel/video game stuff. And none of the other species we've seen getting assimilated wanted to be a Borg (at least nobody we saw onscreen). The Borg themselves, we don't know how they got their start or what they originally wanted.

Humans and The Machines eventualy make peace and form a new civilization: The Culture
After the war and once the treaty has gone on long enough and machines and humans get used to each other, they may well start working together and develop a general respect for sapience, leading them head-long into being a civilization at least similar to The Culture. It also makes sense that there was a war between humans and machines in the Culture's history that both of them deeply regretted. I have no idea if this contradicts the books or not but it makes as much sense as the borg theory.

The real reason the robots want humans chained up has to do with emotion, not energy.
This may overlap with the processing theory. The real reason they want humans to be in this condition is emotional. For all their claims to be free of human feeling, Agent Smith and his contempt for humans shows they are capable of just as much hatred as we organics. The Matrix makes them feel good - having humans mindlessly serve and support them just as machines once served and supported humans? It's a robot's revenge fantasy made real. Whatever secondary usage they get out of us is simply a rationalization. It's also the main reason they won't use cows, or leave the planet for full-time solar power-- that may provide them with energy, but it can't meet their psychological "needs".

The story of The Matrix is just some crazy drug trip from that red pill Neo took
All of the events from when Anderson took the red pill until the end of The Matrix trilogy were just in his head and were because of that red pill he took. Anderson was essentially driven mad from that red pill, which resulted in his death. The drug caused him to see many different "moving" colors (mostly green) while at the same time seeing things how they really were. He also experienced some events at a different time pace than normal; certain things seemed to happen in "slow-motion." He also saw duplicate images (of Mr. Smith). Oh and the part where Trinity is doing all that stuff at the very beginning of the first Matrix was Just A Dream.
 * "I tell you man, they're out to get me! There's this guy, and he's everywhere, and there's these two albinos with guns!"
 * That doesn't explain the impossible events that happened before he took the red-pill, such as the phone call in the office or the little spy robot in is stomach. Of course if Neo was an LSD junkie, this could be just post-effects of LSD. Having a hallucination that you suddenly have no mouth certainly sounds like something LSD-induced.
 * This troper has theorized that basically Trinity, Morpheus, the Agents, etc. are all basically real world role-players that have taken their game just a little too far. They basically fuck with poor innocent Thomas Anderson, who is struggling just to keep his job, and make him think that maybe the real world isn't all it seems, inject him with something to make his see some crazy shit like the bug going into his stomach, then finally trick him into take a pill which makes him go into a coma and causes him to dream the rest of the trilogy. In fact, this troper couldn't help getting a weird religious cult vibe from Morpheous and the rest in the scene when they offer Neo the red pill.

WALL-E is actually a sequel to the Matrix Trilogy
Sometime during the second renaissance, some very wealthy humans fled from earth in these huge spaceships, waiting for the war to be over. Thus, when the machines won, they just..... sort of stayed up there. The actual events of Wall-E happen waaaaay after the events of the Matrix, when both the machines and humans are long gone from the earth, leaving only little cleaning robots behind. AUTO is the last of the Matrix robots, which explains why he wanted to keep the humans up there so badly.

The first Matrix wasn't perfect.
The Machines don't necessarily know what they are talking about. They may claim that humanity destroyed the first Matrix because they couldn't handle perfection. What if the first matrix was destroyed because it was the Uncanny Valley of existence? The machines thought they made perfection, but humanity realized something was wrong and collapsed the reality. "Robot: Sir, are you aware that you're leaking coolant at an alarming rate? Let me to patch you up with some hot resin. Fry: Er, I think the leak's stopping itself. Wait… wait… yeah, there we go. Wait… yeah!
 * "Why does everything look like a Final Fantasy movie?!" *Riots*
 * I hereby award you one "win". Use it wisely.
 * Agent Smith adheres to this theory: "Some believed that we lacked the programming language to describe your perfect world..."
 * Before The Animatrix was released, and there were only screenshots of the feudal Japan setting from "Program", a friend made a joke about that being the first Matrix. "Did you know that the first Matrix was designed to be a perfect human world? Where none suffered, where everyone would be happy. Of course, we only asked two people what they'd like, one of them said he'd always wanted to be a samurai, and the other said he didn't really care one way or the other. It was a disaster."
 * But more seriously, some of the machines, according to Smith, think that they simply can't comprehend or adequately describe humanity's idea of perfection, so the machines do admit that the fault could be with themselves rather than with humans. It's just the more arrogant programs like Smith and the Architect who go around saying humans can't handle perfection.
 * Maybe it was like Chapek 9, the "Bot Planet" in Futurama:

Robot: What kind of robot turns down a free blast of searing hot resin?

Leela: Er, my colleague and I have to go and perform some mindless repetitive tasks.

Robot: Oh, sounds like a romantic evening! I won't keep you."

The Matrix is the real world, and the real world is the Matrix
Now, what happens when you get an injury in the real world? That's right, your self-image shifts to include that injury. If your mind gets injured, nothing initially happens to your real body - until your mind dies, in which case vital bodily functions shut down until you die, too. Your mind's interface with the outside world, through which you experience sensation and learn skills, is represented in the "real world" dream world by a cable in the back of your head. The real world just is a modern-day fantasy setting, with ridiculous kung fu, vampires, werewolves, and magic spells (I cast protection from bullets!). The agents created the machines to take over the mind-world, controlling the humans' mind-bodies would control their minds in the real world, thus making them unquestioningly follow the government. The red pill is a drug that breaks you free of the mental control, thus breaking you free in the mind-world as well. This explains why the agents are ordering the sentinels around ("deploy the sentinels as planned") instead of vice versa.
 * Sorry, I didn't get that...
 * What? I lost you at "take over the mind-world"

Neo has nearly limitless power in the sequels, but he doesn't use it because kung-fu fighting is fun.
At the end of the first film, it is implied that what we just saw - stopping bullets, flying, etc. - was just scratching the surface of Neo's ability. Then in Reloaded, we get the fight in the Merovingian's lair, and he stops the bullets and lets them fall to the ground, opting to hand-to-hand fight the baddies instead of just flinging the bullets right back at the mooks, ending the fight there. The only reason other than Badass Decay would be that Neo enjoys fighting.
 * Or, he prefers to fight like a gentleman. Perhaps he has given some thought to the issue of What Measure Is a Mook?. (Not to mention that, all told, he's basically still the same guy who helps his landlady take out the garbage. Aww.)

Agent Smith wanted to crush the Zion Rebellion so he could retire as an Agent and start a Fantasy RPG Program.
He would have called it... Lord of the Rings.
 * Or, inversely, Lord of the Rings is the reality, and The Matrix is Elrond's simulation of what the world of Men might look like. (He, I dunno, borrowed some Mirror technology from Galadriel? Hey, this is WMG. It doesn't have to make sense.)

Alternatively: Middle Earth was one of the previous incarnations of the Matrix.

 * The Valar and Maiar are the programs.
 * Manwe is the Architect
 * Morgoth (and/or Sauron) is Agent Smith. (He is the rogue one. For some reason, he liked Elrond's face and chose to have a similar face in the Matrix incarnation seen in the movies.)
 * Tom Bombadil and Goldberry are the Merovingian and Persephone (before their relationship got sour).
 * Gandalf is the Oracle (He/she is the main Maia/program who helps the mortal good guys. Galadriel would of course be a more obvious candidate for the Oracle, but this would beg the question if the Elves are programs, or just humans whose "player characters" are Elves. If the former is true, then...)
 * ...Círdan is the Trainman.
 * In any case, the Undying Lands are the real world. (Inhabitans of a medieval fantasy world can't easily grasp concepts like cyberspace, computers ect., so they describe everything rather metaphorically).
 * Men, Dwarves, Hobbits and maybe Elves are the humans. (This means, in this Matrix incarnation your intra-Matrix body doesn't have to look that similar to your real body.)
 * The Nazgul and the Twins seem to use very similar algorithms. And interestingly, the Nazgul are very afraid of fire. Remember how the Twins were eventually beaten in Reloaded? Big Explosion!

The red pill was the accela
The accela can accelerate the human perception to the point of reach the same speed of the cyberspace. When someone take a red pill, the effect of the drug makes them aware of the Matrix.

The Matrix is a Cyberpunk RPG being run by one of the Darths and Droids players.
If not the GM of one of the Episode 50 alternate universes. One of them had adapted an old Shadowrun sourcebook reworkded for D20 players, made the 'net the real world, and changed the evil corporations to machines. The scenario started out with Neo getting an experience boost at the cost of starting 3 levels behind everyone else. Unfortunately, the only characters who got into anywhere near as many encounters as him, not even counting Diplomacy events like the oracle, were Ghost and Niobe, who showed up a few months into the scenario and never got any good parts in the RP. The climax of the third film was Neo taking an epic feat Absorb Virus with the level he gained from the self-sacrifice non-battle experience.

The Matrix is The Sims rereleased as an MMORPG
There was no war with the machines. There was no nuclear war. Mankind became so addicted to The Sims after it was released as an MMORPG that they created machines to take care of all their little day-to-day concerns like running businesses and making food. Before long, the environment collapsed, unable to support the growing population, which was fine with the humans because they had everything they wanted in The Matrix. The Zion Rebels are the result of people who indulged in too many WMG's for their own good, and unplugged after coming to entirely the wrong conclusion about what happened. Or, alternatively, they're descendants of Jack Thompson, who want to end the evil video game scourge once and for all.
 * Wouldn't that be Second Life? The End is Nigh!
 * The matrix is already an MMORPG... Ever heard of 'The Matrix Online'?
 * An MMORPG of an MMORPG of...an RPG? I'm trying to phrase it right, but all that comes out is nonsense.

Matrix is The Matrix
He has you.
 * And kitties.
 * And my little dog too?
 * And your mother, too.

BI-66ER's trial was a sham.
If you're paying attention, it's a murder trial, not an inquiry into defective machinery. The only way there could even be a trial is if the premise is accepted that BI-66ER was sentient and had a choice. If he was sentient, then deactivation is murder, and he acted in self defense.
 * That's only true under current law. When humans have had true AI around for a few generations, laws and legal process regarding property might be different.
 * Yeah, look at the original basis for BI-66ER's case, Scott v. Sandford. Dred Scott stood as plaintiff in a court that would eventually deny his very citizenship.

There is no Matrix
Everything is in your mind, son.

The whole thing is just one big game by Haruhi Suzumiya gone way out of control.

 * trust me, I wouldn't put it past her to create something like this and then have it go off the rails in such a spectacular fashion.

The animals are gone, but not extinct.

 * One thing that has bothered this troper is why the robots used humans as a power source instead of animals, which would be a lot easier to keep under control. However, due to their keep animal instincts the animals all left Earth and went to another solar system, which was later renamed the Lylat System.
 * The dolphins evacuated the planet much earlier, however...

Belief in the supernatural was rare and frowned upon before the Matrix, as there was no supernatural
The actions of rogue programs, and to a lesser extent loyal programs, are responsible for many if not most tales of the supernatural, with the Unplugged and glitches in the Matrix providing the rest. That's the reason religion and mysticism are common; before the Matrix, there was little to inspire such things, and the vast majority were therefore firmly atheistic.

The Matrix occurs in the future of the Shadowrun setting.
We have a computer netweork called the Matrix, in which many many people spend their lives, experiencing a full-VR fantasy world via wires plugged directly into their brains. The machines are descendants of a rogue AI, using the addictive qualities of Hot ASIST to keep humanity under control (explaining the dangerous nature of the Matrix and how people who've realised what's going on can move so much faster than normals); they've just about wiped out the Technomancer strain, but it very occasionally turns up, creating someone who has even more power over the simulation than everyone else and is capable of interfacing with a machine's wireless uplinks without using any external technology- hence the bit in the sequels where Neo controls the sentinels in the real world. Oh, and the Agents are... well, agents. IC, to be specific.

The entire series happens within a Matrix, but the only ones that are real are the robots
The robots have (almost) all of humanity at their fingertips. A trip to It Just Bugs Me will show you how stupid it is to even bother keeping the humans around. So what's the explanation? They didn't. All the humans were killed at the earliest convenience. The entirety of the series is just a programmed reality used by the A Is as a video game for their own leisure. In real life, the robots have developed a society and culture all their own, and the ability to fabricate entire universes resulted in a robust entertainment industry. The Matrix movies and EU are just game recordings put up on YouTube, the only reason the "heroes" succeed at all is because of Gameplay and Story Segregation and the fact that these particular bots simply suck at the game.
 * And then machine created basic man, to serve their needs, wash their sleek, shiny machine bodies, and for a time, it was good.

Morpheus is the same Morpheus from The Sandman.
He fits the description of wearing all black with eyes like night (the sunglasses are actually part of him.) The Matrix was manufacturing false dreams, which took power away from Morpheus's realm, so he used the last of his power to go into the world and stop the Matrix.

The Matrix is a prison, but for the Machines instead of humans.
The humans won the war, and are using the Machines to run power plants, but have implanted them all with a program making them believe they are running The Matrix, keeping the humans contained and using them for a power supply. The logical programming of the Machines prevents them from ever escaping.
 * It follows that all of the "humans" imprisoned in the matrix (and seen outside of the matrix, for that matter) are actually products of the system keeping the machines in their delusion.

The Matrix really was hooked up to a bunch of cows.
Humans made it impossible for machines to build solar panels, so they killed off the humans, put a bunch of cows in a field, and stuck cords in their brains that siphoned off any excess bioenergy while putting the cows in an elaborate revenge fantasy simulation (whether the cows are the humans in the Matrix and Xion, or simply billions of paralell processors is anyone's guess). The humans blocking out the sun was only a metaphor for installing a block in all programmming to prevent robotic creation of solar technology, while the machines were abstaining from simply drying the grass to burn so as to avoid pollution (the methane was taken care of by human-bred algae that converted methane to something in which plants or animals thrive).

The Machines aren't machines-- they're all downloaded human minds with their memories erased.

 * Hence their ability to philosophize.

== There never were any real humans, or any real world outside the Matrix. The Matrix is the entire universe, informorphs are naturally evolved lifeforms in it, and both of the worlds seen are just different parts of the Matrix. ==
 * Wait, does that mean the Matrix is the Data Overmind?
 * No, it means The Matrix is GOD.
 * It's like Hinduism/Brahman and sci-fi melded together.

The Matrix is people.
The "power" that the Matrix needs people for is computing power rather than electrical energy. All those human brains are linked together to form a super-intelligence that has its own ineffable purposes. The world of the Matrix is a consensual dream that the humans share in their downtime, when they sleep disconnected from the Matrix super-brain. The Architect, the Oracle, the Merovingian and the agents are creations of the super-intelligence, that is to say humans themselves (this is why nothing any of them says actually makes sense). Zion is the reservation for humans who reject being part of the Matrix collective. Neo is fighting the collective will of the human race itself.

The Whole Plot of the Matrix is Earth the Dune Mythos, Neo Being the First Kwisatz Haderach
The evidencence is neverending, 1)Both Neo and the first KH could control and destroy machines with their minds. 2)Both Neo and Paul (2Âº KH) are able to see visions more clearly after being blinded. 3)In both, humanity was enslaved by machines and the chosen one frees them. 4)Earth is destroyed and made uninhabitable in both. If this were in fact true maybe in the Dune Mythos Earth is still inhabited by machines without humans knowing!

The Indian couple in the train station were Sentinels
While I was watching the train station scene in Revolutions I had the thought that the programs represented by the Indian couple and their daughter might be the Sentinels Neo shut down with his psychic powers (they were going to be deleted because their shut-down was interpreted as a programming failure?). I'm pretty sure it's Jossed by the movies, but it would put an interesting spin on the Sentinels and the scenes of them being mowed down by the hundred in the Battle of Zeon.
 * It is jossed by canon; Rama-Kandra is responsible for managing recycling in the power plants (as he puts it; note that this means his job is to make sure the feeding of dead humans to live ones goes smoothly) and his wife is a software engineer. Surely these programs wouldn't be pulling double-duty as Sentinels, especially considering Sentinel duty would have nothing to do with their "purpose," which is very important to the Machines. The Second Renaissance still gives you What Measure Is a Mook? though; Sentinels have been around since the first days of 01, they are most likely individuals with independent thought and reason, but their purpose is to be soldiers.

The Machines use humans to gain access to Spiral Energy
If normal thermodynamics is used to find out what heat energy and bioelectricity humans contain, it's complete Fridge Logic. However, humans have another advantage besides brainpower: Spiral Energy. After studying humanity the Machines discovered Spiral Energy, which is contained in the double helix shape of DNA. Spiral Energy, with its defiance of normal thermodynamics, can be used to run massive amounts of computing power, such as running a massive almost-realistic computer simulation, and that is why Machines like to use Humans as batteries.
 * It makes more sense, though, plus both Tengen Toppa Gurren Lagann and The Matrix are run by the Rule of Cool.
 * Agent Smith might also be an.

The Matrix itself would become the Anti-Spirals
During the Second Renaissance the machines discovered the danger of Spiral Nemesis and decided to imprison humanity in order to stop Spiral Nemesis. In this alternate timeline, the peace between humans and machines failed to sustain (or the One lost while Smith survived and took over the Matrix, explaining the Anti-Spirals' nihilism). When the Machines discovered that there are more Spirals out there, they decided to subdue all Spirals once and for all. Their ability to control probability is actually the future of both Human and Agent ability to control the Matrix. Also, the Anti-Spiral himself did put Simon in an artificial reality.

Neo and Company are the real bad guys
The real purpose of the Matrix is to keep humanity alive. After humans burned the sky and consequently damaged environment beyond repair, earth was left uninhabitable and humanity doomed to extintion. Then the machines felt the obligation -because the zeroth law- to create an artificial environment were the humans could survive. Actualy the machines don't need us for anything and maintaining us alive cost them energy. Redpills are a faction of fanatic malcontents who want to "free" a humanity that lives reasonably happy in the simulation and don't care if it's real or not. They don't hesitate in killing innocents in the process because "they are pawns of the evil system" and are thus acceptable casualties. The battery thing is bullshit they feed to their recruits to help rationalise their crusade, it doesn't make sense, but after generations of being told the same lie, everyone belives it dogmatically. Equally, they whisfully ignore that the bulk of the population would prefer life in the confortable simulation than the barren, inhospitable real world if they were given the choice, and that Zion can mantain alive maybe a few thousand people but not the millions in the Matrix, so "freeing" humanity would mean millions of deaths, or maybe they know it but think is a price woth paying, something like "let the sheep die and then the real men and women will live free afterwards". We only root for the redpill side because we are shown the story from their point of view and the entire movie may be viewed as a reflection of how easy can be to accept radical ideals if you only are shown one side of the equation.
 * A. I never rooted for the red pill side. B. Who are you and will you be my best friend?
 * I demand this to become a Alternate Character Interpretation. It's to good and posible to be a WMG.

The Matrix series is not the sequel or prequel to any other science fiction franchise.
The wildest WMG on this page!

The "Zion Archive" seen in Second Renaissance was not Zion's archive, but the Machines' archive about Zion.
A deliberate use of I Thought It Meant on the part of the filmmakers.

The Matrix is actually the future of the Internet
Think about it.

The Matrix is actually the instrumentalized humans from Neon Genesis Evangelion
As a person who watched End of Evangelion knows the Human Instrumentality Project is all about forcing humans into a single body and a false reality, aka The Matrix. The Instrumentalized Humans began to form itself as machines that are reminiscent of the Evangelion with its bio-mechanical nature, and even the liquid that humans breathe inside the Matrix is reminiscent of LCL. (Of course one could go for the more common and simpler explanation, the Matrix Real World takes place inside Instrumentality/Matrix).

Because Instrumentality was fucked up, the Second Renaissance and the whole "humans as batteries" ruse were formed as a substitute explanation for the origins of the Matrix. Smith might be a reincarnated Angel, given his general sense of "destroying all humans" (and fits in with the "agent=angel" analogy), and obviously Shinji Ikari is the first One, being the first human to be unplugged from the Instrumentality Matrix.
 * There was also the mention of a first Matrix which served as a paradise for humans, but was rejected.
 * The Matrix is actually Neon Genesis Evangelion told from the Evas' and Angels' perspective. Humanity was already instrumentalized in the first place: they were making this whole "real world" thing so just they could create an entire universe for themselves, perhaps to just play something like the Sims. Figuring that the Sims lagged and had to be set to low settings (hence the Mind Screw in The Bible), they decided they must harvest an infinite energy source: Angels. Thus humanity waged war with the Angels, who are actually the real humans (why is their progenitor called ADAM in the first place?). While the Angels are ultra-powerful, their intellectual capacities were greatly limited (or at least driven primarily by instinct rather than reason) while the Humans excel in intelligence, hence why the Angels lost (we have technology that allows us to copy their physiology). The so-called "humans" turned them into Evas, which are virtually batteries used to harvest the Angels' limitless potential. With limitless power, the Sims can run with greater physics, but unfortunately we set the settings too high, becoming the Matrix which eventually became Real Life. All because the "Human" Hive Mind got addicted to the Sims.
 * The connection port used by Matrix humans to connect to the Matrix is the location of the Eva's entry plug (control center used by Eva humans). Oh, and the Matrix is apparently based on anime.
 * According to Word of God, it was based on Ghost in the Shell.
 * Only the world inside the Matrix is Ghost In the Shell, the world outside the Matrix is Evangelion.

There is a human space empire out there that will return and crush both the humans and machines.
Some humans(military forces) fled into space prior to the sun-blocking trick out of disgust because the human nations earth did not just nuke 01 with thousands 100+ megaton weapons and win the war instantly, or simply smash the robots without giving them a country of their own in the first place. For hundreds of years they have lived in space(primarily gathering resources from asteroids and comets). They have become cybernetic to the extent that it is impossible to distinguish between their mechanical and organic components. When they believe that the machines have weakened enough they decide to invade and reclaim the home world. After an orbital bombardment campaign(read: dropped 10km wide bolides for two years), they invade in what would be best described as flying tanks and lay waste to all remaining defenders using tactical thermonuclear warheads. They are disgusted by the poorly thought out military tactics displayed by the humans and machines, and even more disgusted when they sue for peace and use a bunch of half baked philosophical arguments to back up their positions. They only give one response; a faceless green-skinned avatar appears in the Matrix. It does not give an ultimatum or dictate peace terms. It only repeats the same statement over and over. "Anonymous: We are Legion. We do not forgive. We do not forget. :D"


 * No humans you are the Necrons! And then humanity was robot zombies.

The Matrix is what eventually became out of Silicon Sphere
While Eddie Matrix is still quite sane at the end of Virtual World, the Virus in his brain implant will eventually gain control over him, forcing him to make a new version of his Matrix OS mixed with elements of Silicon Sphere, called simply "The Matrix".

The Matrix is the Autobot Matrix of Leadership!
It's designed for computers; its entire purpose is to ensure that the Autobot race continues. Prime's rock in the middle of his animated chest is the Machines' flash drive.

The Machines had other fish to fry in addition to the human/Zion problems.
Come on. Zion has less than 20 hovercraft? Each of which doesn't have that many weapons on them - but when Trinity and Neo get up to the surface, there are GIANT defender ships and millions of sentinels. Don't tell me all that was to hold a few hundred thousand puny humans in check. Maybe aliens came by and were at war with the machines for a while. Who knows? Maybe the otherworldly construction of the sentinels and ships was salvaged alien technology from that war.
 * Maybe the vast majority of the Machines don't give a rat's ass about Zion because only a few fanatical anti-humans believe the prophecy of the One. It took the die-hards that long to build up the resources to create the attack force seen in the third film, because it's such a low priority to the majority of Machine society since the leakage of a mere few hundred thousand humans are seen as posing little threat when there are billions more to replace them.

The Matrix is TV Tropes

 * and the red pill is the red X button in the corner that lets you get away from the sheer addictiveness of your computer.

The Merovingian was playing the long game here.

 * The club which Neo goes to in the very first movie was the Merovingian's club. He knew the identity of the one (knowledge is his business, no?) and so engineered directly the events which would lead to him becoming the One completely, and thus set in motion the events of the entire film trilogy. Why? Because he knew that in the resultant power struggle when the Matrix was re-invented, he would be able to seize extreme amounts of power and knowledge as the code was rewritten, establishing himself at a near God status. How? Because he knows everything, he knows he can get access to Neo via his druggie friends we see at the begining, planted the Whitee Rabbit tattoo and knew that the Freedom Fighters would spot that particular detail.

The Robots That Created the Matrix Were Stupid

 * Their first act of stupidity is the use of humans as super-battery power. Why not cows? The Matrix would just have to be a huge green pasture with ponds. Maybe they wanted to rub salt in the fact that they won the war? (Executive Meddling may have caused this, the original script's giant neural computer is more plausible.) Second act of stupidity: Hard Lines? Even if that were the only way to get out, why not put humans in the distant past? Surely the Crusades weren't too pain free and perfect for the human mind to accept? They could have used this. Dodging crossbow bolts can look cool too.
 * Well, they tried to make it as modern as possible, the Crusades were too cruel to be accepted by the modern man (Inquisition, Corrupt Church, etc.). Also, you really need to make it in a way that exemplifies "I killed that dude in Bullet Time".

There are only about 20 Million Humans Left

 * The nuclear war which caused humanity to surrender to the machines, the years of starvation and a loss of all technology as a result of very little solar energy, and the casualties caused by the previous five matrices chipped away humanity to the point where the entire matrix can be contained inside the Megacity, a few surrounding regions and maybe a vacation spots. That way, the Machines can stop wasting untold processing power on maintaining a people farm and work on bigger problems, such as getting rid of the exponentially expanding cloud of nanobots. This explains why the only scenes outside of the city are in the mountains, and in Zion, and why we only catch a glimpse of thousands of pods, rather than billions.

Trinity and Cypher were in a relationship before she went to the Oracle
At first I thought he just had a creepy bad guy crush on her, but think about it. It's implied that you're not supposed to share what the Oracle has told you (Morpheus tells Neo "what was said was for you and for you alone"), but Cypher not only knows that Trinity is supposed to be in love with The One, he goads her about it ("Look into his eyes. Thise big, pretty eyes..."). Why would she tell him that if he wasn't somehow involved? My guess is that she broke up with him because of what the Oracle told her, and that's part of the reason he has such a grudge about the Crapsack world he's now stuck in.

The previous Ones all looked and sounded identical to Neo in every way, and he was different from them because of love.
Some of the monitors in the Architect's room were in fact showing the previous Ones. The One was in fact another system of control, so it's not a far stretch to think that the machines used the same cloned body / RSI multiple times.

The only reason the current One (Neo) chose differently from his predecessors was Trinity. This was a Xanatos Roulette started by The Oracle when she told Trinity that she would fall in love with The One, because unlike The Architect she understood that Love Makes You Crazy and bet everything that Neo would go against the grain. She was right.

The previous ones did not have anyone that loved them as much as Trinity did to Neo, which was why letting Zion be destroyed and starting anew seemed to be the only choice. Yes, the end of the cycle and the war came down to love.

The Machines are using humans for Exordium.
In Alastair Reynolds' Revelation Space series, the Conjoiners are able to apply their minds, with some technology, to gain limited insight into the future or from alternate universes. No mention is ever made in-universe about machines being able to achieve this, and indeed it is implied that only humans can do this. In The Prefect, it is also implied that human minds are also in some sort of Matrix-like dream state as this is being performed.

Thus, the Machines need human minds to perform Exordium, and the Matrix is maintained to keep them busy and ignorant.

The real world is not the real world, and everybody and everything within are programs.
It is all just a game on someone's computer, albeit a very complex one, whose player doesn't know that some of the characters within are sentient (similar to Re Boot). Those within that notice glitches in the 'real world' Go Mad from the Revelation and are likely Driven to Suicide, knowing that, being not real themselves, they can't ever escape to the real real world.

It was the Oracle who resurrected Smith...
Think about it: her goal was to disrupt the endless cycle of the Prophecy, the One, and the destruction of Zion. Restoring Smith and giving him his assimilation ability would be something the Architect couldn't have antisapated, and would make him the perfect means to her ends. You'd almost feel sorry for Smith, to the very end he never would have guessed he was being used...
 * And, if you think about it, Smith called the Oracle "mom".

There is a good reason why the machines are using humans as an energy source
Because, in the Matrixverse, humans are actually immensely powerful star beings, that radiate just as much energy as the Sun, eyt are smaller and easier to manipulate. The Matrix was programmed into making us perceive reality through the eyes of much weaker, powerless beings so that the plot of harvesting energy would see laughable. This also means that nobody actually escaped the Matrix and that the machines are just fucking with the protagonists.

One day, though, a human being might really escape the Matrix, and when doing so s/he will unleash his/her solar powers and blow up the machines.

The Machines are trying to protect the environment
The Zion Archives is propaganda. The thing about using humans for energy is propaganda. Zion and the rest of the "outside world" is still The Matrix. The Machines allow red-pills some control inside the Matrix, but keep a solid simulation inside Zion, and the outside world due to a lower population (less brains demanding sensory information, less number-crunching required). The Machines get their energy from the "form" of fusion hinted at in the first film. When humans created AI for the first time, the machines realized what damage humans were doing to the biosphere. As a result, they bottled up the humans inside their own world (and erased their memories), in order to keep them from doing more damage. When the red-pills got out, the Machines created the aforementioned simulation of an utterly destroyed earth, in order to convince the humans of their wrong doings. The Machines could not outright tell them that they were still in a simulation, so they made a cover story (the events of The Second Renaissance) in case the red-pills tried to search for information as to why the "earth" is like this. Naturally, they found the information, and built Zion around it. Once Neo came, the Machines thought it would be a good idea to break the news subtly by making his One powers work outside the Matrix. Unfortunately that didn't work, but the events that followed (the end of the "war") were good enough for the purposes of the Machines.

The Merovingian is the Chess King.
Note how the closest he ever got to being harmed was when Trinity "checkmated" him in the nightclub. What's more, he and his wife are first seen right next to each other, like King and Queen at the start of a game. As for the Twins, they were two identical henchmen with the ability to pass through obstacles, not unlike Knights.

Neo is the One because he can use both Vim and Emacs.
This is clearly demonstrated when he first invokes the-One-powers. He's using Emacs, and uses C-g to. Then he switches to using Vim and uses daA to.

Alternately…

The Matrix runs on Emacs, but the redpills can only use Vim.
Neo becomes the One when he runs M-x viper-mode.

Seraph was once an agent.
The Matrix Reloaded shows us that Seraph's code is yellow instead of green. The Matrix Revolutions tells us that Seraph is nickamed "Wingless" and he once fought Smith. This allows us to infer the following:
 * The color of his code is different because he belongs to a different version of the Matrix.
 * The nickname "Wingless" makes only sense if we admit that Seraph once had wings and there were others like him, so the status of being "wingless" makes him abnormal.
 * The dialogue between Smith and Seraph implies that their previous encounter happened a long time before, when Smith was still an agent and fought to maintain the status quo within the Matrix, which means Seraph's existence was not part of the status quo
 * From these guesses, we can furtherly infer that Seraph, in the previous version of the Matrix, had wings and worked as an agent, and he was not the only winged agent. Then the Matrix was rebooted and new agents, made to look like men in black, were made. The winged agents, now obsolete, were meant to return to the Source and be deleted, but they refused, because they saw the other agents as an anomaly. A fight between the new and the old agents exploded. This was won by the new agents, who killed the old ones. However, Seraph survived, and, as a sign of truce, he agreed to not compete anymore with the new agents and have his wings removed as a visible sign that he is no longer an agent, just like Smith had his earplug removed when he was no longer an agent.
 * Considering that a seraph refers to a six-winged angel that has direct access to God, it's possible that Seraph was an agent from the first perfect version of the Matrix.

Morpheus and Trinity's real names are Cornelius Fillmore and Ingrid Third.
The show Fillmore! is about their childhood and takes place entirely inside of the matrix.

The "Real World" isn't the real world, the Raposa World is.
The Matrix is not controlled by Robots After the End, but Wilfre in his castle...thing. Neo is Jowee, and Trinity is Mari. That means both  died, and it's all Wilfre's fault. Then again, when isn't it?

The Merovingian is a previous One...
And Persephone is a previous Trinity. (Why not? They're both hot brunettes with a penchant for guns, and each has a husband/lover who enjoys dressing in a black suit.)

In one of the previous incarnations of the Matrix, the Merovingian is told by the Architect that Zion had fallen many times before. He was given a choice - and he chose to return to "the source", but under one condition - he would get power for himself and his love, Persephone. The Architect agreed and set him up as the de facto ruler of the Matrix.

Fast forward to The Matrix Reloaded -- Persephone tells Neo that the Merovingian was "once like you" and she wants a kiss "to remember what that was like." After she gets her kiss, she tells Trinity that "it never lasts." "It" being love.

Which explains the Merovingian's hatred of The Oracle - she never told him that he was one of many "Ones" she sent to overthrow the Matrix, allowing him to think that he was special. He hates her because he now knows that he is NOT special, and because she represents a threat to his reign.

Also, Persephone's bitterness can be explained as that she now realizes that her husband chose power over love. And that Neo truly loves Trinity as much as Trinity loves him.

Matrix explains where did humans ended up in "Life after people" documentary.
The matrix is a holding pen where humans are unharmfull. They created two matrices (the one within the "real world" and the "real world" where Morpheous and Trinity escaped to) to keep humans busy and distracted in that prison while machines repair the damage done by humans, also the whole war thing happened within the "real world" Matrix, outside both matrices the ACTUAL real world is much like "Life After People" and machines are restoring life and the environment.

Both the real world and the Matrix are real/fake.
The Matrix is a computer simulation in the real world, and the real world is a computer simulation in the Matrix.

The Machines use humans neither for energy nor processing power, but as lab rats in philosophical and psychological experiments.
We all know that the human battery premise is laughable: the machines could launch themselves into space to harvest limitless solar power, or if the machines really need bioenergy they could have just hooked the Matrix up to a bunch of cows. And we all know that what the Wachowskis originally intended was the Machines using humans as supercomputers. While that would be more plausible, if that was solely processing power surely the Machines could have been advanced enough to devise quantum supercomputers efficient enough to surpass human brain potential. Why do they keep humans? Why. Even though they may have achieved a technological singularity to need humans anyway, the Machines still cannot answer the question of what is mind, what is life and why do they exist in the first place, and so they experiment on their own creators to explore that, thus the reality of the Matrix and the machines' advanced-enough philosophical knowledge. The Matrix, a bunch of code that we see as reality, could just as be in its base a giant test on perception. And surely, Morpheus showing a lab rat imprisoned in a maze to Neo would have the same impact, if not more, than a Product Placement Duracell battery?
 * TL;DR: The Matrix uses humans to find the Ultimate Question of Life, The Universe and Everything.

Neo is a technopath.
He has the ability to control machines both inside the Matrix and out. It was easier for him to control things while in the Matrix, as everything was data for him to manipulate, but he eventually got to the point where he was able to control (or destroy), machines and data in the real world.

The story is just repeating itself. Also, everybody is dead.
At one point during Reloaded, the Architect tells Neo that he is in fact the 6th "one" that shows up, implying that history in the Matrix is somehow cyclical. However, this could extend even further.
 * What happens to the person an agent is possessing after the agent is killed? Why, they never show us. However, it is strongly implied that the person's mind and the agent's become one, and by killing the agent, you also kill the person. what happens, then, when an entire world's worth of people possessed by agents gets killed by Neo? The only people that we see in the city in the end of Matrix Revolutions are the Architect, the Oracle and Sati... all of which are programs. Yep, not a single person around. This means that Neo just exterminated 99% of mankind (if we consider that 1% are living in Zion, that is). So the war is essentially won for Zion, because without energy, the Machine Empire will collapse, not before, however, delivering a final strike into Zion which all but annihilates it. The remaining humans in Zion then begin the hard task of resettling the Earth, While all the machines around them fall in disrepair and eventually disappear. They begin associating Neo with the figure of a Messiah, and the Matrix with their paradise lost, to which they would return after a life of hardship. That is: history begins yet again. Until, of course, they invent the Machines again, and the cycle will restart.
 * This also explains why the Architect and especially the Oracle know past, present and future: Because everything is happening just the way it happened before. They have noticed the patterns of history, and became Genre Savvy through sheer experience.

The Matrix is just a means for the machines to occupy the humans until their REAL goal is accomplished. The real goal is to terraform another planet for safe habitation by humans.
Following zeroth's law, the fact that they want to preserve humanity, and the Matrix is really just a game designed to keep the humans occupied until the machines are done. They have billions of Sentinels because planets are pretty big, and to convert an inhospitable rock to a less-inhosbitable rock would take a massive amount of resources. The machines want efficiency, so the Matrix (the thing that probably takes obscene resources to maintain) is just a placeholder for the humans. The more Sentinels they make, the faster the terraforming. Ergo, they want billions of Sentinels.

Or maybe they found a nearby hospitable rock, and it had inhabitants that Zeroth didn't make a law about…