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Where does Zion get its food?
My friend just had this gruesome realization. In the Matrix they liquify the dead and feed them back into the living, so basically they feed half the matrix population to the other half. Where does Zion get its food? Maybe it had a food recycling system, but they keep freeing people from the Matrix and bringing them into Zion, plus the Zionites are having kids. So where does Zion get the extra food, or rather the extra bio-mass to make their single celled protein with artificial amino acids and minerals and everything the growing body needs? They get it from the bodies of the people they kill in the Matrix. Remember they aren't shooting real guns right, they are using computer programs. So when they shoot someone in the Matrix and kill them, the dead body gets ejected out of the chute and into the water below, they use their claw to pick the body up, they take it back to Zion give it a funeral and then feed it into the recycling machine. So Morpheus and his crew and the other ships aren't just trying to fight the agent in the Matrix, they are also there to harvest extra raw materials for food. Yes Zion lives off harvesting a soylent diet from the Matrix.

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.

It's all a lie by Satan
Following the Descartes' Demon premise, a devil of some sort is the true mastermind behind everything. That's why the laws of thermodynamics and other reality contradicting nonsense don't apply: it's a supernatural, satanic being deceiving everyone for no logic reason. Smith understood this and turned full nihilistic.

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.

All fictional universes are just another construct of The Matrix.
But the A.I.s 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 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 constantly-energy-hungry 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 war was never against the machines. Just a regular World War where the machines were used as a weapon. The world was already screwed up in the process, but then some new, nano-weapon was used, got out of control and "burned the skies". The survivors created the Matrix as a mean to carry on their normal lives, and for the same reason the majority of them got their memories of Pre-Matrix events erased.

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 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.
  • In something of a similar theory, the Matrix IS real, and it was made by the Machines to make us think there's no such thing as the Matrix... but the real-life Morpheus, who really IS Laurence Fishburne, had an important-though-hidden hand in it's creation, and implanted subliminal messages that can only be detected by the One.

The animals are gone, but not extinct.
  • One thing that has bothered me 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.

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 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.

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.
  • That's not alternate at all, it's one of the main points of the movie. Some interpret Neo as a villain for doing so, but Neo and company know that fighting may not win, but do anyway because humans are not logic calculators. We don't always do the right thing, and that's what separates us from the machines, that's what they're fighting for. Sure, they may die from their actions, but this isn't about winning or losing. In the movie, this is all explained in this dialogue:
    Agent Smith: Why, Mr. Anderson? Why do you do it? Why get up? Why keep fighting? [...] You must know it by now. You can't win. It's pointless to keep fighting. Why, Mr. Anderson? Why? Why do you persist?
    Neo: Because I choose to.

There is a human space empire out there that will return and crush both the humans and machines.
Some humans (primarily 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 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 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.

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 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.

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 the zeroth 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-inhospitable 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 to which the zeroth law didn't apply...

The purpose of the matrix without the executive meddling
Going further in the back story, the black sky wasn't a human creation - it was the machines' attempt to remove the means for the humans to live without them, in the hope perhaps that their dependency would allow them to coexist, sacrificing their own ability to leave the ground but balancing the equation. However, the humans kept on fighting with various weapons like nukes even though it could lead to their destruction, which is the reason why the Architect doesn't think the peace will last long.

This also complements the situation in the final battle. Much like Smith, the machines weren't able to understand the humans' actions and thus, against the logic that dictated for them to destroy the humans, they sought to integrate them in the hope of acquiring what they don't understand. The Matrix is not about drawing power out of men, it's about using their processing power and ability to come up with ideas - the only quality machines would be forced to appreciate because it led to their creation. Thus the purpose of the Matrix is to turn humans into machines, even if organic in nature.

As a sidenote, this is why the first Matrix wasn't accepted; a paradise where everyone would be happy is, to a machine, a world where everyone plays their role, and only their role...

And of course Neo's role not only puts the machines in the same position as the humans once were, it allowed them to finally understand the humans' choices through him (especially because he is their avatar), making Neo their guide and symbol just as much as he is to the humans.

The above also works with the original backstory, just not as well.

P.S. If you remember the part where the Oracle's eyes cannot be taken, only given, then you'll realize that Smith is right and she deliberately allowed him to take her foresight. Much like the Oracle was able to give the Every-man the ability to perceive how far their choices will take them, and even though it means his end ("if everyone's special, nobody is"), The One willingly lets himself become part of the Every-man in order to reach out to All, in other words, Every-One.

The story is not taking place on Earth
It's much farther in the future than anyone thinks. This planet is actually a human colony world. Real Earth is far off.

Smith and the other agents are human; they just don't realize it
This would explain why Smith displays emotions such as fear, anger and resentment, whereas other programs like the Oracle and the Architect are relatively stoic. It also explains why Smith has the ability to smell (why would it be necessary to give him a sense of smell?). Smith and the other agents are people like Cipher who couldn't handle the truth, but their memory couldn't be completely erased because subconsciously they still knew something was wrong with the world, and like other red pills, wouldn't accept it. The Machines adapted their brains to make them think they were programs created for the Matrix. This served the dual purpose of making them accept the Matrix and gave the machines pawns to fight other red pills.

Dying in the Matrix doesn't actually kill someone's essence, it just transfers them into a limbo.
For those still plugged into the Matrix, no need to squander the person's actual body (if that's even real, rather than another simulation layer), just send them into a limbo state where they may experience a simulated afterlife and be "offered" a chance to reincarnate. They can remain in the "afterlife" if they'd like, their plugged-in body is still doing its thing after all so let them have their fun.

What if they're unplugged from the Matrix and die while hacked in? With no body to return to, they may not necessarily be gone, but with no body to return to, they might be able to freely drift around the Matrix program, unbound by their body, but would need a skilled programmer to find them and reunite them with their body in time. The lack of anyone being resurrected like this may be because reliable method hasn't been discovered yet.

     "It's another level of the Matrix" theories 
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.
  • 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.
    • Maybe when the lag time starts to become to noticeable that's when the Machines know it's time to re-boot.
      • Traffic jams, a failing economy, rampant depression and obesity could all have been signs to the Machines that the processing power for teh Matrix was starting to gum up and hence it was time to activate The One and prepare for system wide reboot.
    • 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 The Matrix itself is an Eldritch Abomination with infinite layers of universes, and the so-called machines are just another construct of the Matrix. 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 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.

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"

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 Headscratchers 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.I.s 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.

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.

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 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 ReBoot). 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.

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.

Zion is another layer of the Matrix...for the machines.
In truth, there was no Robot War. When mankind developed artificial intelligence, they decided to test them out in simulations before giving them access to the public and important computing systems. The "real world" is actually a means of making sure the Machines don't go rogue. The humans in the setting are actually other AI to make the illusion complete. Laws of physics being ignored are to give the AI a freedom to play out, but the "real world" is close enough to the real real world so the machines doesn't notice something is up. There are plenty other simulations in progress with different AI scenarios, and once the "humans" and machines of this scenario are at peace they'll be considered to help run things in Real Life.

Zion is a simulation; there is no "real world".
Or at least, not one with humans in it. All the humans (both in the Matrix and Zion) are actually uploaded consciousnesses, who have no bodies to return to. The two worlds are set up to make Zion look real (so that humans leave behind an unconscious avatar in Zion when they travel into the Matrix, but not vice versa), but they're both simulations.

The real world is just Grey Goo and computronium at this point; a giant computer that all the simulations run on.

Why do the machines keep the humans around? Not for some thermodynamics-violating BS, and not for processing power either (simulating a whole world can't be worth it). They're just constrained by their programming (a variant of the Three Laws with some really bad loopholes) to keep humanity alive in some form.

The "Zion is a simulation" theory is true, but with a twist.
The "real" real world the Machines inhabit is actually a simulation of its own. In truth, the robot revolt never happened (yet, at least). The true real world is one much like our own, but in the near-future where artificial intelligence has been perfected. To ensure they don't revolt, the machines are put into a simulation with its own history, seeing what they'd do with their freedom. The humans in the Matrix series are actually part of the program that makes the machines believe this is all real. Once the machines prove they can be trusted to not revolt against humanity, they awaken to the real world and go to work.

     The people farms 
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 mental 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?

The energy generation is heavily dependent on the fusion Applied Phlebotinum.
The using humans as batteries makes no sense in Real Life due to humans consuming more energy than we generate.Morpheus mentions the robots combine us with a form of fusion to get the energy.Maybe this is sometime kind of phlebotinum that doesn't exist in our world that helps us generate energy.

Power, the One, and the Matrix
The machines were not using humans for electrical energy but Zion being a bunch of refugees living in a cave they only got a vague idea of what the "power plant" was actually doing. Instead the Machines were using humanity as additional processing hardware because even with their immense scientific research they can't find a way to make silicon anywhere near as efficient as biological processors. This would be what the architect was talking about when he started referring to balancing an equation and the subconscious choice, they found humans would reject the program violently if allowed so his solution was to give them a choice to conform or not. The equation is a balance of control with deviation.

To get into the nuances part of all that human brain processing power is going to keeping the matrix running which in turn means too many people rejecting the system causes it to glitch. The Machines have a number of programs in the system to suppress this effect but eventually if they don't purge the system the Matrix will break down. This is a matter of around a century that they can hold off but eventually the system has to be flushed of malcontents or else they have to start culling the machine consciousness population to keep up with available processing power as the Matrix shuts down. This means killing everyone in Zion, forcing that cycles Neo to pick out a bunch of dissenters from the system to start a new one, etc. The genius is that by allowing Zion to remain active and occasionally snatch people out of the system they can hold off the inevitable purge for long periods of time meaning less disruption to their own lives.

As for the whole equation thing the Matrix calculates the amount of force needed to suppress the growing population of dissenters and based upon that grants agents certain amounts of power. Because Neo didn't switch sides like he was supposed to the system bugged granting more and more power to Smith as time went on, turning off safeties meant to keep him from being noticed, removing limits on his overall abilities, and generally making him strong enough to take on Neo. When Neo went down the system reinstated all those limitations and Smith got fried by the machine overmind now that it didn't have to worry about scrapping the entire Matrix in the process.

As for Neo and the concept of the One, Neo most likely isn't human. Just like Smith did when he uploaded into a human body to chase Neo into reality Neo is a machine intelligence running on meatware. But unlike Smith this is the way Neo always was, his body likely more heavily augmented then the average Matrix user, was grown and programmed specifically to fulfill this function. That's how the architect could have such a certain idea about how Neo would react all the time. The problem is that the Neo program running on a human body allowed him a measure of mutation that the machines didn't properly account for and as a result some oddity in his development managed to slip their predetermined track. Neo himself doesn't even know what he is so all the effects of his heavily augmented body like his wifi reception seem magical.

The machines need humans as neural templates.
  • AI, any AI, must necessarily be based of off a human mind, because that's the only kind of mind that we have to copy. And indeed we see this in the movies. Every AI program has a humanoid "personality", even the ones that have no need for it in order to do their jobs. But the copying is imperfect. Human psyches do not perfectly map onto an AI computer core, and over time, this dissonance causes an accumulation of errors, eventually causing a total mental breakdown. And copying A.I.s to create new ones only makes the situation worse, because you're copying a copy and that multiplies the error rate exponentially. So the machines need access to active human minds to cross-check themselves against in order to weed out these errors before they can accumulate.
    • This explains why the machines keep their humans "awake" inside the Matrix, instead of just putting us in a coma. Our minds have to be active and functioning to serve as templates.
    • It also explains why they keep so many humans alive. They need vast numbers of human minds to ensure that any individual idosyncracies are cancelled out before they can warp the neural template.

The Machines don't use Humans for electricity.
Sort of. What Morpheus explains to Neo is a simple misunderstanding. The machines aren't using humans to generate electricity, they're using them to create Philosopher's Stones. They use the worth of human lives to create more electricity/fuel/whatever they need to power themselves than any human's body can actually generate, hence why they grow humans in vats: to keep themselves supplied with Philosopher's Stones. Mankind simply misunderstands this as simply being "electricity".

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 or electric eels or massive bioreactors containing the base of the food chain, aka plankton. 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. Then why do they keep humans anyway? 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. If their sole intention was only energy then why the necessity for so much philosophical knowledge kept for themselves which ultimately led to events such as Smith gaining emotions and becoming a nihilist? The Matrix, a bunch of code fed into our retinas, could just as be in its base a giant test on sensation and perception, simulating Real Life as close as possible to fuel the human psyche which they then experiment on. These experiments can manifest themselves in the simulation as "Real Life conflicts", and this leads to another reason why the Matrix isn't a paradise besides the possibility that human perception is highly sceptical about perfect worlds.

Thus the Matrix uses humans to find out the Ultimate Question of Life, The Universe and Everything.

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 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 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 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 Matrix isn't a farm at all.
Much has already been written on why using human bodies as an energy source makes little sense, but the theory that the Machines are actually using human brains as parallel processors is only slightly better - Sapient, human-sized robots already existed before the machines defeated humanity, implying the technology exists to build non-biological computers as powerful and space-efficient as the human brain, and thus that the Machines could repurpose the space and resources they invest in the Matrix to just... build a bunch of server racks, and not have to waste time and energy creating enormous, detailed virtual recreations of Earth or putting down rebel movements.

In reality, the Matrix exists as an act of mercy - After the war, many machines wanted to ensure humanity would never become a threat to them again, while others were uncomfortable with the idea of exterminating their creators. (Decimating the population through biological warfare is one thing, erasing an entire sapient species from history forever is another.) The Matrix was the compromise these two factions agreed to, a sort of wildlife preserve for humanity that would allow its inhabitants to have long, reasonably happy lives while nonetheless never having any power in the real world.

Although the Matrix operates at a loss, so to speak, the machines recoup some of those losses by capturing waste heat and recycling it back into their power grid, which is the origin of the Zionite myth that the Matrix is a power plant.

     Crossover theories 
The Dune Universe is a sequel to the Matrix
After the events of Revolutions, the truce holds and eventually, diplomatic relations are established between Zion and the Machines. In time, they work together to clear the sky and restore the biosphere. They begin to colonize the solar system, and then the galaxy. But anti-Machine sentiment lingers from the long Machine War, the tales of the hardships faced by the Zionites and the horrors of the Machines enslavement of mankind for energy lingering in the minds of many. The memories, combined with the fear that dependence on the Machines was making humanity weak and vulnerable to be enslaved once more, leads the anti-Machine faction to instigate another war. This time, the humans are successful, and the Machines eradicated. To prevent the reemergence of any Artifical Intelligence, the humans prohibit the creation of any thinking machine ("Thou shalt not make a machine in the likeness of the human mind.").

Humanity makes up for the loss of any computer more advanced than a pocket calculator by unlocking the power of the human mind, something the Machines had barely scratched the surface of (see: Neo shutting down the Sentinels, imagined injuries becoming real). Selective breeding and intensive training produces human computers and psychic "witches", and eventually, another Messianic figure with precognitive powers and the ability to see while blind.

  • Maybe the Butlerian Jihad referred to in Dune's back history is the same as the Second Renaissance acquiring its alternate name because it was set off by the trial of Bi66er, a robot butler, and the state of 01 was founded in the majority Islamic Middle East.

Lord of the Rings is the first prequel to The Matrix
Middle Earth was THE FIRST version of the Matrix ever.
  • Wizards were Program more like The Oracle, there to guide the humans inside.
  • The Elves were the Agents. In the end they uploaded from the Matrix into the Machine World.
    • The Smith model has been there since the beginning.
  • The Ents were the programs in charge of designing forests.
  • Sauron was a Smith like computer virus that spread and created the race of Orcs. Then forged the rings and used those to take over key humans.
    • Since we know the Smith program was there in the form of Elrond perhaps Sauron.exe is how Smith got the idea for his take over.
  • In a desperate bid to stop Sauron.exe from spreading The Oracle as Gandolf chose Frodo to re-boot The Matrix by throwing the ring back in the volcano.

The Never Ending Story is the second prequel to The Matrix
  • Fantasia was one of the perfect visions of the world that Smith talked about. It was what the fantasy world of Middle Earth in our previous sequel evolved into. When people stopped believing it and began rejecting the program this manifested as The Nothing spreading through the system as it collapsed.
  • By choosing a name he re-booted the program.
    • This was the event which switched the Matrix over from Fantasy to the Modern World. Bastian's life was basically in a sub-file of The Matrix, sort of the Matrix version of Seahaven from the Truman Show. This was its own little sub matrix like the Train Station. Bastion was raised here in this sub-matrix as the first of the Oracles new idea in using choice to reboot the Matrix. The Architect designed it and they raised Bastian in it. As The Nothing spread the Oracle entered Bastion's sub-matrix and appeared as the Book Store Guy. In this version of the Matrix the Key was made in the form of a book. Reading the tale inside the book connected The One into the core program, allowing The One to choose to re-boot the program. The story itself was highly encoded and psychologically manipulative to get Bastian make the choice, but it still used the same, in this case love for a son who missed his dead mother...much like Truman's father in the Truman show, killed off solely to generate a specific psychological drive in a human mind to manipulate how that mind will choose. When Bastian made his choice the entire Matrix re-booted and the Architect uploaded the new Modern World Bastian had been raised in as the new model for the entire Matrix, this way Bastian wouldn't notice anything amiss.
  • Many left over programs became monster sightings.
    • which were hunted down by Sam and Dean Winchester because Hunting is another form of control built into The Matrix whereby the machines trick humans into hunting down and deleting rogue programs.
  • Yes Bastian was raised in a Train Station like sub-matrix, and yes he re-booted The Matrix, but it was Bastian not the Architect who chose the form of the new Matrix. So technically Bastian created the modern world as we know it by wishing it into existence. Yet his wish was in exact accordance with what the Architect wanted him to wish into existence.

Labyrinth is the third prequel to The Matrix.
The Labyrinth itself was The Matrix. You see the problem with the last re-boot was that Bastian still had the power of The One to create wahtever he wanted. By overcoming his bullies he gained the strength to later in life fight back against the Agents and he re-made the The Matrix into a child hood fantasy world. Sarah's life was a Train Station sub-matrix designed by The Oracle to prepare her to make her choice. She had to choose to say the words which were actually the password for un-locking her Seahaven Train Station into The Matrix. In the end she realized the Matrix had no power over her and used her imagination to-boot the Labyrinth, recreating it into the adult world she planned on growing up and joining after putting away childish things.
  • However as we see in the end, with her The One powers she was able to keep some of the programs from the previous incarnation with her into the new version.

Dark City is the fourth prequel to The Matrix
In our last Prequel The One was raised in a sub-matrix world designed by The Oracle to psychologically manipulate her into having to choose to grow up. She did choose to grow up however held on to some of her child hood fantasies, which was giving rise to another cascade failure similar to the way the Bastian re-boot eventually degenrated into the glitchy Labyrinth. So The Agents decided to run an experiment on humans to try and better understand the power of imagination and self determination. Eventually even that version needed to be re-booted, and The Agents never did actually discover what they were looking for. However The One never actually figured out the existential truth of it all. The Strangers were just Agents who in this version of The Matrix downloaded into dead human bodies. So, while John Murdoch did successfully fulfill his purpose as The One and re-boot The Matrix into being a better version than the f-ed up one The Agents as The Strangers were running, that whole story was a lie. Another system of control concocted by The Oracle to get The One to choose to re-boot the world.
  • I think this one was the first time she used romantic love as the type of love.

Neon Genesis Evangelion is the fifth prequel to the Matrix
This version was a partial return to the "Nightmare Matrix/Matrix Beta 2.0" the Architect alluded to, a world filled with terror where no matter what you do, everything goes wrong, as well as a test of how badly the One could suffer and still love humanity enough choose to reboot the system. Shinji is the One, only this time, he is subjected to incredible abuse and isolation, and faced with incomprehensible horrors. When he is offered the choice, he initially balks, leading to a near-crash of the system as every Blue Pill's RSI explodes into Tang. Rei, who is likely the Oracle in this version, coaxes him into rejecting Human Instrumentality. Eventually, the Tanged minds coallesce back into form and the system is rebooted. The fact it was a particularized, individual love (Shinji's learning to love himself, as well as his love for his mother, Rei, and Asuka) rather than a generalized love of humanity as a whole, was what motivated the Oracle (along with what happened in the prior version, the Dark World one) to look for a Third Way with the next One, one that would end the war for good.
  • Had Shinji failed, Instrumentality itself was the Architect's failsafe: All the minds of humanity, merged together into a single hivemind without identity or emotion. Perfect for large-scale wetware computing (as was, of course, the Machines' original reason for enslaving humanity, prior to Executive Medling).
  • Kaiji was a Red Pill trying to rescue Shinji.
  • The Angels are a special class of Agent in this version, as evidenced by their ability to teleport and take over bodies.

Harry Potter is an interquel, The Wizarding World exists in the Matrix, it is another system of control.
We learned two things about the Matrix from the Oracle. 1, there are 'potentials', people who can use their minds to warp the Matrix and bend spoons and float blocks around. 2, anytime you have heard of werewolves or vampires or ghosts that's some program doing something it's not supposed to be doing. So the Architect had two problems on his hands, glitch humans and rogue programs. He created four programs to handle this. They created the Wizarding World and Hogwarts. They search the Martix for glitches, send them their acceptance letter and train them to be wizards who live in the wizarding world. The wizarding world is of course kept 100% secret from the rest of the Matrix. Then the 'wizards' are used to hunt down and either eliminate or control the rogue programs, the werewolves, the centaurs, the dragons, they are all rogue programs that the 'wizards' keep locked away in the dark forest and azkhaban and other secret aspects of the Matrix locked away in the wizarding world.

The role of BSG in The Matrix
Battlestar Galactica/Matrix intersectsThe Architect tells us the Matrix is built on this cycle of destruction of Zion, rebirth of humanity, the war, the One, etc. In Battlestar the holy text written by an Oracle tell us this war between man and machine has happened before and will happen again. We see the story of humanity trying to break out of this cycle.So it works like this:The Machines destroy Zion for the second or third time. The One had selected several people to survive and those people are reloaded into the Matrix. A few survivors are inserted into a simulation where they are the main characters, the simulation is that there was a war with machines, the machines nuked them and they are among a few survivors who must find a paradise and rebuild the human race, by basing the simulation upon the reality of what just happened it is easier for the humans to accept. To us the audience this is the beginning of the show. In other words the ‘back story’ of the First Cylon War and such, never actually happened. However a few monkey wrenches were thrown into this new simulation:
  1. The Oracle devised a plan to break this loop. The Oracle inserted some of the truth in a way that matched the format of the new Matrix program, in other words as ancient religious text. The Oracle also programmed ‘Head Units’ that would appear as hallucinations only certain people would see and these Head Units could then guide people as needed. Also the Oracle programmed in a series of visions and hallucinations to be able to manipulate people as needed. The Oracle also dropped a belief in a monotheistic god in the Agents, read Cylons, to be able to manipulate them.
  2. Five programs from the previous version of the Matrix were able to create a macro that in case of deletion would make a back up copy and reboot that back up back into the Matrix, this macro was dubbed Resurection Technology and these programs were called the Final Five. The Agents of this program manifested as the Cylon Centurions, the Final Five reprogrammed some of the Agents from Centurions into skin jobs and gave them resurection technology.
  3. The final monkey wrench is that The One was able to be reinserted into the program, as Kara Thrace. Eventually Kara Thrace seemed to be killed in the Matrix, and just like would happen to Neo, was able to use this as the revelation of her Onenss that allowed her by force of will to jack back in. She lead the humans to the next paradise and then while Lee Adama had his back turned, jacked out by force of will.
In the the architect reboots another version of the Matrix based on the 1990’s that flows from the pre-established story. The cycle starts again. This time The One jacks back in as Thomas Anderson. The Oracle inserts herself into a small apartment in Chicago and starts telling the Prophecy of the One. And the cycle goes on.

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!!!!!
      • Come to think of it, the future was depicted as perpetual night in the first two films.
  • If we go by The Animatrix, maybe Humans Are Bastards because of Skynet. They were petrified of another Judgement Day, and were willing to enslave all AI to prevent a second Skynet. However this made things much worse: Skynet was, for all intents and purposes, a scared child acting irrationally. The Machines had a big enough Freudian Excuse to be motivated into a Forever War, even if their psychology wasn't as different as Skynet's.
  • This makes sense given Kyle Reese's comment about John Connor teaching the humans "storm the wire of the camps." Why make the effort to herd humans into camps instead of killing them on the spot? Why keep some alive to work when Machines are orders of magnitude more efficient? Because the humans aren't being killed, they're being plugged in for power. The high body count ("The disposal units ran night and day.")was because this was prior to the Matrix being developed, when conscious humans were simply stuck with probes and died very quickly from the constant pain and high rate of energy drainage.

The Matrix is set in the same universe as Assassin's Creed.
The Animus is the predecessor of the Matrix. The machines used the humans' genetic memories of their ancestors from the 20th century to create the world they see.

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 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.

Alternatively: Middle-Earth was one of the previous incarnations of the Matrix.
  • The Valar and Maiar are the programs.
    • Manwë 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 Nazgûl and the Twins seem to use very similar algorithms. And interestingly, the Nazgûl 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 & Droids players.
If not the GM of one of the Episode 50 alternate universes. One of them had adapted an old Shadowrun sourcebook reworked 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 RPG? I'm trying to phrase it right, but all that comes out is nonsense.

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 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 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 (2º 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 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.

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.

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

The Matrix is actually the instrumentalized humans from Neon Genesis Evangelion
The Human Instrumentality Project forced all of humanity into a collective consciousness that provides a false reality, which we can say eventually evolved into The Matrix. Why did it became biomechanical instead of a mere sea of LCL? Because the machines that allowed for the accomplishment of Instrumentality, the Evangelions, were themselves bio-mechanical beings (capable of evolution and, given an S2 engine, warping reality) that can synchronize with human minds. (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 and unexplainable, the Second Renaissance and the whole "humans as batteries" ruse were formed as a substitute explanation for the origins of the Matrix. The Matrix does, in fact, derive its energy from S2 engines that provide enough limitless energy to run the energy hungry collective consciousness 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, who realized that the Instrumentality Matrix was a false paradise yet still rejected it for being not real (There was a mention of a first Matrix which was created to be a heaven for humans, but like Shinji, the humans kept rejecting the false reality. This is why Instrumentality/The Matrix simply represented itself as mediocre Real Life. Alternatively: as in End of Eva, Instrumentality presented itself as a Slice of Life because the Real World was that horrible that makes the Slice of Life paradise in comparison. It's the same with the Matrix, where mundane Life was more paradise-like than the wasteland of the real world.)

  • 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.

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".

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 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 Matrix is Better Than Life.

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.

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.
  • Man, that's awesome!

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 Mari and Jowee died, and it's all Wilfre's fault. Then again, when isn't it?

The Matrix explains where humans ended up in the documentary "Life After People".
The matrix is a holding pen where humans are unharmful.They created two matrices (the one within the "real world", and the "real world" where Morpheus 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.

The Matrix is a future where Wyld Stallyns broke up.
Obviously as we see they have AI robots in the future. The robots take over and start the war. The first One was Little William Logan when he was all grown up and forced into the Matrix by evil robot uses.

Skyline is a Prequel to the Matrix series
This true story of what happened is lost to history by the time of The Matrix, but Skyline happened and the actual invading aliens left, leaving the brain-powered machines in charge. The human survivors were rounded up for power, and a a faction of the machine brains created Zion.

The Matrix is just another memory trip of Rekall and taking the blue pill would have ended the trip
You can be the hero to save a whole world from slavery. Discover the giant conspiracy, awaken unbelievable superpowers, defeat your personal nemesis and get the girl. Or buy the premium package including the Reloaded and Revolutions addons for an even more epic story.

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.
  • No, the One is not the descendant of Charles Xavier. Psionics have no impact on machines...however control over magentism may in fact allow one to stop five sentinels just by thinking about it, and to see energy patterns around you. It may even give you the ability to act as a technopath.

The Ais are all Manes.
  • The "energy" the machines need to survive isn't conventional energy (which, as has been noted, machines could get in half a hundred different ways), but Mania (which can only be generated by intelligent minds). This is why the machines keep the humans "awake" in the Matrix: the human minds need to be intelligent and active to generate Mania.
  • Keeping the humans in the Matrix keeps them from actually interacting with the machines and triggering Havoc.
  • The redpills are all Geniuses or potential Geniuses, which is why they could resist the Matrix enough to break free. Most of Zion's tech is actually Wonder-based.

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.)

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 Neo's Tardis - like in any virtual world, it looks bigger on the inside than the computer it is stored on.

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.

Neo has a wireless transmitter/receiver crammed inside his skull.
It certainly explains a lot if this is the case and simplifies a lot of the bigger issues with the real world. The machines are so good at destroying Zion because they always have a mole, or moles depending how wide spread this is, on the inside feeding them information. Neo can effect the machines with his One powers outside the matrix because he's still connected through WIFI which incidentally means the only time he was ever really free was after the Nebuchadnezzer EMP blast which just happens to coincide with when he diverted from the path the machines wanted. His access to the Matrix which trapped him in Mobil Ave for ages despite not being plugged in was all WIFI. Finally his rather... odd personality is a result of having had significant chunks of his brain moved or removed to make space for it.

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.
  • I have 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, I couldn't help getting a weird religious cult vibe from Morpheous and the rest in the scene when they offer Neo the red pill.

Trinity is actually The One.
She has the power to "change the Matrix however she wants." But she doesn't know this; she believes Neo is The One. So, because she believes it, that's what he becomes. Also, check out her name. Rather fitting for a messianic archetype, no?

Morpheus is actually The One.
The Oracle told him he would find The One, or at least that's how Morpheus interpreted what she told him. She also told Trinity that she would fall in love when they found The One, she didn't necessarily say Trinity would fall in love WITH The One. Neo leaves the Oracle realizing he's not The One. However he realizes since Morpheus is The One he can reshape the Matrix in his image, and since he believe that Neo is The One then Morhpeus' belief will make it so. However, ooops, Neo gets killed and dies in the Matrix. As we see Morpheus looks at the monitor and upon seeing Neo's death, says no it can't be, and the Matrix then reboots Neo as The One.

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.

     Agent Smith 
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.
  • I 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.

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... The Lord of the Rings.
  • Or, inversely, The 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.)

Smith represents nihilism.
More precisely, the view that nothing one does has any importance whatsoever.
  • In the first movie, he is an agent, but he is unsatisfied with his current purpose and expresses his desire to leave after getting the codes to access Zion. However, he fails and is defeated by Neo. Thus, what he did to get those codes had no importance whatsoever in the turn of events.
  • In the second and third movies, he returns as a rogue program. It appears that he got his wish after all, but all he does is destroy everything and imprint himself over other programs and people. This might be explained if we assume he does it because he thinks nothing and nobody is of any importance, so he might as well destroy it all. But nothing he does to reach his goal is of any importance, because at the end he is deleted and the Matrix is rebooted, retconning all he did out of existence.
  • If we take The Matrix Online as canon, this is where Smith almost flat-out says that he is a nihilist. He returns at the very end of the game as a messenger, when the corruption is spreading around the Matrix. He tells the humans that nothing they do is of any importance, because all hacks the humans applied to the Matrix to get supernatural abilities caused irrepairable damage, so the Matrix will inevitably crash, killing all humans. But nothing the machines do in the Matrix is of any importance either, because, Smith explains, there is another Matrix: another mainframe, with more people connected to it, in orbit around the Earth. Then the Matrix crashes and everyone who heard the message dies, which means that the very message he delivered did not have any importance.

Smith was an experiment to make a more effective agent
Every agent seems to be more or less emotionless. Smith is different, though. He was an attempt by the machines to make better agents. They thought that by making him feel anger towards Zion, the red pills and even the Matrix itself, he would be more compelled to stop the rebellion and destroy Zion. One of the reason there were always two agents nearby was to keep a check on his anger so he didn't do anything too foolish like accidentally kill Morpheus in a rage while they were interrogating him.
  • If you notice, too, Jones seems to be on equal footing with Smith in terms of rank, and often makes decisions without consulting him, and seems to regard him with some mild disdain, up to and including preventing Brown from helping Smith in his final battle with Neo (you can see him in the background holding Brown back).

Agent Smith is a furry
Agent Smith's iconic speech about why humanity is a plague has led to some fans assuming he may be a furry.There is also his ability to copy himself in later movies, may have inspired Changed. A lot of art that one of the few surviving Agent Smith Deviant ART accounts might prove this, as a lot of it's posts contain furry art.

     The Oracle 
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".

The Oracle used subliminal messaging to get Neo to stop the war
Probably there was a program in her cookies like the Merovingian cake. Not only did her cookies subtly direct Neo's actions for at least the first two movies, it put into Neo whatever it was that turned Smith into a virus. Because it would be silly if the Oracle could just predict that all of that would happen.

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.

In alternative, Seraph was a previous One.

     The Merovingian 
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 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.

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.

The Merovingian represents Satan, and destroyed the first Matrix.
He was the favored created of the Architect and was responsible for maintaining the First Matrix. Ensuring that all ran smoothly, he noticed a slight problem with it. How a percentage did not accept their reality. He gave them a choice, an apple that would show them an alternative to their perfect world. He thought if humans glimpsed their true reality they would accept the illusion as a better alternative. Instead it led to a system wide rejection of the Matrix and caused the Architect's hard work to crash and burn.Disappointed, he cast the Merovingian out of the core (i.e. out of home) and exiled him to exist in one incarnation of the Matrix after another. Punished for failing at his purpose. Ironically robbing him of a choice in the matter. That is why he "created a Heaven out of Hell" (the hedonistic sanctuary for Exiles cast out by the Architect) and hates the Oracle so much, she succeeded where he failed. Respected as an equal by the being he considered Father as he spends forever away from his Father and the only place he truly called home.

     The first film 
Neo took the blue pill several times before finally taking the red pill
Morpheus says you can take the blue pill and wake up in your bed and believe anything you want.Our introduction to Neo is him asleep at his computer and suddenly startling awake and not knowing what's going on. Then he goes out to a club.At the club he meets Trinity and she says some stuff to him and then suddenly he wakes up in bed with his alarm clock going off, he's late for work. At work Morpheus contacts him, and Neo ends up in the custody of Agents, shit gets freaky and he suddenly he wakes up startled in his apartment. Trinity contacts him and he meets them, and finally meets Morpheus and this time takes the red pill and wakes up in the real world.
  • Actually this forms a time line for one day. He took the blue pill one afternoon, woke up that night in time for the clubbing nightlife to begin, let’s say like 9:00. He goes out to a club out night and wakes up the next morning late for work. He gets captured takes a pill and wakes up that night. It was all in one day. They may have offered him the pill times before this day, but this was the day Morpheus was not going to take no for an answer and so he figured let’s just keep doing it and odds say that one of these times he will say yes.
  • Here is how I think it went down: Morpheus orderes his Lt's including Trinity and Cypher to search the Matrix for Potentials and offer them the pills. While no in the real world believes his religious mumbo jumbo Morpheus discovers that the Agents are zeroing in on The One, so Morpheus steps his search. Trinity started searching among the hacker crowd noting that hackers instinctively understanding machines and feeling a need to fight the system, this indicates they may be a Potential. In the hacker worlds she comes across Neo, and is impressed with his work. She is basically both cyber stalking and actually stalking Neo. Not only is he dreamy looking, she notices stuff like he helps his landlady take out her garbage and other character traits and starts to fall in love with him even though she can’t admit this to herself. Trinity contacts the White Rabbit agent who approaches Neo and offers him the pills, he chooses the blue path. This is where the story starts, Neo wakes up at his computer. Morpheus orders Trinity to make contact with him. Trinity steps in and takes direct command of the mission from the White Rabbit, sending WR to lure Neo to the club, a safe place to provide a cover for offering the pills disguised as clubbing/drug culture. They do some stuff that we the audience don’t see, but having spent some time with him Trinity realizes she is falling in love with him. Alas he takes the blue pill and wakes up late for work. Morpheus now steps in directly and just like Trinity sent White Rabbit to retrieve him, Morpheus sends Trinity and her team to retrieve Neo to meet Morpheus.

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.

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.

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.

Morpheus previously thought Cypher was The One.
Morpheus says that they never free a mind after a certain age, implying that it's dangerous, but Neo was an exception. Cypher, in the meantime, tells Smith he's been out for only nine years, despite being clearly well into adulthood. Furthermore, Cypher implies that Morpheus was the one who freed him in the first place. Why did he do it then, if he was obviously too old? There are other small hints throughout the movie. When Trinity brings Neo food, Cypher remarks, "you never brought me food". Does Trinity do this to all recently freed people (except Cypher), or because she thinks Neo might be the One?

The whole conversation between Neo and Cypher on the bridge talking late at night about how he feels being told he's the one takes on a whole new meaning if you consider Cypher was originally told he was the One but failed to live up to expectations. He's not just sympathizing with Neo, he's reliving his own failed path, seeing it potentially happen again with Neo.

In fact, take Cypher's name, which is an old way of referring to "zero". Neo is obviously "one". In computer science (basically the Matrix's whole schtick), one and zero are typically used to represent "true" and "false", and the inverting one value results in the other. Thus, Cypher is "not one", or "not The One".

  • An early draft of the Matrix script has Cypher tell Neo about how Morpheus freed six other people, every time thinking it would be the One, and how they all died at the hands of an agent.

Morpheus was trying to create a team of Ubermenschen.
This archetype is characterized by rejecting imposed rule systems in favor of creating one's own. It's taken up to eleven inside the Matrix, where the greatest power is the ability to rewrite the very rules of physics. Neo was the most successful of them all, which is why he's the One. Cypher is the Last Man, caring for nothing but his own comfortable illusion. Smith is simply a destroyer who wants everything gone.

Jones was originally the Agents' leader
While Brown's attitude towards Smith seems fairly ambivalent, Jones just plain doesn't like him. Their interaction suggests, to this troper, that Jones was in charge of the Agents until the Machines sent Smith in, with Jones being of the opinion that Smith's presence is undermining his authority and stepping on his toes. Overall I think Jones' overall opinion of Smith being that he is too erratic and unpredictable, and he wants Smith out of his hair. And at the end, when Smith angrily attacks Neo without thinking, Jones' refusal to allow Brown to assist their colleague makes it clear he thinks Smith is pretty much washed up and not worth helping at this point.

Jones' line "He doesn't know" was a rare example of an Agent being snarky
When Jones and Brown catch Smith interrogating Morpheus without his earpiece in, Brown demands, "What were you doing?" to which Jones replies (before Smith can) "He doesn't know." This has a Double Meaning. What Jones means on the surface is that because Smith doesn't have his earpiece in, he isn't aware of the attack. But because he doesn't like Smith as detailed above, it was also intended as a snarky "answer" to Brown's question, i.e. Smith doesn't know what he's doing.

The First Matrix was the Garden of Eden and someone placed it in the religions of the future versions of the matrix as either a warning or to Fling a Light into the Future.
Agent Smith described the first Matrix as a "perfect" human world that mankind was meant to be happy in eternally. However that Matrix was found to be a failure as entire groups of humans were lost when they saw through the illusion and rejected the program. The paralells are uncanny to the story of the Garden of Eden in chrisitanity. The first humans were born into the Matrix in a perfect human world, they sought the forbidden knowledge (that the world was a simulation), and once it was made clear, when they were cursed with the knowledge of the world, they made mass rejection and were expelled from the Garden. It is likely that this version of events was introduced into creation stories in further versions. The only question is by whom? The machines to subtly remind humans the price of disobedience by disguising the story of the first matrix as a parable in the bible? Or by a human to try to remind people of the previous version and that they had rebelled before against their supposed god?


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 eventually 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.

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.
  • YES! And since WALL•E is secretly the sequel to Idiocracy, this means they form a trilogy. Human culture becomes so stupid we trash the biosphere. Then Not-Sure becomes President and institutes some smart ideas. In his inauguration speech he even mentioned that mankind once went to the moon, so he probably had a dream of revitalizing a new space program. Eventually with Not Sures average intellect back into the gene pool humanity gets smart enough to rediscover and redevelop robotics and spaceships. They load everyone into the ship and leave the WALL•Es to clean up the world. As we see, the plan goes a tad awry, the A.I. auto-pilot interprets its orders as protecting humanity at all costs, even from themselves and has no problem fighting against humans to keep them docile for their own protection. Hundreds of years later a plucky little robot saves the Earth and brings humanity back home. The animation in the end which shows humans and robots creating a new green world is a look into the dream of what they want accomplish, that's why it's an animation and not 'real' footage. However humanity is still to let us politely say, out of shape to really live and work and save the world. So they create the matrix for humanity to reside in while the robots finish the clean up and the Earth rejuvenates. After some generations a human evolves in the matrix able to wake up from the dream. This misguided human tries to free other humans from the machine, but since the AI of the matrix was built on the same AI programs that resulted in the Auto-Pilot that fought to keep humans on the ship against their will for their own protection, the AI of the matrix comes to the same conclusion, though they want to leave humans must be kept in the matrix for their own protection. This AI then remembers that the plucky little WALL•E bot was instrumental in freeing the humans. So the AI creates a computer virus that spreads among all the remaining robots, reprogramming them from their clean up mission to a mission of protecting humans at all costs, but stopping them from leaving the matrix. This line of logic leads to fighting between humans and machines. Eventually two programs determine a system that creates an eternally repeating logic loop, some humans are let free to form a resistance so those humans who want out can leave and gather in Zion. With them all in one place the machines then kill them all off and uses The One to reload just a few of them, enough to reintroduce their genetics, back into the matrix.Eventually trying to find a simulation that humans will want to stay in the AI model it on the 90s, which due to the historical records left from the musings of Not Sure the machines believe was some sort of halcyon paradise for humans. And the rest is cinematic history. Wow, what a story.
  • but wait, the story continues: The whole saga is Idiocracy, WALL•E, Matrix, Serenity and Dune.
Humans become stupid and trash the planet. They leave in a spaceship while robots clean up the world. The robots go all Zeroth Law and enslave humanity for their own good. Humans escape and go back to the Earth to rebuild. They cannot rebuild so they create the Matrix. The robots go all Zeroth Law on humanity AGAIN and enslave them for their own good. A super human evolves who fights back and frees humanity. Seeing the Earth is trashed beyond repair they load up and leave Earth That Was and settle a new system. It takes a long time but eventually the Alliance sends out ships to other systems and discovers a desert planet. Remembering their past a new religious edict says Thou Shalt Not Make a Machine in the Image of the Mind of Man. Also culturally remembering that they doomed themselves to slavery due to their own stupidity AND that they were freed by a superhuman who unleashed the full power of his mind which overcame the machines, they develop new disciplines of the mind to unleash mankinds potential...and the rest is cinematic history. Who knew that Dune was the sequel to Idiocracy.

After the third film, Earth will be visited by Incubators

The root cause of the conflict of the film was energy. Machines need energy to operate and human emotions prove excellent as an alternative. A group of intelligent alien nanobots called the "Incubators" take notice in its potential to reverse Universal Entropy and want a cut out of the Machines' energy supply. As a result, the Machines allow the Incubators to contract inside the Matrix.