Matrix in a Matrix theory: Is Zion real?

Theory 1: Zion is the real world and strange things happen

Important !!
It is impossible to prove that Zion is real.

Why?

Because you can't even prove that the world you (my dear reader) live in right now is real. One can only prove that there is a level above the current level. Not that it's the "abovest" level. Except if you were a god (or a Wachowski).

Thus a great part of the uproar that is caused by claims "Zion is in Matrix" is caused because the counter-believe "Zion is real" cannot be proven.

Moreover the "Zion is in Matrix" theory is partly fueled by unexplained questions (e.g. "Why don't the machines use harmless apes in the cocoons?"). A "Zion is in Matrix" opens a lot of doors to explanations to such questions.

And, no, I personally don't claim that Zion is real or is fake. But until the Wachowski directors don't tell it clearly others must have the right to speculate and phantasize.

Here is what others said to support the "Zion is really real" theory, which is also called

1M theory (1 Matrix)
ZINAM (Zion is not a Matrix)

Zion is real, because it's time for extra-powers

'Neo has gained telekinetical powers (hey, he knows the secrets of the Matrix, now he knows the secrets of the real world)'
'After the deep connection with Agent Smith/the Architect/etc... Neo understands the real-world-rules better now and can break them'
'The Matrix trilogy is a philosophical/religious story of salvation and enlightment. And since Neo is the Messias/ the Savior/ god-like it's obvious that he must have such powers'
'Our brains are just electronical machines. Thus if the Matrix can be influenced then so can reality'
'Matrix 1 explained how much electricity the human body generates. Maybe Neo has found a way to emit an electromagnetic pulse'
'The machines know everything about human bodies. Maybe they can adjust minds, too?'

Well, I personally think that all of the explanations above would break the concept of the Matrix movies according to which the following has always applied:

Philosophical riddles are explained by computers/ programming only.
Superpowers (Telekinesis, ESP (extrasensory perceptions), seeing the green Matrix code...) stem from the fact that programmed rules can be bent within their parameters. There isn't anything supernatural/ paranormal/ metaphysical so far.
Even the Oracle's clairvoyance/ foresight/ prophecy is part of the computer's programming (or a recycling Matrix).
Even ghosts, werewolves and vampires are purely explained by the system of the Matrix system...
Oracle: "Every time you've heard someone say they saw a ghost, or an angel. Every story you've ever heard about vampires, werewolves, or aliens is the system assimilating some program that's doing something they're not supposed to be doing..."
Neo: "Programs hacking programs."
...and I have no doubt that you can extend this list to Chupacabra, Yeti, Ghouls and Men in Black.

Marginal note: Persephone kills Abel with a silver bullet. Was Abel a werewolf? Here is en excerpt from an interview:
Interviewer: "Your character kills with a silver bullet in one scene. Does that mean that the character you kill is a werewolf?"
Monica Bellucci (plays Persephone): "Yes"
- Interesting #1: An emotion vampire (Persephone) kills a werewolf (Abel), who was watching a vampire movie.
- Interesting #2: Gothic legends say that Cain is the father of all vampires.

However, it could turn out that the matrix was invented to enslave persons with telecinetical powers and now Neo rediscovers them.

Zion is real, because it's just Hollywood, baby

'This is a Hollywood movie thus it cannot be that complicated'.
- Well, Matrix 2 is already very complicated for a Hollywood movie. Moreover I think that the Wachowski brothers wanted to make a movie epos that will last a little longer than a summer. Already now the movie is refreshingly different from the standard Hollywood sci-fi flicks.
  Please also note that this argument is the exact opposite of 'That would be lame, because everybody guessed it'
'Why make two movies building up a story only to tear it apart in the 3rd movie?'
- Because that's the style of the Matrix trilogy: Everything changes by 180° from time to time and so many things have hidden meanings. Please read There is more to the Matrix than a Matrix.
'There is only 1 episode left and there's no time to develop confusing answers'
...and...
'Instead of having the third movie action-packed, it would be trying to explain to us what "really" happened as we have just learned that everything that has been said so far is false'
- Well, one episode is left, so what? Who says that at the end there will be no Matrix, every problem will be solved and all questions will be answered?
  Keanu Reeves [in interview]: "Will [Matrix 3] answer all the questions? No. Will it ask more? Yeah."
  - However Nona Gaye (the actress of Zee) says this:
    Nona Gaye [in interview for ScifiWire]: "People will be relieved when they see Revolutions...I know a lot of people are like, 'What's going on?'"
  In another interview he said:
  Keanu Reeves [in interview]: "Some questions of the journey of Neo as The One are answered. And lots of surprises."
  
  That means that some questions will be left unanswered.
- Who says there will be a happy end?
- Who says there won't be more Matrix movies? Matrix Online is said to play after Matrix 3. The show (computer games, comics, TV shows, prequels, sequels) must go on. How about an animated Matrix 4?
- What do you think will happen in Matrix 3? Only fights and explosions and no new answers?
- Maybe the end of Matrix 1 was after the end of Matrix 3 and thus the Matrix simulation will continue to exist. See the section Matrix 3 before Matrix 1?
- Other theories about Matrix 3 (e.g. the machines cannot compute pi and thus need a programmer to help them) seem to me to be even more complicated.
However as one can see from the action-packed Revolutions trailers, it is indeed unlikely to
- let whole wars play in a fake world
- let everybody know it is fake
- and say: Well, the really real world will be featured in comics etc.
Thus this is a somewhat good argument.
'Since the game Matrix Online will play after Matrix Revolutions it means that the Matrix and Zion will still exist. Thus Zion vs. Matrix is Real world vs. Matrix'
- Good point. But maybe it will be 'Real world outside of Zion vs. The Matrix'
- Maybe they will find out, that the Matrix isn't that bad.
- This theory doesn't explain how Neo stopped the sentinels.
'The Wachowski Brothers put these scenes at the very end of Matrix 2. Since they are very intelligent they probably want the audience to seduce into Theory 3 (see below). And this will turn out false'
- Well, who could argue with that? This is one of the cleverer arguments and possibly true.

Zion is real, because you suck!

'Zion IS the real world. Get it, you suckers. You are fooooooolish'

It is interesting how antagonistic people can get (without giving evidence).
Here are a few comments about 'Zion is fake':
- 'WAKE UP!!!!!!!! Dammit'
- 'go have anal sex with your mwm theory while ur at it.'
- 'I mean, come on'
- 'Your retarded theory'
- 'a cheesy explanation'
- 'it calls for a ridiculous plot-line in the third movie'
- 'Even a two-bit director could create that lame storyline. Bleh.'
- 'The worst theory I've ever heard is the matrix within a matrix idea. I wanted to bash that guy's head in..'
- 'If you go on believing that Zion is a simulated world or (Matrix within a Matrix) , then you are going on a wrong path and will end up confusing yourself even more and will never find the answers to tie it all together.'.
- 'unless the entire first two movies are building up a plot only to have it shattered, the idea of another matrix just doesn't make sense'
- 'It would be impossible to determine what's in the matrix and what's not, so the idea HAS to be rejected'
- 'it is really a foolish idea. It serves no purpose in the trilogy, makes no statements and furthers no ideas, it is merly an incorrect interpretation. Why? Why would they have a MwM idea? What purpose would it be to ahve this all a lie? Nothing! It is wrong! Completely and utterly!'
- 'it will reduce the Matrix trilogy to a huge Bobby Ewing-style stunt and alienate a large percentage of the films' fan base.'
- 'The Wachowski's wouldn't settle for such a predictable, crappy ending'
- 'There is no way in hell the brothers are going to cheat people'
- 'makes a mockery of both movies'
- 'MIM junk'
- 'I too hate the MWM theory, it's just too easy a cop out.'
- 'That just goes to show you how much wasted time MWM believers have by thinking up every possibility'
- 'I agree matrix in matrix in not real. people who think it is are stupid, and to lazy to write my reasons but there are a ton'
- 'Wacky theories that people are coming up with.'
- 'I hate it. I can't see why the Wachowski's would spend two movies buiding up the notion of the real world for it to be turned on it's head in the final moments of the third'
- 'Just plain suck'
- 'The wnole storyline would be nullified if Zion was a matrix'
- 'would ruin the plot'
- 'a cheap resolution often used in movies dealing with questions of perception'
- 'If that's true then most of my appeal to The Matrix will be ruined.'
- 'a stupid concept and only people with minds open to stupidity would believe such a thing. I bet you MwM believers would also believe that neo is not human but actually a super monkey from neptune plugged into the 18th matrix.''
- 'A big joke'
- 'The MWAM theory is nothing more than lame.'
- 'i think the MIM theory is boring, and i hope it dies at the release of M3.'
- 'too simplistic, renders aspects of the film puzzling and unnecessary'
- 'A curse upon those 'Zion is fake' infidels!'
- 'I 100% Totally dont believe in this MWM crap'
- 'The Wachowskis would lose a shitload of money'
- 'If the MwM theory is true then the entire Matrix story is just a cheap rip-off of The 13th Floor.'
- 'Please, stop with the weird 'genius' theories that make absolutely no sense at all'
- 'You stupid ZIAM people make me so frustrated. "Neo stopped the sentinels". That doesn't prove shit!'
- 'Oh yeah, sure, and after Matrix 1 I bet you said: "That must mean mirrors eat people in the matrix!"'
- 'I'm utterly appalled that this ridiculous MWAM theory (probably standing for Most Wankerfied Analysis in Memory) is even being discussed. There was no 'second Matrix', no 'hidden level', no fucking Matrix-within-a-Matrix-within-a-Matrix-within-a-Matrix-within-a-Matrix.'
- 'Why the living hell this fucking flame hasn't died out yet I can only attribute to some great plague of stupidity among certain people.'
- 'The Wachowskis may have had a lot of intrinsic meanings, but none of them were ever unfounded as this joke of a 'theory' is.'
Interestingly enough one hardly sees people who support the MwM theory (Matrix within Matrix) getting as angry as the Anti-MwM.
It seems to be MwM-theorists vs. Anti-MwM-terrorists ;-)
What comments like this forget: It's not only what the movie shows (Zion may be real or fake) but how it explains it. Maybe Zion is fake, but in a such an interesting way (with twists and new ideas) that it make everything plausible. Maybe Zion is real, but it's explained in such a way that it's rejectable.

Neo has superpowers, because he is like superman

Superman has superpowers on planets with a yellow sun (= like earth). Neo has super powers when there is no sun (= like in Zion).

Zion cannot be fake, because this collides with the story

'If Zion is part of the Matrix, why don't they simply unplug every one in Zion instead of fighting them for 100 years?'
&
'What do they need the prophecy for?'
- Do you remember what Seraph (the 'friend' of the Oracle) said?
  Seraph: "You do not truly know someone until you fight them"
  ..and combined with the Architect words it makes sense...
  Architect: "An anomaly, which, despite my sincerest efforts, I have been unable to eliminate"
  ...and...
  Architect: "This will be the 6th time we have destroyed it, and we have become exceedingly efficient at it".
  All statements can be read as: We let Zion's population increase, so you can fight us better, so we know you better, so we can destroy you better, because we still have 'sincerest efforts' to eliminate the anomaly.
  'Sincerest efforts' could also mean, that this time (because all past efforts failed) they let Zion become bigger than before.
- The Zionists free individuals and that keeps the internal 'dissatisfaction pressure' within the Matrix minimized (Zion as an outlet).
  Please remember that the Architect wants a new Zion to be populated. He orders Neo to start with 23 new humans.
- The ongoing war distracts the Zionites from realizing that Zion is a fake. The war makes life "realer" than in the Matrix.
  Please also read the section below: "A fake Zion fits perfectly into the concept of deception".
- The prophecy is needed to keep the Zionists busy for 100 years.
  The Zionists want to finally free all humans OR to finally fight against the system when they have freed enough people. Thus for the System it is much more clever to fight against Zionists (= terrorists in the system's sense) every 100 years than all of the time and expecting terroristic attacks anywhere, anytime.
- The prophecy is needed to let the Zionists find the One:
  - Remember, that after the One is found he has to go to the mainframe and he has to choose 23 people and then...? Maybe he is deprogrammed? Maybe he is killed? Thus by keeping the prophecy alive the Zionist find the One for the System and -zap- the System gets rid of him.
  - Also remember, the 'prophecy of The One' is just another form of control. The One has a function:
    Architect: "The function of the One is now to return to the Source, allowing a temporary dissemination of the code you carry, reinserting the prime program."
    Whatever this means, it seems to be important.
    It could very well mean, that the One's memories are used to eliminate unwanted elements better.
'If Zion is just another part of the system, why does the system need the access codes to the Zion mainframe?'
- To keep up the illusion of Zion as the land of the free. Because you could also ask 'Why do they need to fight at all? Why don't they just unplug everybody in Zion?'
- Maybe only Agent Smith needs the codes for whatever reason.
- Maybe the agents are unaware of the bigger picture.
  Agent Smith: "I hate this place...Once Zion is destroyed there is no need for me to be here...I have to get inside Zion...You're going to tell me [Zion's access codes]"
  But this seems to be wrong. From what the Architect says...
  Architect: "[Neo] will be required to select from the Matrix 23 individuals... to rebuild Zion"
  ...agents are needed even after Zion is destroyed (because a new Zion is in the making).
  They also address Neo as "still only human", while he very well might not be as you can read in section Is Neo 100% human?
  However it could be, that Agents are rewarded if they can get the Mainframe codes faster. Maybe they are freed?
- In web forums some users state, that if Zion is part of the Matrix, then the access codes would be known anyway. Maybe a reason why this might not be the case is that the landing/ docking maneuver is controlled from within a navigation program (the white controllers seem to be in a Matrix-like environment). Thus this program might be inaccessible from the Matrix itself.
  However there is a counter-evidence:
  Tank [Original Matrix 1 shooting script]: "Every leader of every ship is given the codes to Zion's mainframe computer which can be accessed only through the Matrix. They are used only in emergencies. If an agent had those codes and got inside Zion's mainframe they could disable the entire defense system. It would be the end of everything."
  Side note: Since the white controllers have to have plugs to be connected to the navigation environment it means that only freed Zionites are able to control the gates. Naturally born Zionites have no plugs. Could this mean that Zions protection (= the gates) depends upon humans who may be deceivable by the matrix? A possible security breach? Is this why Smith wants to have the security codes to Zion gates? To reprogram the white controllers?
'If Zion is just a Matrix, why don't they escape out of it as they did before?'
- You might need a 'One' to escape. In other words: Since there is only Neo in the huge Matrix world, you'd probably need millions of Zionites until a Zion-Neo (Zionio, so to speak) emerges.
- You might need to know how to make a red pill.
- You might need somebody who can self-eject himself first (like the Kid from Animatrix). (Thus he will probably play a substantial role in Matrix Revolutions.)
- Since you don't know what will be outside the Matrix you cannot be sure that awaking from it will put you in a position where you can use weapons, spaceships etc to escape to a 'really real Zion' and to return back to Zion to free the others.
  - Maybe you awake and soon thereafter you die, because there is nothing outside that you can do.
  - Maybe all people who die in Zion come to the real reality, but cannot go back.
  - Maybe you are just a brain connected to the Matrix outside of Zion. Thus Zion is an illusion, but the best world you have.
'It hasn't been mentioned ANYWHERE in the movies so far, that Zion is fake, thus this theory are too far-fetched'
- Well, of course it hasn't been mentioned so far. That's the very surprising deal about this theory. The movies would take a different path if you knew this in Matrix 1 already. Remember The 6th sense and The Others and The Others? You get to know the truth at the very end, everything else would spoil it.
'This requires that we disregard substantial portions of both films and the first movie was a complete lie and both movies had absolutely nothing to do with the story'
The first part ('disregard portions of the movie') is true somehow. More than this: Even portions of Animatrix would be fake.
But maybe they are fake anyway: Think of Agent Smith's speech to Morpheus about the crash of the first Matrix and the redesign:
Agent Smith: "The perfect world would dream that your primitive cerebrum kept trying to wake up from. Which is why the Matrix was redesigned to this, the peak of your civilization."
Now why does Smith say that? Isn't the peak of the human civilization later? When the first robots/machines were invented? Thus maybe the rise of the Artificial Intelligence was a lie.
On the other hand, he continues...
Agent Smith: "I say your civilization because as soon as we started thinking for you it really became our civilization"
...which could mean 'As soon as humans invented machines it started to be a machine's civilization'.
The second part ('both movies had absolutely nothing to do with the story') however is not so true:
- Both movies are the story about the Matrix. They describe the fights within the Matrix and secrets of realities. And, yes, isn't the theme that we are deceived to believe?
- Besides isn't Matrix 2 already the movie that belies the first one (Architect's speech)?
- If Zion is within a Matrix and the Matrix is already, say, thousands of years old, then nothing that has been said is wrong. The whole human history would be correct (but has always played within a Matrix). The only thing we wouldn't know, is: What is outside the Matrix?
- If there is something like a Matrix reboot plus a Zion reboot, then only the reason for the Matrix was a lie. The adventures of real people (Trinity, Neo, Niobe) in the fake Matrix and the fake Zion, would be true anyway. Only the surroundings were virtually created (with a green hue in the Matrix and a blue hue in Zion, I might add).

Zion is real, because Neo didn't stop anything

'The System stopped the sentinels to keep Neo alive, since Neo still needs to rebuild Zion'
- Good point. Could be true, however it doesn't explain:
  Neo: "Something's different. I can feel them."
'The sentinel-stopping and hand-raising was purely coincidental'
- Could be, however it again doesn't explain...
  Neo: "Something's different. I can feel them."
'Neo didn't stop the sentinels. It was the hovercraft 'Hammer' that flew by'
- After analyzing the scene I cannot see anything like this. There are more counter-explanations:
  - Neo says about the sentinels:
    Neo: "Something's different. I can feel them."
  - The sentinels stop in the same moment as Neo moves his hands.
  - There is no EMP effect visible (as was at the end of Matrix 1, where the Morpheus' crew triggered an EMP).
  - Neo falls into a coma, while nothing happens to Trinity (who was standing only a few meters away).
- It was even mentioned that it couldn't have been an EMP (electro-magnetical pulse from a hovercraft) because after the sentinels went down their red 'eye' light was still glowing. I disagree, since you don't see the red light glowing in its full glory but fading away instead.
- However, this proposed answer ('Something else was it') is one of the more attractive ones thus it might be true.
  - But: Would the Wachowski brothers really end Matrix 2 in such a surprising way, only to tell the audience in Matrix 3, it was another ship?
  - A very big counter-argument is what is written on the official matrix site. Warnerbros.com: "At the cliffhanger conclusion of The Matrix Reloaded, Neo lies in a comatose state aboard the rebel hovercraft Mjolnir [= Hammer] after using his powers to terminate several attacking Sentinels – an inexplicable feat given that he was not jacked into the Matrix during the deadly confrontation. In Revolutions, Neo learns the truth behind the source of his powers and why he is able to use them in the real world. Reeves sees Neo as “a lightning rod, a searcher and a witness. In acting out his quest, Neo makes himself available as a conduit for a very powerful energy force, which translates into these extraordinary powers"
    I take it very seriously, that it's stated, that Neo himself stopped the sentinels. However, the term "real world" may not mean "really real world" but "real world as we know it from the story".

Zion is real, because Keanu said so

Keanu Reeves (Neo) said in an interview (while or after shooting Matrix Revolutions):
Question: "Is it possible Neo is not real? Like he is made by the Matrix?"
Keanu Reeves: "I think in terms of the representation of the films, the Brothers don't tend to do things like that, like hood-wink you. It's not like, 'I see dead people' [6th Sense], where you are watching this whole movie and then, 'By the way...'. I don't think they do that kind of cinema. So my answer to your question is 'No'. I don't think it is so boxes within boxes. I think that Zion is Zion. But if you want to go: 'Is it the blink of Vishnu?' Maybe. But in terms of literally and the world of the pictures, no."
Well, what I read from this is, that Matrix Revolution doesn't answer this question. Since Matrix 3 is the last movie from this trilogy it may very well mean, that Zion is really Zion.

Zion is real, because otherwise the matrix would look like Zion

This is a good point: In the matrix Neo can fly thus he can bend the rules. Bending rules is not good for the system. In Zion he can not bend the rules. Thus if Zion was another matrix, it would be an enhanced matrix, which even can suppress the Ones' powers.
In other words: If Zion is so effective in suppressing "Ones" then then why just not design the matrix after the seemingly "more emprisoning" Zion?
- The reason might be very simple: What works for Zionites might not work for 99% of humans. Since Zion is suffering maybe a lot of humans would awake in their cocoons.
- Moreover the system NEEDS the One, as I point out thruout my site. Thus they need a bendable matrix
- Moreover who says that the next matrix upgrade wouldn't look like Zion?

Zion is real, Neo has a wireless connection and was given the access codes

'Neo has a wireless connection with the sentinels and he stopped them'
- This is a very good argument. Why does the brain stick have to be plugged in? Why not wireless data transfer?
  Thus take wireless connection PLUS sentinel accessing codes (given to Neo secretly by the Architect or Smith) and you have the ability to deploy or stop sentinels.
  Think of that, too: Smith has a connection with Neo. Smith has a connection to the sentinels. Smith is in Zion. Thus maybe Neo in Zion has a connection with the sentinels, too.
  - However this doesn't explain, why the sentinels crashed. Neo, not only did stop the sentinels. He destroyed them. They were shaken forcefully. Did he activate a sentinel-self-destruction mechanism?
  By the way: This answer could make it possible, that Neo (in his coma) is inside the Matrix without being hard-wired.
- Maybe Neo could stop the sentinels not because of a wireless connection, but because "a part his mind" is still in the matrix
  Oracle [Enter the Matrix]: "Yes, he touched the source and separated his mind from his body. Now he lies trapped in a place between your world and ours."
  Whatever that means, it could be that he stops the sentinels because he is split and works from within.

Zion is real because Neo is an ape and Zion is Zooon

'The agents' talk about "Only Human" shows that Zion is a big zoo'
- This is somewhat a strange argument. It works only if you interpret the agent's "Only human" talk in the sense of "Zion is a zoo (for our studies, for our fun), thus we need to keep humans in this zoo, thus we blackened the sky, thus you are only an animal".
  Agent Smith supports this argument a bit:
  Agent Smith: "I'm going to be honest with you. I hate this place, this zoo"

Zion is real, because of... (miscellaneous objections)

'Zion is real because they let Zionites alive'
- Zion is used as a security system in case of a matrix system failure (where everybody connected to the matrix would die). Thus the system keep a few Zionites living underground as a reservoir, in case the whole humanity dies.
'If Zion is another layer, it means there are infinite layers without any real reality'
- Who says there are infinite layers? Maybe there are only 2.
- And in fact, even if Zion would be faked, then there is still only 1 matrix. A matrix with several side simulations:
  It's like you sleep and have dreams, side dreams, parallel dreams, dreams in dreams, dreams of traps, dreams of being trapped in dreams etc... but in fact there is only 1 dream. If you stop to dream it, then everything stops.
  Thus there would only the simulation and the world outside of it.
'The simplest explanations are the correct ones.' (William of Occam's philosophical axiom).
- Well, let's not fight about about what is 'simple', what is 'complicated' and what is 'too simple'. Besides: Who says that Okham was right? (Maybe he was just part of the system? ;-)
'Neo thought he can feel the sentinels because he went insane'
- You could destroy any movie with an assumption like that.
'Neo fell in a coma because of stress. A hardworking man needs a break'
- Could be, since Neo was never attacked so directly before.
'Zion is real, because Matrix Revolutions is about a big battle in Zion'
Now this is one of the best arguments to support Zion = real. Joel Silver (the producer) said that one of the scenes will be a big battle in Zion:
Joel Silver: "A 14-minute, $40 million battle scene that is the most complicated sequence ever put on film."
Now what sense would it make to fight wars in Zion, if Neo discovered that it's a simulation anyway?
Another (smaller) argument: In the trailer for Matrix Revolutions you see Neo striking a deal with the machine god. What sense would it make if probably most of the cocoons are a simulation anyway.

What do you think? Is Zion real? Go to the voting booth!

Theory 3: Zion is not real

[Cast your vote]

In other words:
Zion is part of the illusion (or a part of a parallel Matrix)

This theory is also called

MWAM concept (Matrix within a Matrix)
MwM theory (Matrix within Matrix)
MiaM theory (Matrix in a Matrix)
MiM theory (Matrix in Matrix)

Oooh, this theory produces uproars in forums amongst those who believe it and those who reject it. It seems that there is no other single theory that raises such heated up debates.

Please read on...

Stopping the sentinels is NOT THE ONLY clue that Zion is a trap-within-a-trap (=part of the Matrix). There are several other hints that Zion is an illusion:

So yellow I could dream

In the trailers for Matrix Revolutions we see Neo talking to Bane (who is posessed by Smith) and Neo sees him in a yellow fire:

You can recognize Smith by his sunglasses. How can Neo see Smith in such a way if Zion is not in a Matrix? Is it because Neo's eyes are hurt?
Now I must admit that this is just from a trailer. The sequence of trailer scenes is unreliable. Thus we cannot be sure that the fire face is in Zion.

Zion's blood

The trailers for Matrix Revolutions show a fight between Neo and Smith (in the rain). Smith says "Welcome back. We missssed you". But his intonation differs from trailer to trailer. While that might be an interesting way to entertain hardcore fans it could also hint at a time loop. I wouldn't mention it, if there weren't also 2 same-but-differing scenes from Zion:

Both scenes are from trailers, both times Bane says "Look past the flesh and see your enemy" but both times the face looks slightly different. If the intonation means time-loop then the bloody face could mean it, too, and thus hints at Zion=loopable Matrix.
Please remember: The Matrix is probably deteriorating by Smith's influence. In Matrix 1 we saw a black cat followed by the same black cat (deja vu) as a symptom of a glitch in the matrix. Also in Animatrix the falling apart matrix of the haunted house (Episoide "Beyond") shows time loops.
Please also note that Smith's "Welcome back" could also hint at time loops (= repeated scenes).
Maybe I am interpreting to much into this. Maybe the bloody face was cut out by the directors but leaked into the public.

Behind behind the scenes

Here's a transcript of Making the Matrix DVD:
Shots are shown of the interior design of the Nebuchadnezzar, of Neo being freed, of the human crop fields. While these images are being shown Owen Patterson says...
Owen Patterson [production designer]: "We've fallen back on..the original conceptual drawings (Neo is shown being grabbed by a sentinel in the pod), that were trying to promote that idea of reality that isn't real. You look at it and go 'oh, that's a real place', but there are the illusions within it."

More than words: Music

When the sentinels head towards Neo at the end of Matrix Reloaded the music (score) changes to the music they usually play for scenes within the matrix
There is a song by on the Matrix Soundtrack by P.O.D. called "Sleeping awake" with the following lyrics
Dreaming of Zion, Awake
Sleeping Awake
Dreaming of Zion, Awake
Can't stop Sleeping Awake

Well, both arguments are not hard, but interesting anyway.

Dreams

Neo wakes up when Smith enters Zion (thru another person: Bane)
Neo sees what will happen in the Matrix and vice versa the Oracle knows what dreams Neo had in Zion.
Oracle (in the Matrix): "You've seen it, in your dreams [in Zion], haven't you? The door made of light?...You have the sight now"
- However, some argue that this is possible because all happened before and somehow the Oracle and Neo know about this. As Smith states:
  Smith: "It's happening exactly as before."

Smith enters Zion (thru another person: Bane)

How is this possible?
There are counter-thoughts why this Smith's entry indicate that Zion is in a Matrix:
- Not Smith himself gets into Zion.
  Instead Smith 'infects' Bane first and THEN Bane gets (thru the phone) back to Zion. Thus it could be a normal case of 'What affects you in the Matrix can affect you at home'.
- Bane's body doesn't change (well, see the reason above)
- In Matrix 1 fighting techniques is uploaded into Neo's mind. So why shouldn't Smith be able to be uploaded?
  - Contra: Maybe only data can be uploaded, but no executable code. But, who knows?
- Since our brains/bodies are electrical machines we (humans and machines) are basically compatible/the same.
Please note, that it could be the powers of Smith that stopped the sentinels. In Matrix 1 he has the power to deploy them, thus we can assume safely that he has the power to stop them:
Agent Smith [Matrix 1]: "Deploy the sentinels immediately"
In both cases (Neo stopping the sentinels and Bane surviving the sentinel's attack) we could have an infection (=code overwrite, code insertion, re-coding) by Agent Smith.
However Smith's ability to stop the sentinels doesn't explain why the sentinels have been destroyed, instead of just stopped.

Blues get me the blues

The color blue is missing or unfriendly (e.g. danger, sentinels lightning).
The same as in the Matrix.
Interestingly Neo had to take the RED pill to leave the Matrix, while RED may mean, that he'll get again into an illusion.
The Wachowski brothers told, that inside the Matrix there is a green hue, and in Zion there is a blue hue. This could mean, that both worlds are a simulation.

Red candy: We all like to know the truth

The Oracle is giving neo a red candy which is probably her hidden reference to Morpheus' red pill in Matrix 1.
Oracle: "You [Neo] didn't come here to make the choice, you've already made it. You're here to try to understand why you made it..."
Neo: "Why are you here?"
Oracle: "Same reason. I love candy."
A similar conversation in Matrix 1:
Morpheus: "You take the red pill...and I show you how deep the rabbit hole goes...I'm offering you...the truth"
Well, the truth in Matrix 1 was, that there is another level of life (= Zion). Maybe this time, too. However, a weak argument.

ArchieTV, Blue screen of death

This would be the ultimate proof that Zion is in the Matrix, if scenes from Neo's life outside of the Matrix had been shown on the TV screens.
I looked and looked and looked, but there is no single scene I identify as playing in Zion. If you see one please write me an email ! This is important!

There is a scene from the trailer of Matrix 1 showing Neo in Morpheus' ship:

This could be considered a proof, but since it is only a trailer, it could just be a fancy visual gimmick, as is the next scene, where the monitors show "The Matrix" title:

Dig me deeper?

Architect: "You are here because Zion is about to be destroyed."
Neo: "Bullshit."
Architect: "Denial is the most predictable of all human responses, but rest assured, this will be the sixth time we have destroyed it"
What the heck? Zion has been destroyed 5 times already? How is this possible? Always starting with 23 humans and ending up with huge underground cities a few years later? This is indeed a hint, that Zion is in a Matrix and every time they start newly, they start in the fantasy world with a Zion where the sentinels have to dig again. As a counter-argument you might say
- by 'Zion' the Architect merely means 'human city, where the escapers are'. Thus Zion is another Zion every time around. Please note that 'Zion' sound similar to 'scion'.
- the Architect maybe talks about destruction of denial, rather than about the destruction of Zion. Read his words again.

Fake humans and fake machines

Oracle (about Neo) [Enter the Matrix]: "Now he lies trapped in a place between your world and ours."
...and...
Oracle [Matrix 3 trailer]: "He is trapped in a place between this world and the machine world."
Now why does she say "machine world"? Why not "real world"?
The reason could be that the world of the machines is a fake. However, the reason could also be simple:
- She didn't say "real world", so what?
- What is real, how do you define real? Both worlds could be considered being real.
- It is the machines' world after all.
- Neo himself says:
  Neo (about the Oracle) [Matrix 2]: "If I had to guess, I'd say you're a program from the machine world."

Dark side of the spoon

Neo gets a battered-looking silver spoon from an orphan in Zion.
This spoon looks as if the orphan (from Matrix 1) has bent it like within the Matrix.
Please also note, that in Matrix 1 an orphan (=spoon boy) who shows Neo the spoon is doing so right before Neo goes to the Oracle. The same happens in Matrix 2: Just before Neo wants to leave Zion to meet the Oracle the spoon is given to him.
There are however some who state
- The spoon is just a gift to say 'Hello, Neo, I made it out of the Matrix, too'
- The spoon is just reminder, that Neo leaves reality behind
I disagree.
- First of all the spoon has dents as if it was bent (telekinetically) in Zion.
  - Contra: It looks shabby, because everything in Zion looks crappy. Thus the spoon could be a simple reminder of the real world's ugliness. In other words: 'Look, Neo. This time the spoon is real'
    - BUT: In an interview Clayton Watson (who plays The Kid) says:
      Clayton Watson [in interview at the Reloaded premiere in LA]: "My favorite scene was...with the spoon - the old bendy spoon."
    - It would be strange if Zion's machines and hovercrafts worked, but they had no good spoons.
- The spoon seems to have been bent forcefully (=with more difficulties). This may be wrong, but if it's true it could mean, that Zion has a different 'Matrix structure'. And it would explain why Neo's stopping the sentinels needed such an effort that Neo falls into a coma.
- Kid runs to Neo and says:
  Kid: "I'm sorry...I just have to give something to Neo...[The orphan] made me swear to get it to you before you left. He said you'd understand."
  Since this orphan was one of the 'One' candidates this clearly means
  - that it's very important. It's not just 'another gift'.
  - that there is something to understand. If it was just a 'Hello, it's me, I am in Zion, too' then why not saying it like: 'The orphan has a gift for you, he wishes you luck'
  - Is there anything in the Matrix movies that is just accidental? I don't think so. Nearly every word and every sentence has a meaning. Thus I cannot believe that a whole scene (in which a 'One'-candidate makes an urgent gift to the 'One') is purely coincidental.
There is also another thing. Maybe Kid and the Orphan hang out together usually or sometimes. This would explain the following:
- When Neo arrives in Zion and comes out of the ship Kid comes running immediately to welcome him:
  Kid: "Neo!!"
  Trinity: "How does he always know?"
- Just before going to the Oracle (Matrix 2):
  Kid: "Neo!!" (Maybe he even saved Neo's life by interrupting Bane's assassination)
  Kid: "Neo!! Just in time. You're gonna see the Oracle, aren't you?"
How is this perfect timing explained? How did he know that Neo is going to the Oracle? This timing is not chance. And this spoon is something special with a deeper meaning.

Alive and bleeding

If you are hurt in the Matrix you bleed in Zion.
Something that doesn't make a lot of sense. Dying makes sense, but bleeding?

No chance in Zion

This is an interesting theory. And it works only if you assume that the system wanted Trinity to go into the Matrix (at the end of Matrix Reloaded) to complete her mission. Why? Maybe to make Neo choose the left door (when he heard that Trinity has enetered the Matrix). OK, here is the theory: The system forces Trinity to enter the Matrix by bombing the ship of Soren (= the captain who failed) in the right moment. Since nearly everything in the Matrix is forseeable it means that bombing to cause something wanted is practically only possible within the control of the system (= Zion is within a matrix).
- Counterargument: Since the system has access to all memory banks and emotion profiles and character characteristics of all humans, it maybe is calculated anyway.

Residual without mirror?

Why do you look like yourself if you haven't ever seen yourself?
Morpheus [Matrix 1]: "Your appearance...is what we call residual self image"
In reality (=in Zion) you never looked into a mirror, but you know how you look like? Do you conclude your outlook from 'feeling' your DNA (which can only be felt outside of the Matrix, because inside you have only a virtual DNA).

Trinity empowers Neo

There are a few scenes where Trinity talks onboard Morpheus' ship and Neo seems to react in the Matrix as if he could hear that:
- After Neo dies (Matrix 1) Trinity talks to him in Zion and he rises from the dead in the Matrix.
- After he rises in the Matrix Trinity shouts "Neo!" and he reacts instantly and runs to the phone.
- When Neo is covered all over by the agents Trinity says...
  Trinity: "Come on, get out of there."
  ...and Neo flies away.

Freed individuals aren't killed immediately in their cocoons/ Harmless machines

Since bodies (in the cocoons) are supported with oxygen, minerals, vitamins and anything they need AND dead bodies are disconnected, rinsed off and liquefied (thus are recognized as being dead/ disconnected) AND the system even knows if somebody becomes aware of the Matrix (as seen in the Animatrix story 'World Record'), it makes one wonder why the machines don't immediately poison/ electrocute the affected cocoon. It seems that they don't care or that they even want that somebody is freed and reaches Morpheus.
Why aren't the machines using bombs since the beginning? They were strong enough to win against the combined forces of the human armies, but cannot fight a few outdated ships? How about using gas flowing down to Zion? How about lethal radiation? Nope, the machines behave as if they had time.

Why should human bodies be a power generator? Why should humans be kept alive, after the machines have won the war against humans?

This is one of most stupid ideas machines could have, it doesn't make much sense for the 'real' world and thus supports that Zion is fake.
Is this a giant plot hole in the Matrix movies ('It's just Hollywood, dude')?
The original script describes the procedure a little deeper, but it still is somehow unbelievable:
Morpheus [Original Matrix 1 shooting script]: "The Machines discovered a new form of fusion. All they needed was a small electrical charge [delivered by human bodies] to initiate the reaction."
Ahem, what? Need HUMAN BODIES to spark something up? Well, well, sparks parks. And think of that, too:
- One has to subtract the energy needed to keep the Matrix running.
- One has to subtract the energy needed to service the cocoon piles.
- Getting the energy from the food directly would be more effective.
- Creating oxygen for humans is probably not energy effective, too, since nowadays oxygen is created by plants and the sea, that both need the sun to do so. But the sun was clouded.
- How often do you have to eat a day? Quite often. The human body really needs a lot of energy for itself and is a poor energy supplier.
- If it has to be HUMAN bodies, then why plug something into the brains? Why not run the Matrix brainless? (The Matrix could be a no-brainer, so to speak.)
  A reason for the need of a Matrix simulation could be that the machines try to solve a problem inherent in the programming of the machines themselves. Remember Artificial Intelligence was created by humans, and maybe humans programmed an incapability into them as a security measure. Thus to solve it, they need a human programmer's mind. Remember, that Morpheus and Trinity and Neo are programmers.
- Why not use wind, fossil or atomic sources?
- Why not use horse bodies? Or cows? They would deliver more energy and would never rise against the machines. Here are counter-arguments:
  - Hey, it's the Matrix not the Mootrix ;-)
  - A very good argument, why the machines don't use cows is the following: There are no cows anymore. All animals are dead! All plants are dead. The earth is too cold and shattered. In Matrix 1 the crew had to eat "bowls of snot" and they didn't know how chicken tastes.
    However this does not answer the question, why a human body needs a real world simulation.
It is also quite unbelievable that humans had to darken the sky. The sentinels are still prone to EMP, thus using EMP back then against machines seems to be satisfactory. Why scorch the skies? Could you imagine a war where humans voluntarily cloud the sky for centuries? Maybe humans had a method to 'uncloud' the sky, but then again (since the machines are intelligent), why couldn't the machines uncloud it for centuries?
Since the body = battery thing is quite unbelievable, then maybe the 'humans clouded the sky' thing is also a deception.
Maybe the machines keep the sky clouded to keep the humans underground (where it's still warm). Thus the machines don't need the humans because of the clouded sky, but vice versa they need the clouded sky because of the humans.
- However, since this would turn parts of the Animatrix stories into a lie (and people already hate the 'Zion is a lie' theory) this could really upset movie viewers.

Click to vote: Is the "humans=batteries" theory true?

Science fiction is no fantasy

Having PSI powers in the real world turns a science-fiction movie into a fantasy movie (like Lord of the Rings, where speaking trees come to rescue you). This introduces an inconsistency into the movie. Please note, that even the resurrections (Neo dies in Matrix 1 and Trinity dies in Matrix 2) are within seconds of the deaths, thus nothing paranormal or metaphysical.

Keymaker's systems on systems

Keymaker: "But like all systems it has a weakness. The system is based on the rules of a building. One system built on another."
Maybe the Keymaker hints at the matrix being funded upon Zion and Zion upon another system? A weak argument though.

Sixth sense

At the very end of Matrix 1 Neo states:
Neo: "I know you're out there. I can feel you now...You're afraid of change."
This marks the change in Neo's perceptions, because he can see-through-the-Matrix now. And at the end of Matrix 2 right before the Neo-stops-the-sentinels-scene he says...
Neo: "Something's different. I can feel them."
...which could also mean, that he see thru the Matrix now.

However, believe it or not, it is not clear, what scene is first. The ending scene of Matrix 1 or the ending scene of Matrix 2? See the section Was 'The Matrix' after 'Matrix Revolutions'?

Marginal note: In the trailer for Matrix Revolutions Niobe (while outside the Matrix) says something similar:
Ghost: "What if they don't find us?"
Niobe: "They will."
Ghost: "How do you know?"
Niobe: "I just know."
Ghost: "What do you think will happen after that?"
Niobe: "I don't know, but I got a feeling it's going to be one hell of a ride."
Well it's not that proving. But I wanted to mention it anyway, because it could very well mean, that Zion is in a Matrix, because Niobe has 'the second sight' now

A fake Zion fits perfectly into the concept of deception

Zion fits into the concept of traps-within-traps
Well these are not really arguments, but show that a Matrix-within-Matrix could be a very typical machine's deception technique:

Happier suffering
Agent Smith states in Matrix 1:
Agent Smith: "But I believe that...human beings define their reality through misery and suffering."
There is no doubt that Zion is a more dangerous place with a more miserable existence than the Matrix world. How would you like it to live in a world with giant spiders haunting you (the sentinels and the cocoon-keeping machines look spider-like)? Making something more threatening makes it more real.
This could mean that Zion the perfect place for the outcast people of the Matrix: If you don't like the 'reality' of the Matrix then you probably like the 'super-reality' of Zion.
Matrix is a prison for the mind, while Zion would be additionally a prison for the body.
Less than choiceless
There isn't good food in Zion. Nowhere to go. No sun, no rain, no snow. Always the same people, the same council. To sum it up: There is less choice than in the Matrix. Thus if you didn't accept the illusion of choice in the Matrix, then maybe you accept the illusion of 'no choice' in Zion. If "nearly 99%...accepted the program, as long as they were given a choice", then maybe 1% accepted the program, as long as they were not given a choice: Predestined prophecy and same food every day.
Once Zion and back, please. The land of the fried.
The real world is so bad off (= Zion is a Matrix simulating misery), that it makes you want to go back (like Cypher). Matrix 'frees' you into Zion and Zion 'frees' you into the Matrix: Artificially comfortable vs. Really uncomfortable.
Please choose your Matrix
Since 99% accept the program if choice is given, then the freedom to choose between the Matrix and Zion could be very well part of the machine's calculation while still keeping everything under control.
Blinder than blind, foolisher than foolish
The concept of reality-within-a-reality to blind people (as introduced in Matrix 1) is continued and extended.
Morpheus: "It is the world that has been pulled over your eyes to blind you from the truth."
What is worse than being blind? Being blind and thinking one can see (= being more blind):
Morpheus [Matrix 1]: "Welcome to the real world."
...and then...
Morpheus: "What is real? How do you define real?...What you can...see...is simply electrical signals interpreted by your brain"
...and then (what a fool, you might say!)...
Morpheus: "For the longest time I wouldn't believe it, and then I saw...with my own eyes."
Concept of trapping lies
The 1st Matrix crashed because it simulated a perfect world. A perfect world is a lie, so why shouldn't all Matrixes be built upon lies? Even in the current Matrix, choice is implemented as a lie. Thus deceiving humans might be the common denominator of all machine-human relations.
It's your own world, happy now?
If you didn't like the big fat Matrix, you probably like your own small world (= Zion). Moreover in Zion you can fight what you didn't like: The Matrix.
I forgot to go home...I had to fight
Fighting and fighting and surviving for 100 years. Maybe this ties the concentration so much that it's impossible to find out that Zion is just another simulation. Please note, that Commander Lock (who doesn't believe the prophecy) is in charge of the defense system, thus the man who doubts the prophecy is the one who has to keep Zion alive!
Perfect world for perfect believers
The escapers believed that something is wrong with the world (= the Matrix). Thus they took the red pill. But what do they do in Zion? They still believe that something is wrong with the world.
The escapers are believers. They form the perfect crowd to be amused for 100 years with prophecies, higher goals and a chance to win against the machines.
Which predestination do you want?
You didn't like the Matrix' fake choices (= everything is predestined)? So why do you like the prophecy (= predestination, too)?
Probably those who don't accept the Predestination A in the Matrix are prone to accept Predestination B in Zion (= predestination that Predestination A will end).
What a wonderful deception: You don't like the Matrix? Hey, there is a place where you can meet friends who don't like it, too. And look what this place offers you: Broadband connections to the Matrix, hacking, rave and sex, the prophecy, the feeling of being alive...
Zion must be real, because everybody talks about The One coming to us
Did you ever think of the prophecy as the reason why the Zionites believe that Zion is real?
'We are in Zion - we fight the Matrix - we are in Zion - we fight the Matrix'. Well then it must be real, because nobody ever said a word about the possibility to shut down Zion.
Zion is real, because the Matrix is unreal
Everybody knows, that the Matrix is unreal and you have to plug-it-in. This alone creates a kind of illusion, that 'Zion therefore must be real'.
Zion is real, because it's your home
Most Zionites are freed when they are young. Thus Zion becomes the very place they accept as home. Do you rember what happened to Neo when Morpheus told him, that the Matrix is a artificial universe?
Neo: "No. I don't believe it. It's not possible...Stop. Let me out. Let me out. I want out."
Thus maybe the Zionites refuse a Zion-is-fake idea by themselves. It would be a home taken away from them for the second time and that is just too much to bear.
More hope for the people or more dope for the people?
If the essence of human behaviour is hope...
Architect: "Hope. It is the quintessential human delusion"
... then by giving humans something to hope for makes them fullfilled maybe. Well, in Zion you really can hope as much as you want. Bad conditions+prophecy let hope pour into your thinking and doing. Thus if the matrix leaves you hopeless (because there lies no hope in a programmed world), then maybe the overkill of hope in Zion satisfies you.
And also think of this: Suffer+Prophecies are the very glue used by religions to bind members. Thus we could conclude by the combination of "suffering" and "the prophecy" alone that Zion turns into a religious place. And how does it look like in Zion? They pray, they give religious gifts to Neo.
Are religions making people stronger or more foolish?
Architect: "Hope. It is the quintessential human delusion, simultaneously the source of your greatest strength and your greatest weakness."
Are Zionites strong or foolish? Hard to say.

Maybe each 100 years (or each 250'000 inhabitants) Zion has to be destroeyed, because the possibility is too high, that indeed somebody finds out that Zion is fake.

More 's' than revolutions?

A weak argument (but nevertheless for the sake of completeness): Matrix 3 is called Matrix Revolutions. That's plural. Well, it's clear that a big fight between machines and humans is underway. That's Revolution #1. But what are the other revolutions?
An even weaker argument: The movie is called Matrix Reloaded. Thus it could be that the Matrix in Zion is just a reloaded Matrix of the outer Matrix (= Zion), so to speak.
Another weak but interesting argument:
"Reload" could implement a reboot and "Revolutions" could implement "Revolving" (= cycle).

Zion in a blink of time

A weak argument: At the beginning of Matrix Reloaded.you see the green matrix code and some of the scene angles can be interpreted as Zion's tubular construction.

Census thru sensus?

Morpheus: "And does the Commander have a plan for stopping 250'000 sentinels?"
Morpheus: "A sentinel for every man, woman, and child in Zion. That sounds exactly like the thinking of a machine to me."
This has been pointed out as one of the proofs that the machines know exactly how many citizens of Zions exist, and therefore all 'Zionists' still are connected somehow to the Matrix. Well I don't know: Since the system knows the approximate number of freed people and can extrapolate birth rates, this seems to be a weak argument.

The suit of freedom

A picture from Matrix Revolutions shows Neo in a suit he never wore before. It doesn't really fit Zion nor the Matrix. So where is it? Is Neo free at last?

However, it has been reported that this picture is a fake.

Sunglasses in the Matrix

At the end of Animatrix' story 'The second renaissance 2' you see a child running home (among the radioactive ruins of the real world) to his parents and both turn out to be agents and the child turns out to be in a cocoon.
- Counter-argument: This could however play already within the Matrix. This could be the very time the Matrix was installed: The child was living in the 'real world', was captured, was put into the Matrix, the environment was duplicated for the 'best Matrix experience' and the child continued living (within the Matrix) where it stopped living in the 'real world'.

The Merovingian is a program, thus Neo, too?

Neo shows similarities to Merovingian, who is most probably a program himself. See the Merovingian section. Thus if the Merovingian was a former one, Neo could be one, too. Thus if Neo is a program Zion could be a simulation.

Wachowskis talks

The Wachowski brothers [in a web chat]: "Reflections in general are a significant theme in the film. The ideas of worlds within worlds"

The rabbit is still laughing

I think it would make sense, if the Wachowskis left the audience (even after Matrix Revolutions) uncertain whether the movie played in a Matrix or not. And whether we (= the audience) live in a Matrix or not. How deep does the rabbit hole go? Is the rabbit laughing at us?

Zions 1-5 in only a few years?

Maybe the most important reason is that (according to the Architect) there have been 5 Zion destructions before, but according to the timeline as we know it, there has been no time. Read on:

The timeline as we know it from the plot and from Morpheus:

Morpheus: "In the early twenty-first century all of mankind was united in celebration. We marveled at our own magnificence as we gave birth to AI"
The Nebuchadnezzar (Morpheus' ship) is manmade and from the year 2069.
The Osiris (the ship from Animatrix) is USA-made and from the year 2079.
Morpheus: "For 100 years we have fought these machines"
Morpheus: "You believe it's the year 1999 when in fact it's closer to 2199"
Architect: "This will be the sixth time we have destroyed [Zion]"
Morpheus [Original Matrix 1 script/Apr.1996]: "It started early in the twenty-first century, with the birth of artificial intelligence, a singular consciousness that spawned an entire race of machines...Sometime at the end of the twenty-first century the battle was joined. The war raged for generations and turned the face of our planet from green and blue to black and red."
Weak hint, but nevertheless:
The first rise of the machines was when the robot 'B1-66-ER' killed humans. The '66' could mean that he has been produced in the year 2066.

Additional thoughts about the Morpheus' timeline:

On account of Morpheus' timeline Zion destructions 1-5 must have occurred approx. between 2060 and 2100. This may differ a little bit but the main point is: It's hardly believable.
The Nebuchadnezzar (Morpheus' ship) is man-made and from the year 2069. It still functions, so it's not too far away from 2199 (imagine using a 130 year old car).
If Zion is about 100 years old it is quite impossible that a few people can build a city near the earth's core with all the technology and ships you see in the movie just within 100 years:
- They don't even have good food, instead you see the crew eating "a bowl of snot" / "the same god-damn goop everyday".
  They never ate 'tasty wheat':
  Mouse: "Did you ever eat Tasty Wheat?"
  Switch: "No, but technically, neither did you"
- You see them dancing and living in a quite primitive environment running around in rags and living in stone houses.
- Their only weapon against the sentinels is the electromagnetic pulse.
  Trinity: "[The EMP] is the only weapon we have against the machines."
- The freeing out of the Matrix and inserting into Zion started about 100 years ago, thus a lot of freed persons have skills like 1900-1980. Not too high.
Thus:
1. The Nebuchadnezzar and all the tech you see was made before the first could flee out of the Matrix to build Zion 6.
2. It's either made by inhabitants of Zions 1-5 or made by people before the Matrix was established. The Architect points to the conclusion that it is not Zion 1/2/3/4/5 technology:
  Architect: "You are here because Zion is about to be destroyed - its every living inhabitant terminated, its entire existence eradicated"
  The Architect wants to eradicate everything, so why should there be anything left from former Zions?
One has to add additional time between each Zion, since it would also take its time for a 'One' to be born, grow up and appear/wake up.
How big have former Zions been?
- The machines wait now until about 250'000 people are accumulated (=freed and newly born) in Zion 6.
  Binary: "That'd mean there are a quarter of a million sentinels out there."
  Morpheus: "A sentinel for every man, woman, and child in Zion. That sounds exactly like the thinking of a machine to me."
  It makes sense that the machines haven't destroyed former Zions immediately, but have previously waited, too.
- Architect: "This will be the 6th time we have destroyed it, and we have become exceedingly efficient at it".
  It either means that
  - now they can kill more humans at a time
    That means that more survived the last times, means that more could tell the story how old Zion is, which obviously didn't happen
    OR
  - now they can eliminate Zion faster
    That means it took them even more than 100 years to eliminate Zion 1-5, which collides with the timeline
    OR
  - the time from the attack to eradication has decreased. The last time Zion was destroyed in 72 hours:
    Trainman (played by Bruce Spence) [Enter the Matrix]: "72 hours...That's exactly how long Zion lasted last time...Hahaha... 72 hours."
Architect: "The first Matrix I designed was quite naturally perfect... its doom is apparent to me now as a consequence of the imperfection... in every human being."
As you see it is nowhere stated that the first 'Matrix crash' had anything to do with Zion. Thus it could be that several matrixes crashed (=more time goes by) without even the first Zion having appeared. This would make the Matrix even older. However it could be, that the first Zion was already inhabited at the time of the first Matrixes, this would make 5 Zions more probable.

Thus the above timeline clashes with the idea of six really real Zions.

More hints that something is older than we know:

Architect: "The Matrix is older than you know"
Persephone [about Cain and Abel]: "They come from a much older version of the Matrix, but like so many back then, they caused more problems than they solved".
Please note that Cain and Abel were persons (in the old testament) who caused problems as did so many back then.
Oracle: "Every time you've heard someone say they saw a ghost, or an angel. Every story you've ever heard about vampires, werewolves, or aliens is the system assimilating some program that's doing something they're not supposed to be doing."
Since stories about angels/ demons etc. are very old this could mean that the Matrix is thousands of years old.
- But it could also mean that programs must behave (at least to a certain degree) within parameters of the 'known and handed down' world. Thus if ghosts and goblins were known in the world before the Matrix, then programs wouldn't invent any new form of existence, but behave (or copy behaviour respectively) 'within the body of human knowledge'.
When the Architect speaks of human history...
Architect: "I redesigned [the Matrix] based on your history"
...Hitler is shown. If the Architect had to redesign the Matrix because of Hitler (and others), then
- Hitler's appearance played already in the Matrix
  OR
- Hitler's was outside the Matrix and a Matrix existed somewhere else.
However this might just be an example and not a real reference.

What do you think? Is Zion real? Go to the voting booth!

Possible conclusions from Theories 1-3

[Cast your vote]

None of the Theories 1-3 can be proved or disproved right now. That makes this movie really unique. But there are possible conclusions from theory 1-3 (maybe a combination of the conclusions applies):

Possible Conclusion 1: Zion in a Matrix

The shown real world including Zion is within the Matrix: Zion is part of the illusion (a trap to blind the Matrix escapers). Nobody ever escaped the Matrix. Zion functions as an outlet to minimize the anomaly pressure inside of the Matrix. Also Zion may be a failsafe, thus everybody who awakes from the Matrix (into the desert of the real) wants to get back.
Like in the movie Virtual Nightmare (I haven't seen the movie).

Possible Conclusion 2: Zion in a greater Matrix

Zion (and its surrounding world with all the disintegrated cities) is already within a Matrix. Thus 'The Matrix' (=the fake world) of the movie is just a Matrix within a bigger Matrix.
So what is the difference then to 'Possible Conclusion 1'?

Zion is not a special outlet, but it's the 'real world' as humans always knew it. Then something happened and a Matrix-within-a-Matrix was installed. Thus Zion is an illusion and is the 'real' world.
This is the best unification theory. This could bring an end to fights between 'Zion is real' vs. 'Zion is fake' believers.
The world of Zion could be what the Architect calls 'an older Matrix'. Maybe in the future something will happen in the fake world (= the world inside the Matrix) and it has to be destroyed, too, and a new Matrix is installed inside it 'again'.
Thus Zion could be a Matrix-within-Matrix-within-Matrix...
The planet earth (with all its destroyed cities) itself could be a huge Zion which was destroyed.

Possible Conclusion 3: Blatant lies

The Architect (or someone else) is lying, please see section Is the Architect lying?

Possible Conclusion 4: Superman in a real world

Zion is the really the real real world
Neo is not a human like others
OR
Neo is the first one to discover super abilities
And/OR
Every human has super powers and the Matrix is a way to deceive humans into the belief that they are powerless
There are other Matrixes (Matrizes? Matrices?) besides this one
OR
the real world coexisted for a long time with a Matrix running somewhere aside, and nobody knew about it.

That would explain the talk about 'Matrix is older than you know' and 'This is Zion 6'

Possible Conclusion 5: Matrix outside Zion (Ever-cycle)

The Matrix is older than we know in the sense of restarting over and over again. E.g. starting always in the 1980ies running for, say, about 30 years (1980-2009) and then starting again.

Other possibility: The Matrix is restarted to the state of, say, -100'000 years and goes on to the year approx. 2050 where again machines fight with humans.

Hints at the ever-cycle theory:

It is said that in an old script draft for the Matrix the Wachowski Brothers planned to implement the Matrix as ever-restarting.
Smith: "It's happening exactly as before."
The symbol π (Pi=3.14...) hints at that. Pi is is used from time to time in the movies, maybe to point out the circularity of the events:
- As a symbol, e.g. sprayed on a wall
- Bane (infected by Smith) cuts his hand: 2 parallel cuts and 1 vertical (you don't see the vertical cut in Matrix 2 though, but in the game Enter the Matrix).
- As a number (314 seconds to enter the door to the Architect)
The train from Matrix 1 and Matrix 3 has "Loop" written on it.
Merovingian (when Neo comes in): "Aha, here he is at last. Neo, the One himself, right? And the legendary Morpheus. And Trinity, of course"
He talks as if everything if history would repeat itself.
Agent Smith [Matrix 1]: "The great Morpheus. We meet at last."
The Oracle knows the future. This could mean that it happened before.
Keymaker [Enter the Matrix]: "It's a very special key, meant only for the One. Will you bring it to him?"
Ghost: "What does it unlock?"
Keymaker: "The future."
...thus stopping the resetting to the past
The Merovingian could have been afraid, that Neo goes to the mainframe and chooses the right door (= the restarting). Thus he wanted to stop Neo and keep the Keymaker:
The Merovingian: "If we do not ever take time, how can we ever have time?"
The (albino) Twins smile and nod.
Side note #1: "ever take time"
Side note #2: "take time" = 'keep the Keymaker'? Thus the Merovingian is the Timemaker? Hehe...

It could be that Neo's choosing the left door stopped the re-beginning (highly speculative).

However, there is a counter-argument for the ever-cycle 1980-2009 theory:
Since the fight in Zion goes on for about 100 years already, that means, that the Zionites would have noticed 3 restarts already. Nobody mentioned that in the movies so far. A possible explanation is that the time runs faster in Zion and slower in the Matrix. 100 years of fights in Zion -> only a few years in the Matrix. Remember the Neo-Smith subway fight scene in Matrix 1? They used superfast moves to hit each other. Maybe they can change the time speed.

However this would mean, that if somebody enters the Matrix for a few hours he could die of dehydration while plugged in.
A slower running Matrix gives you a lot of trouble if you have to find an exit (in the Matrix) fast, because sentinels (in Zion) are attacking.
A faster running Matrix gives you problems if you have to get out of the Matrix fast (e.g. because agents are attacking), and your operator (in Zion) has to look for a solution.
Since all your thinking stems from your brain in Zion, it means, that either everything is too slow in the Matrix (= boring) or too fast (= too fast to grasp by your brain).
Your residual image (= your digital image of your real body) would differ on re-entering the Matrix.

But let's suppose that the evercycle does not cycle from 1980 to 2006, but from, say, 1980 to 2130 (150 years). Let's suppose that not only the Matrix snaps back (e.g. to 1980) but also Zion (e.g. to 2100). Then nobody would ever notice anything. This would explain how there could have been 5 Zion before, and this would explain, that the Matrix much older.

Possible Conclusion 6: Human-Machine-Fusion

Zion and all the human bodies in this world are in fact the robots, the 'artificial intelligence' as is shown in Animatrix. Or maybe they are cyborgs/ androids (=half-human and half-robot). Maybe in the war between humans and machines both couldn't survive anymore (the sky was too clouded and temperature was too low) thus they had to fuse (or the machines forced the humans to fuse, or vice versa). Therefore every human who escaped the Matrix and lives in Zion is a cyborg:
Morpheus: "Combined with a form of fusion the machines have found all the energy they would ever need."
Aaah, now that makes sense. It would explain a lot of the Matrix plot...

It would explain why the robots didn't exterminate humans, their enemy.
It would explain the otherwise pretty strange theory about energy production. As it turns out this human-machine fusion would be a win-win situation: Humans keep their world (at least as an illusion) and machines get their energy.
However this doesn't solve the question: "Why aren't the machines genius enough to tap other energy sources?". Maybe this means, that humans won the war, couldn't live in a shattered world and 'enslaved' the machines to keep humans alive.
This would also explain why the sentinels attack: The sentinels could be part of the old armed forces of the humans! Attacking every robot and android.
- This theory is unlikely though. Animatrix shows the sentinels as machine-made, not human-made.
a lot more....

Please also read section Is Neo a machine?

Possible Conclusion 7: The matrix is an illusion for the machines

The matrix (and Zion) is a simulation created by humans for the machines after the machines have been defeated (the war in Animatrix) (or even the war itself is untrue).
Aaah, this would also be Wachowski style: You think the matrix was created by machines for humans? Think again: The matrix could be an illusion for the machines.
Thus agents and everybody who seeks to keep the Matrix going (Architect) could be human or under the controls of humans.

But why? Why should humans make such a simulation?
To let machines understand humans. To reverse machines. To raise a new kind of artificial intelligence that has a profound attachment to humans. Think of the episode "Matriculated" in The Animatrix.

Possible Conclusion 8: Zion helps the evolution of Artificial Intelligence

Zion and everything inside (including the Matrix) is a simulation created by whomever (probably humans) to facilitate the development of a truly intelligent Artificial Intelligence, that will have an awareness and a free will as similar as possible to humans. Thus all 'cocoon prisoners' are in reality programs, that just think of themselves as 'humans'.

Possible Conclusion 9: Parallel Zions around the world

Maybe there are a lot of underground movements like Morpheus and Trinity and Neo. At the same time other Neos and Trinities try to fight the system. Thus 5 Zions have already been destroyed not long ago around the world.

However, why then the Architect's words:
Architect: "The Matrix is older than you know"

Possible Conclusion 10: We don't know what is outside the Matrix

Since Zion might be in the Matrix, too, we have never seen what is really outside of the Matrix. Thus:

It is possible that all dreamers are prisoners on an ice planet, being plugged and observed by prison personnel
It is possible that all dreamers are amoeba like giant jelly fish floating in oceans of sulphur.
It is possible that all dreamers are playing multiple personalities at the same time. Trinity could be played by somebody who also plays Morpheus and Commander Lock.

Possible Conclusion 11: Architect's small world

While the destructions the last 5 times happened as a simulation (simulated by AI higher than the Architect), this time around Zion is for real. The Architect tells from his own point of view that Neo is the 6th anomaly. While this is true, Neo is the 1st really real anomaly.

Possible Conclusion 12: There are no humans

What if all humans are in fact a creation of the machines? Not vice versa.

Possible Conclusion 13: Matrix is real, Zion is fake

OK, I don't know what I am trying to say with this idea, but I list it here to make your thought machine go boom.

Possible Conclusion 14: The evolution of Matrixes

Zion is a special outlet for unhappy Matrix citizens (= Zion is a Matrix) and is about to become the future Matrix, where all current inhabitants of the current matrix will live. Thus the current matrix is just a better verison of an older matrix and Zion is a better matrix of the current matrix. If again a One arises in Zion then a "Zion Zion" would be created and all humans (are they really humans?) would be put into it again. This way the machines upgrade their matrix versions and less and less humans escape.

Possible Conclusion 15: Neo is a machine

What if all Zionites are machines? What if Neo is some sort of a robot with EMP powers that could stop the incoming sentinels? What if Smith is a code inserted by humans to destroy the machines? Would Neo still be your hero? Would you be happy when he lost and the humans win?

Possible Conclusion 16: Machines have always ruled

What if human bodies in cocoons are the normal condition of existence? What if machines have always been the rulers of the world?

What do you think? Is Zion real? Go to the voting booth!

Zeeon, Sion, Zeon, Xion, Xeon, transscript, transexual, the merovingina, Morpheous

Matrix within a Matrix

Is Zion just another Matrix? Thoughts and consequences

Matrix-within-a-Matrix Theory

Theory 1: Zion is the real world and strange things happen

Zion is real, because it's time for extra-powers

Zion is real, because it's just Hollywood, baby

Zion is real, because you suck!

Neo has superpowers, because he is like superman

Zion cannot be fake, because this collides with the story

Zion is real, because Neo didn't stop anything

Zion is real, because Keanu said so

Zion is real, because otherwise the matrix would look like Zion

Zion is real, Neo has a wireless connection and was given the access codes

Zion is real because Neo is an ape and Zion is Zooon

Zion is real, because of... (miscellaneous objections)

Theory 2: Zion is not Zion

Dreamish

Something is different -> This is not Zion

Where is Neo?

Possible: Wrong door

Theory 3: Zion is not real

So yellow I could dream

Zion's blood

Behind behind the scenes

More than words: Music

Dreams

Smith enters Zion (thru another person: Bane)

Blues get me the blues

Red candy: We all like to know the truth

ArchieTV, Blue screen of death

Dig me deeper?

Fake humans and fake machines

Dark side of the spoon

Alive and bleeding

No chance in Zion

Residual without mirror?

Trinity empowers Neo

Freed individuals aren't killed immediately in their cocoons/ Harmless machines

Why should human bodies be a power generator? Why should humans be kept alive, after the machines have won the war against humans?

Science fiction is no fantasy

Keymaker's systems on systems

Sixth sense

A fake Zion fits perfectly into the concept of deception

More 's' than revolutions?

Zion in a blink of time

Census thru sensus?

The suit of freedom

Sunglasses in the Matrix

The Merovingian is a program, thus Neo, too?

Wachowskis talks

The rabbit is still laughing

Zions 1-5 in only a few years?

Possible conclusions from Theories 1-3

Possible Conclusion 1: Zion in a Matrix

Possible Conclusion 2: Zion in a greater Matrix

Possible Conclusion 3: Blatant lies

Possible Conclusion 4: Superman in a real world

Possible Conclusion 5: Matrix outside Zion (Ever-cycle)

Possible Conclusion 6: Human-Machine-Fusion

Possible Conclusion 7: The matrix is an illusion for the machines

Possible Conclusion 8: Zion helps the evolution of Artificial Intelligence

Possible Conclusion 9: Parallel Zions around the world

Possible Conclusion 10: We don't know what is outside the Matrix

Possible Conclusion 11: Architect's small world

Possible Conclusion 12: There are no humans

Possible Conclusion 13: Matrix is real, Zion is fake

Possible Conclusion 14: The evolution of Matrixes

Possible Conclusion 15: Neo is a machine

Possible Conclusion 16: Machines have always ruled

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