Warning, major
plot points revealed! Do not read this if you have not seen
the series.
Morpheus: The Matrix is the world that has been pulled over your eyes to blind you from the truth...
If real is what you can feel, smell, taste and see, then 'real' is simply electrical signals interpreted by your brain...
What is the Matrix? Control. The Matrix is a computer-generated dream world built to keep us under control
...

What is The Matrix? The Matrix is,
without a doubt, the greatest Sci-Fi movie series in the history of the
world. There is no legitimate intelligent argument to the contrary.
Despite the idiotic, simple minded, cry-baby opinions of most movie critics who
obviously understand nothing, The Matrix will always and forever be one
of the most triumphant accomplishments ever filmed.
First, if you are one of those who say, "I liked the first one
better" be advised that this statement makes no sense and irritates me every time I hear it. The Matrix is a trilogy. It is a single story that was conceived from beginning (The
Matrix) to end (Reloaded/Revolutions) and then filmed in 3 parts.
It is ONE story. It is not possible to like one more than the other. That's like saying "I thought
The Fellowship of the Ring was a great movie but that sequel The Two Towers was a bunch of crap!" You either like
The Lord of the Rings Trilogy or you don't. And likewise you either like
The Matrix Trilogy or you don't. Remember, "It's better to stay quiet and be thought a fool than to open your mouth and remove all doubt."
Now that I got that out of the way again I can
proceed. I am going to assume that anyone interested in reading this has
actually seen all three films plus the Animatrix
shorts and therefore
knows the general synopsis. If you don't, I summarize the second and third
parts in my reviews and there are probably tens of thousands of
resources on the web that will give you the back story.

After I saw the second part, The Matrix: Reloaded,
I came up with a idea based on what I saw in that film and what I knew from the
first. Then when I saw the final part of the series, The Matrix:
Revolutions, I had doubts and admitted that my initial, loudly postulated,
beliefs were probably false. Now that I have
seen all three parts of the Matrix and the Animatrix prequels in
order, I can give my final analysis of what I believe happens in the film, and in
effect, I've returned to my original theory which was:
Neo is a necessary aberration in the Matrix. Free will and choice eventually destroy the Matrix so a controlled crash and "Reloading" has been written into the program. Neo and the people of Zion are the facilitators of that crash. Zion is built up with the assistance of The One, and then systematically torn down and destroyed at the end of each cycle of the program. What we have seen, starting with the first Matrix film, is the sixth cycle of the program. The battle of the machines versus Neo and the Zionists has been played out five times previous and is completely controlled by the Architect, and his program. At the end of each cycle Neo, the aberration, makes a choice, and the cycle begins anew.
The choice, this time, is to save Trinity or humanity. Door number one or door number two. Five times Neo has apparently chosen the door to save humanity but this Neo is making different choices and he decides to save Trinity, which he does.
Back in the "real" world the Sentinels have smashed a pre-emptive attack by the humans that is discovered to have failed because of a traitor. That traitor is Bane, who has been inexplicably infested by Agent Smith. As they out run the Sentinels sent to destroy their ships, Neo senses and is able to disable them with a debilitating pulse, a power that should only have been available to him inside the Matrix.
What is the primary lesson that we have learned from Reloaded? The Matrix is not real (but we knew this.) It is part of the program designed by The Architect. The rebellion of Zion and The One (Neo) are also part of The Matrix program and it's predetermined failsafe mechanism. And finally, the most important thing to know, based on the Smith / Bane incident and the disabling of the Sentinels in the real world by Neo at the end of the film,
THE REAL WORLD IS NOT REAL EITHER. It is just another layer of The Matrix. No one is free. Neo, Morpheus, Trinity and even those who are supposedly born inside Zion, are all plugged into the machine and have never been released from
their pods.
I once again believe that the Matrix is a multi tiered
virtual reality and
we never, at any time in the film series, actually "see" the real
world. I will explain my reasons for this again in more detail in a
moment.
One essential thing to first understand about my new
improved theory is that it requires an understanding of computer virus
protection software. In a nutshell, your computer's anti-virus software
seeks out and finds destructive programs (virus') and either destroys or
isolates them so that they can not harm the functionality of your
system. I believe that the matrix has a similar security system and I will
apply this analogy to my analysis.
In the first film Agent Smith said:
Agent Smith: I'd like to share a revelation that I've had during my time here. It came to me when I tried to classify your species. I realized that you're not actually mammals. Every mammal on this planet instinctively develops a natural equilibrium with the surrounding environment, but you humans do not. You move to an area, and you multiply, and multiply, until every natural resource is consumed. The only way you can survive is to spread to another area. There is another organism on this planet that follows the same pattern. A virus. Human beings are a disease, a cancer of this planet, you are a plague, and we are the cure.

Smith and the other agent's are indeed the cure.
They are the anti-virus software that is tasked with removing programs that are
dangerous or foreign to the system. There are numerous subversive programs
in the Matrix and not just Zionists.
Neo: Are there other programs like you?
The Oracle: Oh, well, not like me. But... look, see those birds? At some point a program was written to govern them. A program was written to watch over the trees, and the wind, the sunrise, and sunset. There are programs running all over the place. The ones doing their job, doing what they were meant to do, are invisible. You'd never even know they were here. But the other ones, well, we hear about them all the time.
Neo: I've never heard of them.
The Oracle: Oh, of course you have. 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.
Persephone: They come from a much older version of the Matrix, but like so many back then they caused more problems than they solved. My husband saved them because they are notoriously difficult to terminate.

The characters in the films referred to as
"exiles" are the programs that have either
gone rogue like The Merovingian and his henchmen, Persephone, The Trainman, The
Keymaker, Seraph, etc. or programs that have been created by elements of the
system for superfluous personal reasons like Sati. The above mentioned
rogue programs survive from one version of the matrix to another and actually
seem to grow stronger.
Merovingian: Mark my words boy, Mark them well, I have survived your predecessors and I will survive you.
This is probably due to their ability to retain
information from one cycle to the next. Neo's strength grows with each
progression as well.
During this string, Smith goes rogue and due to his
infusion of Neo 6.0, he becomes unstable and very powerful. In a sense he
and Neo become one at the end of the first film, then The One splits into his
two complementary selves. Good/Evil, Yin Yang,
Neo/Smith, etc. Perhaps it is this split that causes Neo to choose the
different (Trinity saving) door during his 6th encounter with The Architect.
Devoid of the Smith half of his consciousness he chooses the "love"
door instead of the one that saves humanity and reloads the Matrix
program. I also believe that Neo 6.0 makes this new choice for other
reasons. First, I think this Neo believes he can save both Trinity
and humanity. He is stronger and more sure of himself. This comes as
a surprise to The Architect:
Neo: Why am I here?
The Architect: Your life is the sum of a remainder of an unbalanced equation inherent to the programming of the matrix. You are the eventuality of an anomaly, which despite my sincerest efforts I have been unable to eliminate from what is otherwise a harmony of mathematical precision. While it remains a burden assiduously avoided, it is not unexpected, and thus not beyond a measure of control. Which has led you, inexorably, here.
Neo: You haven't answered my question.
The Architect: Quite right. Interesting. That was quicker than the others.
At this point The Architect realizes that something is
different. He is a program too so he does not show an emotional response
to this revelation. He does however quickly surmise the change.
The Architect: It is interesting reading your reactions. Your five predecessors were, by design, based on a similar predication: a contingent affirmation that was meant to create a profound attachment to the rest of your species, facilitating the function of the One. While the others experienced this in a general way, your experience is far more specific. Vis-à-vis: love.

The other difference this time around is that Smith has gone
rogue and is taking control of the entire first level of the Matrix. The
machines cannot control him and as he absorbs the avatars of each human's
residual self image he also is able to absorb the exiles like Sati and utility
programs within the Matrix like the Oracle.
[Talking to the machines]
Neo: The program Smith has grown beyond your control. Soon he will spread throughout your city, as he has spread throughout the Matrix. You cannot stop him... but I can.
The Oracle is the program that is ultimately orchestrating
this change in The Matrix. Neo and Smith are her puppets. In the
past she has guided their efforts toward the standard reboot cycle but her
perspective inside the Matrix has shown her how the bad exiles like The
Merovingian have grown stronger (The Merovingian actually destroys her avatar as
punishment for helping Neo on this new unpredictable cycle of change.)
The Architect: You played a very dangerous game.
The Oracle: Change always is.
Working from the inside as a supposed confederate of the
resistance, The Oracle was the one who first came across the solution to the
problem with people rejecting the Matrix. She understood the danger of
this and thus the second tier of the matrix was created as a safe controlled
recycle bin for those who would not accept the program.
The Architect: As I was saying, she stumbled upon a solution whereby nearly ninety-nine percent of the test subjects accepted the program provided they were given a choice - even if they were only aware of it at a near-unconscious level. While this solution worked, it was fundamentally flawed, creating the otherwise contradictory systemic anomaly, that, if left unchecked, might threaten the system itself. Ergo, those who refused the program, while a minority, would constitute an escalating probability of disaster.
Neo: This is about Zion.
The "Real World" and Zion is the
place that the machines created to harbor the people that could not be
controlled from within the Matrix. The real world is crawling with
sentinels that would not be tolerated in the first level of the Matrix (It would
break the illusion, so agents are used instead.) The people of Zion
are also conveniently settled in one location, a corral if you will, that
continues to facilitate control by the machines. This is like when
virus protection software quarantines a virus. It can't remove it without
disrupting the system but it can isolate it so that it can do no real
harm.
The following are some of the reasons that I
believe the "Real" world and Zion are still a part of the Matrix:
As mentioned above, Smith's ability to affect
things both inside and outside of the Matrix would be impossible unless he never
actually leaves the Matrix. His ability to pass his consciousness into
Bane is only achievable if Bane is also jacked into the system.
And speaking of being "jacked in",
remember when Neo was in a coma in the "real" world but also trapped
in the train station at the same time? The woman monitoring his brain waves said, "I've seen these patterns before... On someone
who's jacked in...."
I also mentioned before that Neo was able to
disable sentinels outside of the matrix. If he was really in the
"real" world he could not do this. We see him do it at the end
of Reloaded and then on a grand scale in Revolutions when he and Trinity take the
hovership to the machine city. Here he disables 100's of sentinel bombs at
one time. Again, this would not be possible unless he is still in the
matrix.
Also, once he arrives, notice how Neo sees
the machine city. The same way he sees the code of the Matrix. This
is a big clue. If the machine city which supposedly resides in the
"real" world appears to Neo as more matrix code then it can only be
because it is part of the matrix.
Finally, and this is the last thing I will
say in support of my theory, in the Animatrix short story The Kid.
The Kid is actually able to cross over into the real world by way of
transubstantiation. He basically commits suicide in the matrix and wakes
up in the "real" world. This moving from one world to the
next, after death, is reminiscent of the concepts of Heaven or The Afterlife,
but actually his communications with Neo outside the Matrix afford him a
knowledge of the "real" world and the system then permits his move
from the primary 1st level of the Matrix to the 2nd "real" world/Zion
level where he can still be monitored and controlled.
The Architect: Denial is the most predictable of all human responses.
You may or may not agree with this theory
about what the Matrix is. But after viewing the entire three parts of the
film and the Animatrix shorts, in what I believe to be their correct
chronological order, this is the conclusion that I believe. Keep it in
mind next time you watch and let me know what you think.

The
Chronology
If you own all three parts of The Matrix and
The Animatrix on DVD and you want to watch the whole Matrix experience
from beginning to end like I did then the following is chronology I recommend:
-
The Second Renaissance, Part 1
(The obvious pre-story)
-
The Second Renaissance, Part 2 (The
obvious second part of the pre-story)
-
Matriculated (I believe
this story represents the early attempts to fight against the
machines. And most importantly, they try to reprogram the machine by
jacking it into a construct where they can manipulate it. They
fail but I believe the machines then adapt this technology and use it to
create what later becomes The Matrix.)
-
World Record (This is an
early version of The Matrix where people were apparently able to break free
by acts of will. The Agents in this version had the primary
responsibility of monitoring and locating weaknesses in the control.)
-
Beyond (This is another
example of early malfunctions of The Matrix.)
-
Detective Story (We meet
Trinity for the first time and she is still working alone as a renegade
hacker. I believe this tells the story of what she was up to before
she met Neo and joined Morpheus' crusade.)
-
The Matrix
-
Program (This is a sparring
program similar to the one used by Morpheus and Neo in the first
movie. They have the same type of ship as the one's we see in the
movies as well. The main point of the exercise seems to be a test of
loyalty. An argument could probably be made that this "test"
was created to prevent "The Cipher Situation" where someone
decides they will strike a deal with the Agents and betray their shipmates.)
-
Kid's Story (Neo is talking
to The Kid from "outside" of The Matrix so this must be after the
first film.)
-
Final Flight of the Osiris (This
is the story that sets the stage for the final two movies. We see the sentinels
burrowing toward Zion and it is referenced early on in Reloaded.)
-
The Matrix: Reloaded
-
The Matrix: Revolutions
Also See:
The Matrix
The Matrix Revisited
The Matrix Reloaded
The Matrix
Revolutions
The
Animatrix