Here is an explaination to whats going on in this remarkable series of films:-

The Masked Reviewer has now seen both The Matrix and The Matrix Reloaded. The question is...what will happen in the third part of the trilogy? Good question. For those of you who can't wait, or for those of you who just like to be "wowed" by the awesome predictive power of the Masked Reviewer, read on.
First, let's discuss the fact that the Warchowski brothers have clearly been influenced by an impressive array of philosophers and science fiction writers. There's nothing in The Matrix so far that hasn't been dealt with in sci-fi. But there are a number of ways the story could be resolved. Let's look at a few clues...but before we do, the warning will be repeated: what follows may contain spoilers to the plot of The Matrix: Revolutions. It certainly contains spoilers to both The Matrix and The Matrix Reloaded. If you don't know what a spoiler is, you might want to look it up now. On the other hand, it is possible that the Masked Reviewer will be totally wrong in his guesses. We'll have to wait until November to know for sure.
Based on clues from the first two films, the Masked Reviewer postulates the following:
Neo is not human. He is a program.
Not only is this a good excuse for Keanu Reeves' robotic performance, but it explains a lot. The Architect says to him:
Your life is the sum of a remainder of an unbalanced equation inherent in 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 deciduously avoided it is not unexpected and thus not beyond a measure of control.
Neo's "life" is the result of programming problems. He has free will, but he is still guided by the program of the Matrix. Other programs exist in the Matrix to keep him moving towards his reason for existing.
What is his purpose? To help understand human nature and thus more effectively control it. We learn that there were five "One"s before Neo. Each time, they attempted to learn what was needed to keep everyone happy, thus maintaining the symbiotic relationship between man and machine to insure the survival of both.
Morpheus talks about the first "One" in The Matrix:
When the Matrix was first built, there was a man born inside who had the ability to change whatever he wanted, to remake the Matrix as he saw fit. It was he who freed the first of us, taught us the truth. As long as the Matrix exists the human race will never be free.
That person was a program. And the Masked Reviewer believes that program appears in The Matrix Reloaded as...the Merovingian. But how could he free anyone if he was born inside? Neo had to be rescued by other people, picked up in a ship, and healed. Unless...
The "real world" outside the Matrix is not real. It is another virtual world, linked to the Matrix.
The Masked Reviewer believes the strongest evidence for this is that at the end of Reloaded, when Neo is able to affect the squid robots in Zion using powers similar to what he has in the Matrix. First he can "sense" them, then he can destroy them. He was programmed to be flexible and grow, but not intended to be aware that Zion is also virtual reality.

Also, there is a human who is "infected" by Agent Smith, who is lying unconscious on a table next to Neo at the end of Reloaded. Perhaps this person is a program, like the Agents in the Matrix, who has been infected by Smith's virus. If not, what mechanism would allow Smith to control him?
"Everything happens for a reason." This is spoken just as, in the end of Reloaded, a gangplank breaks as a crewman runs in his ship in Zion. That "random event" allowed the chain of events that Neo dreamed about to happen. The computer was only able to force that chain of events by controlling both worlds.
Items have been passed from the virtual world to the real world, such as a cartridge given in an envelope to be delivered to Neo in Reloaded. Though there may be another explanation for this, the most logical is that they are both virtual worlds controlled by the same computer.
And, of course, the Oracle seems to have a knowledge of what happens both in the "real world" of Zion and the virtual world of the Matrix.
There are some visual clues, such as the color coding: everything in the Matrix is tinted green, everything in Zion is tinted blue. Perhaps we will see the real world in Revolutions, with normal colors?
Remember Plato's cave? The real world is the cave. Perhaps there is no reality outside of the Matrix? At least, no habitable reality. We learned in The Matrix that the humans scorched the sky to stop the machines. How do the humans survive? How do they grow food? Now the machines and humans are dependent on each other, and all that is left for the humans is the Matrix and Zion.
The purpose of the second virtual reality is to give the people who reject the Matrix (according to the Architecht in Reloaded, it's about 1% of people) a place to go.
Humans need at least the illusion of free will, or they will revolt ("The humans are revolting!" "I know, they smell bad too"). Thus a place was created for this 1% of people to go.
The agents exist to keep too many people from going to Zion; the system will become unbalanced if too many people go there.
The agents are programs that don't know that Zion is a 2nd virtual reality. They don't need to. Just like real computers, not every program knows what every other program is doing. Agents exist to stop too many people from being transferred to Zion. Neo exists to improve the parameters of control. The Oracle exists to keep Neo in line.
Neo's program is altered through his mouth.
Remember the woman who was affected by the cake that the Merovingian gave her in Reloaded? She ate the cake, she changed. How did Neo leave the Matrix in the first film? He swallowed a pill. Why did Persephone kiss him in Reloaded? She wanted to download information from him. How about the Oracle? Did you notice that whenever they meet, she gives him something to eat? In The Matrix, she gives him a cookie and tells him that by the time he finishes the cookie, he'll feel better. Hmm. The Oracle is also a program. Her job is to keep Neo on track...because he is the product of several efforts to perfectly emulate and understand humanity, he is hard to control, and thus she guides him. And when he's too far off course, she alters his program. She also gives him candy in Reloaded.
What information did Persephone want? She is the one referred to by the Architecht as "the mother of the Matrix". Her job is to understand the emotions of humans. She is also a program.
The Merovingian is the first "One".
After freeing the first minds into the "real world" of Zion, the Merovingian was integrated into the code of the Matrix. How would a human mind become part of a program? He must be a program himself. What he learned about humanity and love was downloaded to Persephone through their kiss. That is why Persephone will only help Neo if she kisses him, just like Neo kisses Trinity. She wants to experience it, to download it, because that's her purpose.
There are many programs hiding as humans in the Matrix and in Zion.
Neo, the Oracle, Merovingian, and Persephone. But...how about Morpheus? How about Niobe? Morpheus is single-minded in his quest to find "The One". The system would want to dedicate a program to finding the next one and guiding him. As the Architecht mentioned, he is not beyond control. Morpheus is a religious figure, providing hope and stability to the people of Zion. It seems logical that the computer would want him. Also, he does speak in a manner very similar to Agent Smith. Morpheus and Niobe aren't aware of the fact that they're programs. And Trinity? She's probably human...but an argument could be made against that, too.
Perhaps Morpheus was an earlier One? Where are the rest of the Ones?
Neo's main purpose is to help the computer understand the nature of love. This is so that the computer can better facilitate control over people.
It's a love story. Neo is fascinated with Trinity from the first moment. The first Matrix failed because it was "too perfect". To be real, one of the elements that the machines must understand is love.
The difference in this iteration of the Matrix is that Agent Smith has developed a bug in which his code has merged with Neo's, producing a virus.
He replicates himself. He infected a program in Zion, spreading there as well (the guy lying next to Neo on the table at the end of Reloaded who cut his hand and sabotaged things). The only one who can prevent a cataclysmic crash which will destroy the Matrix and Zion will be Neo. "Revolutions" refers to both a revolution against the system (by both man and computer intelligence as well as the revolution of the process, the constant turning of the giant wheel. Revolution: revolt. Humans provide power. Voltage. Re-volt. Okay, that's nonsense.
The Masked Reviewer predicts that The Matrix: Revolutions will be a huge blockbuster. The Masked Reviewer isn't afraid to go out on a limb. In the end, Neo will destroy the virus Smith, but no one will be freed. No one but Neo, Morpheus, and Trinity will know that everything is an illusion. Thus, the trilogy will end with humanity saved from the threat of Smith's virus destroying everyone, but no one actually being free. And, the possibility of future Matrix films will be left wide open.

Damn, I bet your fingers hurt.

looks like a trekkie, in the club :P

(star trekkie or someone that loves sci-fi)

No, havent you heard of cut and paste??

Also more of a Star Wars fan than a Trekkie but more of a Petrol Head than anything!!

more of a Petrol Head than anything!!

thats what i like to hear:) or a datto freak like me

Matrix Reloaded? More like Matrix Real Bloated!
I apologize if you have covered this above. I must admit I didn't read your whole review, yet. Here's my take, the whole thing took itself waaaaaaaaaaaaaaaaaaaaaaaaaaaaaay too seriously. C'mon, The Matrix was just a little throwaway sci-fi action romp with lots of special effects. The, for lack of a less insulting term, Matrix geeks read so much into it that they HAD to bloat the thing up with so much philosophy 101 that the whole thing was almost unwatchable. And what was up with the lame and boring fight scenes? Why didn't Neo just run away to begin with and save some time? And don't even get me started on that whole time waste of a rave/orgy scene! Where the hell did THAT come from?
Now, having said all of that, I do plan to receive my "three hour beating" and watch the (hopefully) final episode when it comes out.

After seeing it two weeks ago, I thought it was okay, but did take itself WAAAAY too seriously. After having thought about it for some time... I think it sucks

Ok Ok I concede..you guys are hard nuts to crack I only cut a pasted it from an email I received and thought you guys would be interested..but I was wrong.

Quote:

That "smiley" is cracking me up!

The Matrix is the Gospel from beginning to end.They got the storyline frome the greatest book of all..the BIBLE!!Think about it.