Ok, here is what I think is going on. I’m aware of the few lose ends in the story… I think human has created the matrix to survive a global disaster. Think of a meteor hitting earth or a nuclear explosion. The matrix consists out of two parts, the matrix as we know it and Zion. Zion is created to “host” the people who are not accepted by (or who do not except) the matrix. This should be 1% of all people hooked to the system (This is explained by the Architect). This secondary system is absolutely necessary to make sure people do not wake up and pull the plug. The system, the matrix, however has seen the “future” and knows when it ends (lose end, how can programs see the upcoming statements?). This would be the time that earth is safe to live in again. Therefore it has changed the program to loop endlessly. This loop consists of the choice between destruction of Zion or, in this case the choice Neo made, saving the girl. At this moment the system is in its 6th loop. As the Architect says, there have been 5 before Neo. This has been the ones that did actualy get the the mainframe. Maybe there where more, but they didn’t get that far. Because of this a virus has been developed which main purpose is ending the system loop and free all people of there “prison”. This virus is called Neo. This virus has been created by “obsolete” programs or programs that have been up-dated and did not return to the core system. This would be Morpheus and his gang. They found a program that could be reprogrammed to act as a virus. And they did as you can see in Matrix 1. Now that this virus is created it’s looking at (gathering) all possible variables (and right values) to get to the core system (main frame) and stop the looping. But the system fights back. It has developed (or was created by humen to ensure the system would not stop before the ending-date) an anti-virus program which purpose is to stop Neo. This anti-virus program is called Agent Smith. Because of an “agent up-date” Smith, who should have returned to the core system as all programs should if they have been up-dated, is now an anti-virus program on the lose, behaving as a multiplying virus. And because of that, Agent Smith has access to the second matrix being Zion? This is explained by both the Oracle and the visions of Neo. I think it to the up most importance the system has Zion as a secondary matrix. As I explained before, if Zion does not longer exist the change is that people wake up outside the matrix and pull the systems’ plug. Therefore Agent Smith, which infiltrated into Zion and sabotaged the defence against the Sentinels, is actually helping Neo (the virus) ending the loop. This would all mean that all leading characters we see in the movie are programs within the system. This makes cense if you think about it. Take the key-maker for example. We all used his skills to hack or crack a program or a game. He’s just a key-generator. I would like to end this with the following quote of the Oracle. (btw, I think the Oracle was the old architect (main frame). But because the system has been up-dated with the new loop, it became a free program. This Oracle can see all five (or more) loops, and she knows what values Neo should have to end the loop.) “You have already made your choice. You now have to understand why you choose it.” (or something like that) Doesn’t that sound just like a program? Everything is predefined. Every statement is there, it’s just finding a way to flow trough the right statements with the right values. Example: REPEAT RunMatrix; UNTIL Neo = RightValue; EndMatrix;
Very good analysis! I think there is something left: Morpheus told Neo that mankind created the AI. As seen in “Animatrix” - the AI build the matrix to survive after mankind darkened the sky! Im sure youre right meaning that the oracle is the former architect (or something related). The oracle helps Neo finding a way out of this mysery. The machines are going to take the same path a sixth time: Attacking Zion, chossing some Humans to rebuild Zion and are waiting for the next anomaly (this time called Neo). The architect told Neo if he chooses to save the girl (he did it yeah!) he will cause the destruction of entire Zion and the he would break the cycle of the matrix ERGO he would be responsible for the eliminiation of MANKIND ! As youve seen at the end of Reloaded - Neo was able to influence/stop the sentinels who chased the crew of the “Nebucad Nezza”. I think this is the key Neo has searched for he needs for stopping the machines! Lets wait until November to see how the Revolutions i going…
Well… somethings you can notice… there’s a matrix inside the matrix… that’s the trick of the movie. The Matrix is inside another Matrix that resembles the real world where Zion was. That’s why Neo can still has powers in the “real” world, that’s why Agent Smith can infiltrate into their minds in the “real” world… because it’s not a real world. It’s just still the Matrix. What’s the best way for not having the humans desiring to be free??? Easy, make them feel they already are. If they dream they’ve awake from the Matrix… why to try to continue waking up?
A bit of trivia for persons that have seen both films; In Reloaded, remember the room in which Neo talks with the architect - well this room actually features in The Matrix!!! [:0] Where? [?] When Keanu is going to be interrogated by Agent Smith (early on), there’s a frame showing him sat at a table, being displayed by a surveillance camera in this room! If you don’t believe me, check it out!!!
Yes youre right - I can remember it! I think the theory that Zion is somekind of another/secondary matrix is a good one but isnt the key to the end of the 3rd Matrix “Revolutions”! 
There has to be a 2nd matrix or Matrix within a matrix. How else was nero able to stop the flying robot thingies (forgot their name) at the end of the Reloaded movie? [:)]. Its frustrating finding people that actually could follow the whole Matrix idea properly. I think that the 2nd one must have really confused a lot of people (especially my girlfried)