[carrrnuttt]

I have never encountered a movie that has made me think LONG after the movie as this one has.

Here are some of the theories that stemmed from Matrix Reloaded:
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The Religious Theory or the Zion is Real Theory

Neo is a Christ figure. He is supported by Trinity (the Holy Trinity) to save mankind (Zion). At the end of M2 he uses supernatural powers in the “real” world because he is actually a higher being. Unlike the other 6 matrices, he made the choice to fight the system, by picking the door to save Trinity and his friends in Zion, instead of “Reloading” the program for another cycle.

His encounter with Merovingian (the French guy) is significant because Merovingian is a former “One” that faced the same choice as Neo but decided to take the other door. The name Merovingian comes from the original bloodline of the Kings of France. The lore surrounding the Merovingian line is that they were descended from Jesus and Mary Magdalene when Jesus escaped from the cross and fled to some part of France. This fallen savior no longer cares for humanity, only his own power. His wife, Persephone (the name of Zeus’s daughter that married Hades lord of the underworld), once played a role like Trinity supporting Neo. She longs for a kiss to recapture those days before her husband made his choice.
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The Blue/Green Matrix Theory

Zion is not real. It is just another Matrix (Blue) for those 0.1% that cannot accept the Green Matrix that imprisons most of humanity. Zion’s (Blue Matrix) existence is essential for the survival of the Green Matrix.

The Matrix imprisons the human mind by treating it like a computer program. This works to a degree (99.9%) because human minds are logical and rational like computer programs. But minds are not completely logical. This is the fundamental flaw with the Green Matrix. Eventually enough minds rebel to crash the entire system.

The Blue Matrix was created as a place to put the people that were rebelling. It creates the illusion of choice (between blue and green). Yet this is only a temporary solution. Over time those that are rebelling will become so great in number they will be able to crash the entire system from Zion (Blue Matrix). Thus the inherent flaw of the system remains, but it is mitigated by the existence of the blue matrix. Zion can destroy the system, that is why it must be purged when it gets too strong and a new Zion created. This is the program loop that has been “Reloaded” six times.

Neo’s role in the Machines’ plan is to make the choice to create a new Zion, thus both saving and imprisoning humans, if one believes the machines’ possible bluff that they would allow humanity to die.

This is why Neo can use his powers in Zion as he does at the end of M2. He isn’t superhuman, he just realized that the spoon given to him in Zion isn’t real, just like the one he bent in the green matrix isn’t either. Perhaps we will see that the coma he went into at the end of M2 is his emergence into the Real world.

Under this theory, Merovingian, is a former “One” that made the choice to create a new Zion.

Councilor Hamann is either a former “One” or in league with the machines. In his discussion with Neo in the reactors of Zion he alludes that the Machines maintaining Zion, just as they are maintaining the Green Matrix. He stresses they symbiotic nature of existence and conflict between the Machines and humanity.

Agent Smith is an unwitting weapon created by Neo with the potential to destroy the Matrix. Smith’s bloodlust for Neo may destroy the vary Matrix that he used to protect as he assimilates more and more of it to increase his own power.
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Tron Theory

There are no humans, not yet anyway. The Matrix movie is like a version of Tron with no human watchers (Jeff Bridges), of a computer running through a simulation with all possible factors being worked first, before it initializes the program for real.

The main computer has been caught in a loop cycle for 5 iterations, and it is trying to find a variance that will break this cycle by utilizing a random bit anomaly piece of software (Neo), to allow it to fully complete its cycle. It has tried this before, but has always failed and in its attempts.

Matrix - main base operating system.

Zion - secondary operating system for software that can no longer can function in main system - but can be utilized to build a new matrix system.

Neo - Random bit anomaly software for breaking loop cycle – utilized by the Oracle and Architect software to be a random variable to upgrade itself.

Trinity - complement software to aid in Neo's completion of purpose.

Morpheus and crew - collector programs for mainframe to try to enable the end of the loop cycle.

Architect - Mainframe operating system.

Oracle - old Macro Software that has been part of all 5 iterations of the loop and can see all variances.

Oracle's Protector, Seraph - Mainframe hard code software.

Merovingian - old Neo that did not fully implement objective in beta 5.0.

Merovingian's wife - Old Trinity code.

Twins, and Merovingian's guards - old base black ice protector code.

Councilor Hamann in Zion - Advisor for Mainframe that advises Neo along his upgrade to not touch the main bios (engineering) systems.

Key Maker - come on now, too easy, a simple keygen.

Smith – originally an anti-virus program, now a self-replicating virus - now capable of moving to either system – infused with anomaly code from Neo.
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Being that I am a Programmer by trade, I am quite fond of the last theory...