Major Spoilers below.
KenM said:
2. Why do they need to go into the matrix programs anyway? If it is the computer that is doing it, get as many ships as you can, fully armed and destroy the computer. They don't need to hack into it.
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WARNING
# MAJOR #
SPOILERS
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Really, don't read this unless you have seen the movie
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You can bet that they do NOT know where the true mainframe lies. Even if they did they sure don't have the military power to destroy it. Even if they had the military power to destroy that would kill eveyone still hooked up to the matrix. Even if all of that happened you can be assured that the Architect has taken steps to ensure his survival.
The only reason that Zion exists is that it is part of the control mechanism that the Architect maintains over the human race. He would prefer a system that was linearly stable but he wasn't able to create one. Instead the AI(s) settle for one that is cyclicly stable. The Arch. created the Oracle to help understand human nature and help create a stable system.
Zion has always only existed at the sufferance of the AI(s). It is the like the trap in your kitchen drain that captures all of the detritus. Every once in a while you go in and clean all of it out. Zion is the place to the put those who don't conform and accept the matrix as real.
If Zion ever became a true threat before the appearence of the one it would be destroyed immediately. It would probably throw off the Architect's cylce a bit but I'm sure he would adjust.
The agents have always LET people escape because that is part of the process of the cyclic stability. My guess is that the instability that results in the creation of 'the one' would only be accelerated if they just killed those who did not except the programming. So, to keep the cycle on longer iterations they let the misfits escape to Zion where they can keep an eye on them.
Once 'the one' appears, it is time to go and clean out the trap and start the cycle over again.
Remember this is the 6th appearenc of 'the one'. That is part of the control system. It was understood by the Architect that this would happen every so often. In fact, he does not count the age of the system in terms of minutes, hours, seconds; he counts the age of the system in terms of the cycle he has created.
Think of the most twisted and evil genious villain in a D&D game and you might come close to the Architect. Even at the end of the second movie The ARch. doesn't feel threatened. He might be annoyed because it will take him a long time to rebuid the matrix after it crashes but it could be done.
Now, one of the things I hope they don't do is to make Zion another level of the Matrix. i.e., Zion is just another program that runs for those who don't accept the first level of reality. This would make it similiar to the movie: 'The thirteenth floor'.
later,
Ysgarran.