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Life in the Matrix Continues
Okay, so Neo saves Zion, now what happens next? Does life continue as normal or does the whole process start again? Neo wanted peace, but can peace truly be achieved if you do not stop entering the Matrix and trying to convert people? I am sure Morpheus would go back to his old ways? What do you think?
They mentioned that anyone who wanted to be free would be freed. The only way they would know is to be told and given the choice. There would likely be subversive division within the Matrix about this that would cause fighting under ground, and yes, I'm sure Morpheus would be highly involved in this. The question about lasting peace was asked at the end of Revolutions and the answer was that peace will last as long as it can. Ultimately, humanity cannot accept being slaves, secondary creatures to the machines. In the end, they either have to learn to become equals, or one will exterminate the other.
You will notice that all the programs were 'resurrected' by the end of the trilogy (remember the scene with the Oracle and the little girl), and I believe that all of this commotion was like one big study of human affairs. The robots, no matter how powerful, still need humans, and vice versa, but it is a case of ying and yang where a balance must be kept. If life in the Matrix is to continue then there must be a balance. However, what enables them to now find people to take the pill? Are they allowed 'evangelical' revival sessions in the Matrix? Maybe Neo appears as an alien in a UFO and explains that he is giving opportunity for people to go to another world? Who knows?