As I've said before, "The Matrix Reloaded" and "The Matrix Revolutions" are two halves of the same film. They should be watched back to back, as I've done by watching them yesterday and today.
The rogue programs play more of a role in the the third film. We find a program called the Trainman, whose duty it is to smuggle programs in and out of the Matrix. Programs hacking programs? Things are getting complicated. Sati, who has the appearance of a young girl, is a program due to be deleted because she has no apparent purpose. Her parents, also programs, love her and want her to survive, so they use the Trainman to bring her to the Oracle for protection. This shows that although the Oracle is working for the machines she's willing to be rebellious and follow her own agenda.
Smith has now become a virus, infecting all of the Matrix. He's become so powerful that he could infect and destroy all the programs in the real world. Only Neo is capable of destroying Smith, with the Oracle's help, so he makes a deal with the machines. If he destroys Smith the Matrix will be upgraded to the next version, Matrix 7.0, without Zion being destroyed. In the new version it will be made easier for people to unplug themselves, if they wish to. To round things off, Sati's purpose is revealed in the new Matrix. Remember that the next time you want to delete a program.
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