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1. I'm not sure exactly, but I think when they did whatever they did to Neo, since he was Smithized, it killed the rest of them.
2. He defeated them, by letting him win. The machines had to kill Neo then, because he would have destroyed the machine world. Therefore, Neo won, since the machines died.
3. I think this was answered in the end, when the Architect was talking with the Oracle. She asked him "Are the all free?". He replied "Yes.". I assume they were talking about this.
4. The train took her out of the Matrix.
5. Umm...she was bored? [img]tongue.gif[/img]
Your last comment was answered, at least I think, when the Architect said to the Oracle "What, you think I'm a human?" after she said "I have your word" (After the conversation in #3.). I think that sorta means that he's a machine, and he doesn't lie, etc.
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