Matrix Reloaded Explained?

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MAJOR SPOILER ALERT!!!
If you’ve not seen the film yet do not read any further!!!
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Been trying to get my head around this one, and came across a fascinating post in a film forum: Reloaded didn’t make sense to you?

It matches some of my initial thoughts, although I hadn’t pursued them as far, and backups the fans that say that this isn’t just an action movie.