Matrix Revolutions has hit the theathres, and from the comments and reviews, I learn it's the worst movie of the trilogy. MattW has written down some answers on the open questions from the 'Matrix Reloaded' (spoiler warning).
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Spoiler
/spoiler/
Near the end, Agent Smith reveals that he is Neo's father.
/spoiler/
Well, OK, not really.
Religion
I have never read a better explanation than this one - be sure to read the rest of the thread too -- very interesting stuff... Including Greek mythology and some major religions.
Bible
In reply to Religion by Anonymous
Looks from this site that the W brothers got their inspiration mostly from the Bible...
New link
In reply to Bible by Anonymous
Check this
chronological
Here's a chronological explanation... In case the Google cache expires, here's a mirror.
Own site
Dude, this movie is so complex, it has its own explained site.