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Persephone's origin is not mentioned in the movie. But she mentions about silver bullets ,thus suggesting that Merovingian has a werewolf background. The DVD Behind the scenes mentions that she is a vampire that seeks after emotions. She admires the love that Trinity and Neo holds for each other. She also mentions about the love that she had once enjoyed, ...

It relates to the training areas of the first movie. If you recall, the ships are there in order to broadcast a 'hacker signal' into the Matrix in order to get their people inside it. This requires them to travel a great distance away from Zion. From this we can deduce that this is not the Matrix. Further, recall that where they trained Neo (and ...

No, a pretty much official explanation exists. And the question is not really "open". As I've stated in this answer, it's explained by the fact that when Neo comes into contact with the Source (i.e. when he meets the Architect), his brain becomes a wireless connection. After all, the real time in the Matrix franchise is set in a tech-wise advanced future, ...

I think the answer is that it was suggested a supermatrix, because it's more likely within the matrix's universe, considering the machine's cold logic, but the idea was possible abandoned. Why a super-matrix? The machines where able to defeat Neo and Agent Smith, and his viral propagation, at the same time, and took Zion after the battle. If the machines' ...