The Problem of Free Will gets a good outing: are we free to do was we please, or does the chemical nature of the brain, and the fundamental laws of cause and effect, mean that we are not? And in the matrix itself all is not quite what you might expect: Both Neo's in-Matrix boss and Agent Smith offer Neo specific (if perhaps Hobson's) choices: turn up at work on time, or find another job; help track down Morpheus, or suffer the consequences; in any event on your own head be it. Contrast that with Morpheus' first instruction to Neo: "Do exactly as I tell you": Not what you'd expect from the arch-libertarian. The notion of choice, and the value of choice, thereafter reverberates through the film.
This of course implies the question of Mind: do chemical and electrical reactions in the brain fully explain consciousness? Is human consciousness simply the product of a glorified organic computer? And if that's the case, what is the difference between the digital consciousness presented by the Matrix, and the "actual" consciousness our own brain gives us? Is there a difference? Segue to Descartes' "Cogito Ergo Sum", an analysis explicitly referred to in Reloaded.
All this isn't to say that the Wachowski brothers are necessarily coherent in their philosophy or that they're doing anything other than name-checking famous dead people, (as yet, I'm not sure what point they're making with all this learning) but it does catapult the Matrix beyond the realms of your common sci-fi/action movie, and leaves you pondering all the iterations into the night. Some folk don't want that sort of thing in a kung fu movie, but for me it justifies the price of admission. And then to see Carrie-Ann Moss kicking butt in skin tight patent leather on top of that ... well, it don't get any better than that.
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