I really liked The Matrix, as an action film and an intellectual film. My favorite scene was when Agent Smith was attempting to break Morpheus. He began to compare humans to viruses saying that we spread and destroy everything. In reality, the machines have taken over the planet and have decimated all natural resources. It seems that the programs that protect the matrix cannot see outside of it and observe what the world actually looks like.
My second favorite scene is when Neo comes back to life and accepts that he is "The One." He fights with Agent Smith then enters inside of him and destroys/infects him from the inside, like a virus. After seeing this the other agents run away in fear. This is significant because throughout the movie Neo is constantly told to run away from the agents because they are too strong. Also in the movie, the agents are able to take over other people's bodies. In the end, Neo does both of these: takes over an agent's body and strikes fear in them to make them flee.
I think that the observations that you make about the virus aspect is very interesting. I think that overall though it leads to a very interesting point about self-perception. The agents don't perceive themselves to be a plague in the world just like Neo doesn't become "The One" until he perceives himself to be worthy.
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