Screw the haters - Matrix pwned

[EarlyDawn]

This is my theory and I'm sticking to it:

SPOILER WARNING
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When Neo jumped into Smith at the end of the original movie, he "imprinted" something on him, as Smith suggests in Reloaded. What I think is that Smith (And Johnson and whoever the other agents were) is the distributed intelligence for the Sentnals and the other robots. This is alluded to because they are refered to as "sentient programs" in the original by Morpheus.

When Neo defeated Smith in the original, not only did he break Smith free of his constraints, but affected the sentenals in the real world, in a way which he could destroy them because, again, like Smith suggests, just as Neo imprinted something on him, Smith altered Neo in some way.

As to how Neo interfaces with them, you could argue some kind of ultrabroadband radio or electromagnetic transmission from his jack, or because he could transmit from the hovercrafts' core based on proximity and an (subconcious) understanding of how the Matrix was structured in the real world. (Think understanding the best router path on the internet, or whathaveyou.) For the sake of argument, how he was wirelessly interfacing with the Matrix is really nonessential.