YOU KNOW YOU WANT TO HEAR MY IDEA
EVERYBODY is a computer program. Even Neo.
(that would explain his wide emotional range)
Seeing as how the idea of imprisoning humans in a simulation just to siphon their body heat is STUPID,
It is instead revealed to us at the end of Maalox Reloaded that humans were imprisoned in this simulation for study, like a human zoo.
Recognizing that humans must have some value because they, after all, created the machines, the machines are using humans in order to create a true hybrid of man and machine. Yet another step in the evolutionary process.
(before monkeys destroy the earth in a huge cataclysmic crap-throwing-fest)
Busting out and joining Zion is also part of the simulation - a specially designed offshoot developed for this experiment.
And Neo is their latest attempt. BUT HE FAILED their crucial test of alleigence, and now they want him wiped out.
(before he breeds... STINKYNESS)
Unfortunately, Agent Smith has mutated into some matrix-destroying virus, and actually poses a very real threat to the integrity of the machines.
(by corrupting the speech patterns of MIB everywhere with Australian accents)
In the end, Smith and Neo do battle, destroying the entire matrix and the core of the machines in the process. Neo turns out to be the next evolutionary step after all - because he is apparently the only one immune to Smith.
(and he can say "Whoa" the most times in a minute.)