basically it tells the story of a group of humans in the real world who are trying to condition the machines to not kill them.
Quote from Peter:"I decided to take a radically different approach and view the world from the point of view of the machines. After all, a robot would be more susceptible to delusion than a human. Also, I wanted to show that the human mind is just as capable of creating a rich and seductive dream world as a computer is."
Here is an interview with Peter about Matriculated (& the possibility of more Aeon Flux):
http://dvd.ign.com/articles/409/409846p1.html