After reading the two reviews submitted to this and the first part which were topically concerned with simply retelling the plot as it occurred, I felt it more relevant to create a discussion to explore what I feel to be the heart of what the two episodes were trying to convey: whether religious wars have less to do with religion than they have to do with human nature. The juxtaposition is our modern era which is overwrought with religious extremism and war (which is mentioned by Richard Dawkins in the first part) and a future without religion but competing powers of atheistic organizations (who are fundamentally fighting each other for power rather than any religious dominance.)
If I was forced to come up with the message Tre and Matt were trying to prove ultimately with this episode (and I do believe nearly every episode of South Park in the last 6+ seasons has had a moral/ideological message), then my guess would be that although religion is often blamed for "holy wars," "jihads," or violence by those who oppose religion, it is likely simply a matter of human nature to be territorial and divisive and have wars against others... almost as sensible and self-conclusive as the theory of evolution might be.
If I was forced to come up with the message Tre and Matt were trying to prove ultimately with this episode (and I do believe nearly every episode of South Park in the last 6+ seasons has had a moral/ideological message), then my guess would be that although religion is often blamed for "holy wars," "jihads," or violence by those who oppose religion, it is likely simply a matter of human nature to be territorial and divisive and have wars against others... almost as sensible and self-conclusive as the theory of evolution might be.