Sam Haverson, by way of the fine folks at the GameFAQs forum (email@example.com) writes:
There's been some speculation as to the purpose of the war. I found this theory extremely plausible: the Humans are Forerunners... and the Prophets know it. The Elites, Brutes, Jackals, Grunts, and Hunters don't. Now see, the Prophets know that the Humans are Forerunners that are rather inferior to the original type. They, being smart creatures, know that if the Elites and other races see that their gods are these inferior beings with low technology, they will inevitably turn against them; their point being something like "You had us worshiping these things?". The Prophets, to make sure this doesn't happen, immediately declare that the gods hate humanity and that they have told them to destroy it.
One of the more intriguing things about the approach of Halo 2 is the possibility of some significant Prophet interactions. They seem to hold most, if not all of the keys in the Covenant empire. After all this time, aren't we entitled to some Tru7h?