Oooh, I was wondering when someone would post a topic like this!
In my occasional visits to HBO, I found a page that I liked tremendously that was very similar to it. On it, they discussed and argued about the Halo story and connections to other things, etc. A very interesting page, which enlightened me a lot on the mysteries surrounding Halo. Could be a good tool to any wanting to discuss such things here.
Link
here.
Warning! Minor Halo and Halo 2 spoilers ahead!
Good questions to start with:
Who were the Forerunner?
Why did the Forerunner build the Halos?
What connections do the Forerunner have to the Covenent?
What destroyed the Forerunner?
Why did the Forerunner create the Flood?
What is the significence of the "Ark" in Halo 2?
What is the significence between humans and the Forerunner?
Why are the symbols on the Elites and the Forerunner runes so similar?
I will come up with more once I think of them.
I think that the Covenent hate the humans because the humans were encroaching (unknowingly) on the Forerunner artifacts. If you read the books, you notice that almost all the important Forerunner artfacts were found on human worlds. The Slipstream bending crystal on Reach, the coordinates for Halo at Cote d' Azure, and obvious things on Earth, since the Covenent came there as well, and not because they knew it was the human home, but because they were looking for another artifact there, which explains the "small" fleet sent there at the beginning of Halo 2. The Covenent consider the Forerunner artifacts to be holy relics of their ancestors or creators, and think that the humans were trying to steal them for their own purposes. So, they attacked the humans in a holy jihad, and are attempting to annilhate their supposed "rivals" for the rights to the artifacts. These artifacts are obviously holy to them, or at least wanted by their Prophets, who can use their power in the Covenent to call a holy jihad on the humans for these much-desired artifacts that can tell them more about their predecessors and can find more Halos to help in their "Great Journey". Overall, the humans are getting between the Covenent and their means of starting the "Great Journey", the Halos, so the Covenent have chosen to crush the humans.