Another vote for the theory that the Covenant are annihilating everything in order to stop the Flood.
Brandon Merrell (email@example.com) writes:
maybe the flood are THE SOLE reason for the covenant... the covenant want to kill the flood by killing all organic life in the galaxy, and they obviously wanted to use halo for their holy war... it would make their job that much easier, rather than killing everyone else off then committing suicide. Glassing planets would kill off everything with sufficient mass to sustain the flood, and maybe thats what theyre doing... killing everything off, then getting ready to kill themselves.
"We are the tools/instruments of the gods" they follow GS? perhaps the prophets are under the influence of someone or something else... someone who is not organic that wants the flood gone, someone who has a way to stop the flood from infecting them, or someone can survive when halo fires.