I remember reading one headcanon that the "Sharqoi" spoken of in "Conversations from the Universe" were destructive Kaiju that the Covenant had found on a planet. They planned to transport them to Humanity's homeworld because the Sharquoi are less devastating to the ecosystem than glassing, but they were more than powerful enough to exterminate the human population. However, since the Covenant didn't dare breed the things, there were only enough Sharquoi to invade one or two planets.

Would have made for a different Halo 2...