The Covenant Jackals are pretty much space pirates and one of their ships ventured out pretty far and ended up near the planet Harvest. Johnson and this other guy had a fight. And then a Brute ship came and the humans tried to offer peace, but hey they were Brutes. The humans sent for reinforcements from other planets but they lost contact. After the Brutes were killed, a whole fleet arrived and attacked the humans because by then they were believed to be heretics. "Your destrcution is the will of the gods." The Covenant 'glassed' Harvest. The Prophet of Truth thought that some of the Forerunners were left behind after the Great Journey (the humans) and he didn't want this to ruin the Covenant's Great Journey, so he told the Elites that the humans were heretics and a threat to the Covenant religion.
Well, if i'm remember it right i think the Earth got over populated and they moved out in space to colonize new worlds. And then they colonized some planet in the Covenant controlled area and the Covenant thougt the humans were intruders against their religion and wanted to stop "The Great Journey". So they needed to stop the humans that just happened to find a planet they liked.