Thousands of years ago, a race called the Forerunners encountered a parasitic alien race called the Flood. The Forerunners constructed weapons that could destroy organic life called Halos. The Forerunners used the Halos and (possibly) destroyed their own race. Sometime afterwards, two races called the Elites and Prophets fight a holy war of left over artifacts of the Forerunners who they regarded as their gods. The war ends and the Elites and Prophets join together and create the Covenant. The Covenant seeks to go on "The Great Journey" which makes all followers ascend to godhood. They claim that the reason the Forerunners disappeared because they were the first to travel on "The Great Journey." They go around the galaxy searching for Forerunner artifacts and assimilating other races into the Covenant.
Meanwhile on Earth, the nations of the world join together and create the United Earth Government and the United Nations Space Command. They begin colonizing other planets and the UNSC wages war against rebels that seek their independence. The UNSC kidnaps various children across human space and puts them through the Spartan-II program to fight the rebels.
Eventually a small Covenant ship discovers a planet called Harvest inhabited by humans. The Covenant discovers "relics" on Harvest and sends a force to retrieve them. The two Prophets in charge of this seek the blessing of an "Oracle" which is a Forerunner AI. They meet with a Prophet Priest in charge of the Oracle and see it awaken. The Oracle tells them their religion is misinterpreted and claims that the "relics" on Harvest are his makers. The three Prophets launch a plot to take over the Covenant and start a genocidal war on the humans to cover up the truth to prevent the Covenant from fracturing. Hilarity ensues.