8 Video Game Plot Twists Revealed OUTSIDE The Main Story
2. The Reason Behind The Covenant-Human War - Halo
In the first Halo game, you didn't really need a reason to shoot the aliens that were trying to kill you. They were aliens trying to exterminate mankind after all, and it didn't really matter why they were doing what they were doing, only that they needed to be stopped.
Sure, the series is much more complex than that and the wider mythology does explain how the war started and who everyone involved is, but the real reason as to why the Covenant have such a hard-on for exterminating humanity is never addressed in-game. It is a pretty big mystery though, especially because so many other species were offered to join the Covenant, yet humans were treated as an instant threat and war was waged.
Well, it turns out that the reason is way more complex than it first appears. The leaders of the entire Covenant force were the Prophets, a small group who resided over all of the species under the worship of the Forerunners and Forerunner technology. Books and other supplementary material revealed that it was the Prophets realising the similarity between the Forerunners and humans, including the ability for humanity to wield Forerunner tech, which led to a war waged out of fear.
Through propaganda, the Covenant armies became convinced that humans were an affront to their gods, and that only total genocide would be the appropriate response.