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I need to explain a few things to make this story make sense. First, before the Covenant was formed the Elites and Prophets, the first and founding member races, fought a bloody war. In the canon, they both realized they could benefit from an alliance so they formed the Covenant. In this story, instead the Elites decided it was dishonorable to accept peace so instead both species' were driven to extinction. The Brutes, Drones, Grunts, and Jackals all still exist but without the Elites and Prophets they are stuck in their own solar systems.