|Warning: This article may contain plot spoilers.|
The Covenant is the alliance of martial and theocratics of who dole to be the foremost opposed antagonistic obligement of humanity. The Covenant is composed of a diverse variety of species, unified under the religious commitment of the Forerunners, along with their belief that the Halos are the path to salvation. Throughout the Halo series, the Covenant is the chief opposing coalition against the UNSC (United Nations Space Command).
However, by the end of Halo 2, this theocratic society is ripped apart by civil war as the Prophets secretly order the Brutes to exterminate the Elites, who, led by the Arbiter, fight back. By the start of Halo 3, the Elites have allied with Humanity in their struggle against the Prophets.
The Covenant is a caste based society with many species under its government, all are capable in combat some more so then others. As Master Chief and the Arbiter you could be aiming your crosshairs at any number of these.
Little is known about the Prophets, beyond the fact that they are the sole members of the leadership caste of the Covenant hierarchy. They believe themselves to be representatives of the gods and as such are protected heavily by up until Halo 2 Elite Honor Guards. Physically frail and weak , Prophets move using Gravity Thrones and Gravity Belts. In Halo 2 we are first introduced to Prophets on the Covenant High Council, and then later to the three most prominent Prophets, known as the Prophet Hierarch's individually known as Truth, Mercy and Regret it is these Prophets that lead the Covenant. As Master Chief in Halo 2 you get to kill Regret on the level "Regret" however Mercy is killed by a flood infection form at the end of Halo 2 and Truth is killed by the Arbiter in Halo 3. Both of these are cinematic deaths however and Regret is the only Prophet you can actually fight in combat.
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