Covenant Loyalists

The Covenant Loyalists are made up of the Prophets, Brutes, Jackals, Drones, and some Grunts castes within the Covenant's hierarchical society. This faction is made up of those who (as of the end of Halo 2) still remain in the Covenant and are set on activating the Halos and starting the Great Journey. Since the beginning of the Covenant Civil War, they have been fighting the Covenant Separatists, led by the Elites and their Grunts and Hunter supporters. Fronts of this war include High Charity, Delta Halo, and areas of space where Covenant ships operate.

This is not necessarily the first internal dispute in the Covenant's society; when the current Arbiter was assigned to his office, he was reminded by the High Prophet of Mercy that an Arbiter was necessary during the Grunt Rebellion, a conflict between the Covenant and its lowest caste, the Grunts.

Origins of the Faction
The High Prophet of Regret led a botched mission to Earth and was forced into The First Battle of Earth upon discovering what turns out to be the UNSC home world. He escapes to Delta Halo but is killed by the Master Chief, which is considered a significant failure in the Elites' mission to protect the leading caste of the Covenant. The Master Chief was assigned on a mission to capture and later kill Regret. The remaining Prophets, led by the High Prophet of Truth, use this opportunity to replace the Elites with Brutes as their protectors. However, this move effectively shames and angers the Elites, who have been in such a position since the founding of the Covenant, and they threaten to resign from the High Council.

Truth then gives command of the Covenant fleets (the Elites' job) to the Brutes. Once there are enough Brutes in place, he secretly orders the Brutes to instigate a brutal genocide of the Elites, so they might replace them in society, disguised as a Brute insurrection against the Covenant to the Elites, the Hunters, and most Grunts, and as an Elite revolt to the other factions (excluding the Brutes and the Prophets). The Elites respond, with the help of the Hunters and the Grunts, and war breaks out in High Charity. Later, the Elite Councilors are assassinated by the Brutes at the behest of the Prophets. When the Elites learn the truth about the Halos, it changes the war significantly and adds the humans to the struggle. Instead of a Great Journey, the Gravemind's revelation regarding the super weapon contradicts the Covenant's belief system and is motivating at least the Arbiter in his eventual opposition to the Covenant as they try to activate Delta Halo later in the game.

Military Forces: The Prophets and their supporters
Commanded by Truth, the Loyalists include Brutes, Jackals, Drones, and a few Grunt castes, along with loyal ships of various classes to their cause.