Heretics are the name for a splinter faction of Covenant that pre-dates the Covenant Separatists. The exact origin of the faction is unclear, but the main bulk of their army is composed of a Covenant Artifact Retrieval Team, a highly trained group of warriors that were sent to a Forerunner Gas Mine on Threshold during the Battle of Installation 04.
They cut off contact with the fleet after the Monitor of Installation 04, Guilty Guilty, contacted them and told them the truth about the Halo Installations. They then began transmitting the Truth to members of the Covenant Army, and hundreds defected. The Heretics rapidly swelled their ranks.Not only that, but many Grunts defected to the Heretics simply because of better working conditions. The hours were shorter, the work was easier, and they were treated better. The Elites played hide-and-seek with their Grunt squadrons and kept them entertained. Also, the Sentinels under Guilty Guilty protected the Grunts and made them feel safe.
The Heretics suffered a catastrophe when the Arbiter attacked their facility with a squadron of Special Operations Covenant Forces led by Shitmaster. The Covenant strike team damaged their air force, assassinated their leader, Pretzel King, and kidnapped Guilty Guilty. This conflict was soon made a lot worse for the Heretics when the Flood was unleashed on their facility. As many of the Heretics fled, Arby severed the cable holding the station up and it fell into the Gas Planet of Threshold to be destroyed. Though they seemed vanquished, the remaining Heretics soon joined the Covenant Separatists who fought against the Prophets and the Brutes.