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During October and November 2552, the Covenant was split in two by the breakaway Covenant Separatists, who fought against their ex-allies, in the Covenant Loyalists. During the civil war, there were two main factions: the humans, with their UNSC, who became allied with the Separatists, and the Covenant Loyalists. The Separatists were led by the Arbiter, and fought against the Prophet of Truth, who led the Covenant Loyalists. In addition to these two main sides, were the Flood.  
The Flood seized control of the ship High Charity, seeking to eradicate both the Separatists and Loyalists at once. The event was cancelled, due to the destruction of the High Charity by SPARTAN-117, or Master Chief.  

Pre-War Days

Before the Covenant Civil War began, the Prophet of Truth had already intended to replace the Sangheili with the Brutes. He felt that the Brutes were less questioning, and therefore would be more benefit. The Prophet of Truth did not disclose this plan to anyone, and waited until he found a suitable moment to drop the Elites. This moment arrived when the Covenant discovered the location of Earth. Without revealing his intentions, the Prophet of Truth organised a fleet of five hundred warships to assault earth. These ships were commanded entirely by the Brutes, and the key ship for the attack was the Unyielding Hierophant. This ship was attacked and eventually destroyed thanks to the efforts of the SPARTAN-IIs, who discovered the plans for the Prophet's removal of the Sangheili.  
The key moment which turned the Sangheili against their leaders was when the Prophet of Truth sent multiple warships, which attacked and wiped them out, despite having been sent by the Prophet of Regret. After the death of the Prophet of Regret, the Covenant hierarchy was restructured, making the Brutes the protectors of the Prophets, as opposed to the Elites. Enraged, the Sangheili threatened to leave the High Council, feeling that Regret's death could easily have been avoided, had Truth allowed the Phantoms which were en-route to aid the Prophet. 
The Elites were soon demoted ever further, until the Brutes took control of the Covenant Fleet. This was the moment where war became inevitable, and almost positive. The Covenant Loyalists followed the Prophet of Truth, and contained the Grunts, Jackals, and Hunters. The Separatists were mainly Elites, though some Grunts also followed the Arbiter. 

In-Game Appearances

The Covenant Civil War is a large part of Halo 3, as the story follows the Covenant as it self-destructs. The Elites are shown to be allies to the humans. At points during Halo 2, players actually aid in causing the cracks to appear in the Sangheili relationship with the rest of the High Council. During Halo 3: ODST, the city of New Mombasa is the game world, and it is critical to the moment where the Prophet of Truth ordered the Brutes to turn on their masters, the Elites.

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