High Prophets

The three High Prophets serve as the highest leaders of the Covenant High Council, being theocratic and known as "Hierarchs". The Hierarchs are thin, hunched creatures with large craniums that float on levitating Gravity Thrones decorated with golden backs, equipped with energy shielding and armed with Gravity Cannons. Also, they seem to be armed with their own sidearm, Regret having his Plasma Pistol while Truth having his Spiker; it is unknown if Mercy has one of his own. They wear crowns adorned with small holographic projections of Halo; they have the ability to access teleportation grids.

Prophet of Truth
Little is known about Truth, except that he is the remaining Hierarch at the end of Halo 2 who offered the former Commander of Alpha Halo to become the Arbiter and ordered him to defeat the Heretics, rebels that regarded Covenant teachings as false, and to retrieve the Sacred Icon on Delta Halo.

He spearheaded the purge of the Sangheili councilors for their opposition to the Brutes, becoming the new Honor Guards of the Prophets, sparking the Covenant Civil War.

When Gravemind teleported Master Chief to High Charity, Truth betrayed Mercy, who was under attack by a Flood Infection Form. He prevented Tartarus from aiding Mercy and escaped to his Forerunner flagship, but not before Master Chief realizes his aim and pursues.

Aboard the Forerunner Dreadnought, Truth then led the Covenant Armada to Earth in order to activate the portal to the Ark. Once there, he set the Forerunner Ship at the base of Mount Kilimanjaro, and began excavating the Ark with Loyalist plasma bursts. Once activated, the excavation triggered a large, stable Slipspace portal to Installation 00. Truth took up residence in the Installation's Control Room in preparation for the Array activation.

Soon after, the Humans and Elites followed through the portal to the Ark. They took down the fortified defenses surrounding the Control Room and deactivated the shield protecting the Citadel just as High Charity exited the portal, spewing Flood forces in every direction. Flood projectiles crippled the Separatist flagship, the Shadow of Intent and prevented the Elite forces from being able to enact that planned mass assault against Truth's final forces. As a result, the Master Chief and Arbiter proceeded into the Control Room, unexpectedly aided by the Flood. The Arbiter then impaled Truth with his Energy Sword, finally putting an end to the deceitful Prophet and the triumvirate of Hierarchs.

Prophet of Mercy
The Prophet of Mercy is much older than the other two Hierarchs. Mercy was first seen during the trial of the Supreme Commander of the Fleet of Particular Justice and agrees with Truth to promote the disgraced Elite to the rank of Arbiter in a bid for redemption and the eradication of the Heretics.

Mercy, with Truth, crafted the plans to invade Earth a second time after Regret's initial botched invasion - this time perhaps to secure the Ark, begin the Great Journey, and wipe out the Humans. Before he can act, however, he is attacked by a Flood Infection Form on High Charity. Seeing this, Truth tells Tartarus to "let him be" and then tells Mercy, "The Great Journey waits for no one, brother, not even you." The Master Chief finds Mercy being consumed by a Flood spore, and kills it, preventing Mercy from being infected. In return, Mercy tells the Chief of Truth's plans, then collapses dead from the trauma of being attacked.

Prophet of Regret
Regret is the youngest of the High Prophets and contrary to his name he appears to be reckless and headstrong.

Regret led the initial, failed attack on Earth with two Assault Carriers and a small contingent of battle cruisers. After one of the Assault Carriers was destroyed by the Master Chief, he ran through the gauntlet of MAC stations and landed troops in New Mombasa, part of the East African Protectorate, the only place the Covenant landed on Earth. After being repelled by marine forces, he initiates a slipspace jump to Delta Halo, destroying New Mombasa in the process. It is speculated that he was not at all aware of the centrality of Earth to Humanity and simply assumed it was another world that had, at one point, been inhabited or manipulated by the Forerunner. This accounts for his Fleet being far smaller and much less prepared than the Fleet that destroyed Reach and other high-profile colonies.

His actions did not win him a reprieve as Master Chief pursued him through Covenant forces on Delta Halo. Truth, in an apparent attempt to increase his power, called off reinforcement Phantoms, which gave the Master Chief a sufficient window to assassinate him.

However the Prophet of Regret makes a final appearance later in the game, revived to a degree by the apparent Flood leader Gravemind as a Prophet Form and argues with 2401 Penitent Tangent, condemning the ineptitude of the Holy Oracles. It is unknown how the Gravemind managed to retrieve his corpse, as the entire area was seared and destroyed by Covenant Energy Projectors immediately after his death.

Past High Prophets
The High Prophets are usually replaced all at the same time through political machinations. Previous High Prophets include the High Prophet of Restraint, the High Prophet of Tolerance and the High Prophetess of Obligation. These three hierarchs were disposed of when Truth, Mercy and Regret came to power.

Trivia

 * The song 'What I've Done' by Linkin Park has a line which mentions the names of the Hierarchs (Regret, Truth, Mercy). This is likely a co-incidence.