Three of the four Ancient Essences are contained within a room at the very beginning of the game. The word artifact and essence are used interchangably. This room lies within an ancient temple (The Forbidden City) near Persia-Mesoptamia (present day Iraq-Iran). Pious chooses one of the three essences which determine which of the Ancients he will align with. The other two essences/artifacts that remain are eventually delivered to Alexandra Roivas so that she can power the summoning spires in the city of Ehn'gha allowing her to summon her Ancient to defeat Pious'. During the fight, Roivas, alongside the ghosts of past Tome Bearers, proceeded to attack Pious' Ancient Essence, eventually doing enough damage to the essence to completely destroy it. Depending on the level of strength the Essence has compared to the Ancient Pious aligned himself with, the essences locations and exact fates varied. The weaker of the two remained in the Forbidden City, and nearly turned Karim into its host before his then-recently deceased lover Chandra interfered, and instead had him sacrifice his life to guard it, with it eventually falling into the hands of Roberto Bianchi before he ultimately was killed shortly thereafter by being thrown into the foundation of the pillar of flesh just above the Forbidden City, and it eventually fell into Michael Edwards' possession who managed to survive from the ordeal long enough to arrange for it to be supplied to the Roivas. The stronger of the two, most likely due to just how much of a threat it posed to Pious Augustus and the ancient he served under, was later relocated to Oublié Cathedral by the 15th century (at least sometime before 1485 AD, due to the pilgrimage to the Hand of Jude used as bait being in effect by that time), even going as far as to summon a Black Guardian to guard the Ancient Essence, at least until the planetary alignment occurred in the year 2000. Paul Luther heard of the artifact's existence after discovering that the Cathedral was housing a pagan religion, but was unable to actually find the artifact before being slaughtered by the Black Guardian. Eventually, due to the Black Guardian becoming restless far earlier than anticipated, Augustus, in order to stave off the Black Guardian's hunger to keep it to its duty, was implied to have instigated World War I, or at the very least the Battle of the Somme, where Peter Jacob ultimately killed the Black Guardian and retrieved the artifact, eventually giving it to Edward Roivas by 1985. The Black Heart was supplied to the Cambodian slave-girl Ellia by its keeper shortly after Mantorok was bound by Pious Augustus, and did not divulge its location to Augustus when he attempted to interrogate her, at the cost of her life. Eventually, Ellia, who survived in a state between death and life, proceeded to supply Edwin Lindsey with the Black Heart by 1983, several centuries later, which he then supplied to Edward Roivas a year later.
These essences are perhaps the physical and magical remnants from the time the Ancients once existed in our universe, before they were sealed away eons ago. They also seem to live up to their name of "essence" as they contain a great deal of the Ancient's magical power and may even be tied to their "life-force." Touching any of these essences/artifacts without protective clothing can result in severe burning as they are formed of highly corrosive energies, and will also result in possession by the Ancients, with the side effects being great power at the cost of becoming a Liche. Even being in close proximity to the essences may have adverse side-effects, as Peter Jacob when relinquishing the Essence that was strongest against Pious' ancient implied the possibility that the essence he guarded had been responsible for his long periods of insomnia after the events of the Battle of the Somme when meeting with Edward Roivas. Although the three Ancients' essences can instantly turn anyone into a Liche upon physical contact with unprotected clothing, Mantorok's essence apparently takes a significantly long time for any significant changes to occur upon contact, as evidenced by Ellia retaining her human form when she obtained the Black Heart until she was killed by Pious Augustus.
In all there are four Ancient Essences:
The Black Heart of Mantorok
The Blue Veil of Ulyaoth
The Green Sigil of Xel'lotath
The Red Claw of Chattur'gha
By choosing a different artifact each time a new game is started, the storyline shifts perspective to the ancient the chosen essence represents. Eventually, after completing all of the alignments a bonus ending is activated. It explains that Mantorok manipulated the holders of the Tomb of Eternal Darkness into doing its bidding. It is even hinted at that Mantorok influences Pious to choose a different artifact each time around. Mantorok combined the various time streams thus all the Ancients were destroyed. Only Mantorok remains.