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The inside of Essence's unblemished state is only seen once, when The Witness is revealed at the end of The Witch Queen. The chamber it stands in during this cutscene would later be identified as Macrocosm.
When The Guardian visits Essence in person, it is fractured and leveled by the influence of the Traveler's terraforming. Its spaces are wide and open in a similar manner to The Sunken Pyramid, but makes heavier use of temple-like architecture and introduces fossils reminiscent of Earth's animals scattered throughout the walls of Pyramid architecture. Rather than gravity lifts, long-distance travel within the ship is achieved by kinetic launch pads that physically push the user towards the intended destination.
Scattered throughout Essence are numerous urn-like containers, each using the power of the Darkness to hold a memory from a civilization the Witness or its agents had visited in the past, including humanity and the Guardians. When recovered by the Guardian, each memory transformed into a regular data storage medium and was found to contain numerous references and retrospectives on the Final Shape, the Witness's beliefs, and the use of the Darkness as a force throughout history — including some that had previously been excised from all other historical records encountered thus far.
During the opening events of the Lightfall campaign, Essence was fired upon by a beam generated by the Traveler, with the intended target being the Witness. This attack dug open a massive hole in the pyramid's hull, as well as terraformed the interior which, likely unknowingly, provided the necessary conditions for the resurrection of Nezarec, Final God of Pain.
- Throughout most encounters of the Root of Nightmares raid, a massive Tree of Silver Wings can be seen in the distance, growing at different stages. The tree has similar features to that of the Tree of Silver Wings that was seen on Io prior to its capture by the Black Fleet.
- Although not outright stated, given that this pyramidal ship was the one the Witness was seen in the most, it can be suggested that Essence is actually the command ship for the whole Black Fleet.