The nature and purpose of the Black Garden was one of the longest-running mysteries known to the scholars of the Tower. It is intrinsically tied to both the Light and the Darkness having existed before the current universe. According to Pujari, the Black Garden is a reflection of the Traveler's actions: when it terraformed the "iron world," the Garden either came to be or changed to match.

The mesa-like structure in the center of the Garden strongly resembles the Cradle left behind by the Traveler on Io, which was also seemingly a product of the Traveler's terraforming activities. However, it was not created by the Traveler. When the Vex arrived, they attempted to control it and impose their own changes through rigorous engineering and earth-moving. The Black Garden is a place where "everything grows" and where "abstract patterns war for survival, fighting to propagate themselves by preying on each other."

Ideas and concepts are carried on the wind in the form of whispers, "sentences with just the beginnings of syntax". Introducing new ideas into its conceptual environment, such as through speech, causes those ideas to "take root" in the Black Garden, changing the concepts present. Uldren conversing to a Cabal Legionary in Ulurant led to the whispers taking on aspects of Ulurant grammar. The Vex there sing ("faint, wraithlike notes of inhuman clarity") to "see how the Garden changes their song."

The Vex are particularly interested in the Black Garden because its effects on them "[grow] them toward what they want to be." Prolonged exposure to the Black Garden's environment can be dangerous. The concepts being whispered there are potentially a contagious brainstain hazard. The Legionary who Uldren spoke to, who had been exposed to the Garden for an unknown length of time, ended up having its "secrets" grown into him in the form of thousands of tiny seeds pockmarking his skull, incidentally imparting him with some knowledge of the Vex.

The sky of the Garden has shifted from one covered in a thick, green veil, to one containing three suns and a planet with an orbiting moon.