These are consumed as the Nihilanth suffers damage from the player, but specialized crystals within the upper portion of its chamber replenish the spheres as they vanish. A series of gold-colored 'energy spheres' orbit around the Nihilanth's head, rendering it impervious to damage. This may not be intended as the creatures appear only when the green orb flies into a wall or rock or is destroyed by the player and triggers the teleportation. It also uses these green orbs to teleport Vortigaunts and other Xen creatures into its main chamber to help defend it against intruders. The Nihilanth attacks by launching energy balls, which come in two types: a swarm of purple-colored electrical orbs that causes immense damage, and a slow-moving, green-colored orb (similar in appearance to the teleportation portals constructed in the Black Mesa Research Facility) which homes in on and teleports its target to other sections of its lair populated by Xen aliens.

Its unusually long arms end in disproportionately huge hands and fingers, and it wears metallic wristbands, which look similar to bands worn by the Vortigaunts. Like the rest of the intelligent Xen races, the Nihilanth has a third appendage protruding from the middle of its pectoral chest region.

The creature sits on a large mechanical levitating contraption consisting of a large base with spikes underneath.

Its legs, minuscule in relation to its body, appear either to be vestigial, or are the remains of amputation. Physically, the Nihilanth resembles a gigantic, oddly-proportioned fetus with its head alone outsizing the rest of the body, and its brain cavity forming most of the head's bulk.

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