Metroid Prime Lair was the deepest room in the Impact Crater and by extension, the last room in the Metroid Prime game. It was where Samus Aran faced the Core Essence of the Metroid Prime, and the only place in which Samus could use the Phazon Beam via Metroid Prime's pure Phazon deposits. In the room, the empty shell of the Metroid Prime's exoskeleton could be seen, surrounded by solid blue Phazon. It is unknown if this Phazon was present before the creature fell here, or was released upon the latter's impact. Samus could stand on it while the creature performed its shockwave attacks.
Several odd growths, named cancerous rock nubs in the game's Concept Gallery, surround the room and are quickly destroyed by Metroid Prime's first shockwave attack. The hole in the roof of the Lair from which Samus descends has a ring of what appear to be teeth surrounding it.
- Subchamber 5 (Long drop from above; one-way entrance)
- Despite being called "Metroid Prime Lair", it does not seem possible for the creature to have entered the room before, as the way it is entered in the boss battle with Samus seems accidental. It is plausible that the room could have been accessed by another tunnel, however. Additionally, the way the creature entered the room could also be perceived as throwing itself in, possibly implying it meant to enter the room.
- A dark red variant of butterflies can be found clustered around several fleshy holes in the room's floor.
- The room bears several similarities to the Sanctum on Phaaze. The room is the Lair of Metroid Prime - Sanctum is where Dark Samus resides. Additionally, the rooms are the last ones playable in Metroid Prime and Metroid Prime 3: Corruption. Both can only be entered through a long vertical drop, and also are seemingly impossible to get out of - how Samus escaped from these rooms after she defeated Metroid Prime and Dark Samus is a mystery.
- The actual map model contains a large hole roughly the size of the ones from the previous Subchambers located on the wall adjacent from Metroid Prime's husk. This hole is patched over in-game with a stone wall. The map wireframe still reflects this hole, possibly a remnant from a scrapped countdown sequence.