The Hunter Cave is a very large cave with many doors on high ledges around the edge of the room; in the centre and much lower down is a lake containing some Jelzaps. Flickerbats fly around the lower part of the cave, near the surface of the water.
To reach other doors in the room, there are three weakly connected stalactites on the ceiling that can be dislodged with a Missile to make a path across the lake; two of these kill Jelzaps in the lake when they fall. The two highest doors can only be reached from the lower section using the Grapple Beam with the Grapple Point revealed when one of the stalactites is removed. It is also possible to reach these without the Grapple Beam by approaching the room from another direction.
- Lower Edge Tunnel (via Purple Door)
- Lake Tunnel (via Purple Door)
- Chamber Access (via Purple Door)
- Hunter Cave Access (via Purple Door)
- In a wall next to the lower door leading to the Gravity Chamber a frozen fish can be found inside a phazon like ice formation.
- Ironically, no Hunter Metroids can be found in the Hunter Cave, although in some versions of the game one does appear in the nearby Frost Cave.