The Quarantine Cave is where Samus acquires the Spider Ball. When she first enters the cave, she sees a pile of large rocks. These rocks are actually Thardus, a Phazon-enhanced monster. Once Thardus is defeated, Samus gets the Spider Ball and the only way out is to use it. In Space Pirate logs it is revealed that they are keeping Thardus in Quarantine there because he became too powerful. After Thardus has been defeated, and Samus returns to this room, a Sheegoth will be slumbering where Thardus originally was.
The "Ice Connect" theme plays in this room before and after the Thardus battle, and on subsequent visits.
- North Quarantine Tunnel (via Purple Door)
- South Quarantine Tunnel (via Purple Door)
- Quarantine Monitor (via Morph Ball Door)
It is possible to access the Quarantine Monitor room without the Grappling Beam by luring the Sheegoth near the Quarantine Monitor ledge, and then killing it. Samus can then jump on its corpse and to the ledge.
It is also possible to quickly reach North Quarantine Tunnel if accessed from South Quarantine Tunnel without beating Thardus. This technique is called the "Thardus Dash". It is performed by first either Scan Dashing off of the Grapple Point to land on Thardus (only in the original NTSC version) or using a Space Jump to get on top of Thardus. In the original NTSC version of Metroid Prime, one would then do another Scan Dash off of a Spider Ball Track to land near the door leading to North Quarantine Tunnel. In other versions, the player has to face near the same Spider Ball Track, holding L, and rely on a damage boost from Thardus to make it across.