The Omega Pirate rests in the center of the chamber in a stasis tank below a huge glob of pure Phazon. There are doors that are opened regularly to examine the creature's vital signs and if necessary, call in Trooper Pirates for intruder annihilation. Three pools of Phazon sit in the corners and power the stasis tank. The scaffolding in the higher part of the elite quarters was an optimal place for troopers to drop into battle. When Samus arrives in this room, she faces the Omega Pirate in battle. After its defeat, Samus obtains the Phazon Suit. She can then operate a lift in the room to reach the balcony area.
According to the map, this chamber rests below the Impact Crater, suggesting that the Leviathan Seed that impacted Tallon IV landed above the quarters and spread Phazon to this room in vast amounts. There were two ways out of the Elite Quarters. One was back through a Metroid Quarantine or through a Phazon infested hall. The Phazon Suit is vital in passing through the latter area, which contains an Energy Tank.
The music that plays in this room prior to the battle is internally named "Music Mines Dark".
- Omega Pirate
- Trooper Pirates (During Omega Pirate fight)
- Fission Metroids (PAL/Wii only) (After defeating the Omega Pirate)
- Elevator/Interface Module
- "Platform active."