This room, as its name implies, contains a lot of Phazon in the lower level. The center is full of Trooper Pirates and, in the PAL and Wii versions, after the Omega Pirate has been defeated, Fission Metroids appear. The main purpose of this room is to provide a shortcut to the Magmoor Caverns.
- Transport Access (via White Door)
- Maintenance Tunnel (via White Door)
- Processing Center Access (via Red Door)
- 2 Fission Metroids (PAL, New Play Control! and Metroid Prime Trilogy versions only, after defeating the Omega Pirate)
- 2 Space Pirates (before Plasma Beam)
- Plasma Trooper (after Plasma Beam)
- Wave Trooper (after Plasma Beam)
- Power Trooper (after Plasma Beam)
- 2 Mega Turrets
- Missile Expansion
- On the eastern side of the room, there is a Missile Expansion hidden inside a wall that can be seen using the X-Ray Visor. Because the wall is made of Bendezium, it can be destroyed with a Power Bomb to get the Expansion.
- If Samus knocks one of the Troopers off the platforms, they will instantly die when they hit the Phazon, showing how dangerous the substance can be for unprotected individuals.
- The Mega Turrets' shots can hit the Fission Metroids in the room, killing them instantly.
- The Fission Metroids in this room are surprisingly fragile. If they come into contact with Doors or other features of the room they may die instantly. For example, there if they charge at Samus while she is just outside the door leading to Processing Center Access, they will hit an invisible wall and die. They will also die if they touch any of the Phazon formations in the room. Also, just a few shots are sometimes sufficient to destroy them. Nowhere else in the game are the Fission Metroids this weak.