The Main Reactor is located in the Space Pirate mining facility on Aether. It is where the Pirates keep most of their Phazon. The Main Reactor is where Samus engages Dark Samus for the first time. Dark Samus is found absorbing the large Phazon crystal in the central Kellium energy reactor when Samus enters the room. During the ensuing battle, four of the surrounding tanks in the room are destroyed by Dark Samus's attacks, leaving patches of burning fire where they once stood.
After the battle, Dark Samus turns into Phazon particles and causes the covers of several tanks in the back of the rupture, exposing the Phazon within. The elevator in the room activates as well. To the left of the remaining tanks is a Spider Ball Track and a dead Luminoth, B-Stl. There is another Spider Ball track to the right of the former one that leads up above the tanks in the back of the room.
- Sand Processing (via Blue Door)
- Storage D (via Blue Door)
- Security Station B (via purple hatch)
- Ventilation Area A (via white hatch)
- Dark Oasis (via one-way Light Portal)
- Dark Samus
- "Morphology: Dark Samus
Powerful distance attacks. Phazon energy shield repels all weapons: wait until it is down to attack. Avoid close contact with target."
- Missile Expansion
- Samus must go up the Spider Ball Track that leads up above the tanks to the end of the track, and then use the Boost Ball to reach the tracks on the moving mechanisms above the tanks. Once Samus reaches the end, she must use a Bomb, Power Bomb, or a Missile on the hatch on the ground to destroy it. Inside is the Expansion.
- "Security systems active.
Unique energy required for door access. Energize door with dark energy to open it."
- Spider Ball Track
- "System: Spider Ball Track
Magnetic rail system track.
In Morph Ball mode, press and hold R* when close to this type of surface. Use Control Stick to move the Ball along the track. Release R* to disengage from the surface.
CAUTION: A Morph Ball Bomb will briefly disengage the Ball from the track."
- "Element: Phazon
Volatile ore with biomutagenic properties.
Origin point of Phazon unknown. First detection of element on planet Tallon IV. Used by Space Pirates to produce vast levels of energy."
- Elevator hologram
- "Elevator platform active."
- B-Stl's Testament
- "I can go no further. Here in this reactor, I go to join my fallen mate, J-Stl, in final rest. Though I die with honor, a shame falls on my house until the key I seek reaches its destination. May my brothers find my burden, that the way to the Sky Temple will be opened at last."
- Kellium energy reactor (Metroid Prime Trilogy only)
- "This is a standard Kellium energy reactor, converted by the Space Pirates to process Phazon energy. Shielding levels at 220% and holding."
- Stasis chamber
- "Object scan complete.
Unit is in a sophisticated stasis chamber.
Xenotech designed to encase small objects in a stasis field.
Field is durable, but can be destroyed by explosives."
- Though it requires precise aiming, it is possible to obtain the Missile Expansion using the Screw Attack.
- A glitch may occur in the original GameCube version if Samus enters the window overlooking the Kellium energy reactor very slowly. If done correctly, Samus's movie model is briefly seen before she activates the pre-battle cutscene, creating another Samus in addition to the player.
- Another glitch may occur where if Samus triggers the pre-battle cutscene whilst entering through the window from extremely high up (sometimes done with the Screw Attack via Sequence Breaking), Samus will be missing from the pre-battle cutscene.