The Command Center is the hub of all Pirate activity in the Agon Wastes. As such, it contains many terminals and computers for receiving and sending reports to Pirate squads in the area. Much of the data concerning the Pirate's knowledge of Aether and Dark Aether is stored here. The lower level contains a scorched crater in the wall where a Dark Portal rift resides. This portal can only be opened by use of a dark matter blast, which will allow beings to enter the portal and travel to the Dark world. Most of the room's floor is metal grates placed over natural rock formation and a sand pit. A small alcove is in the far north west contains an entrance to a system of tunnels underneath the grates, protected by surging Electric Gates to kill pests. This tunnel leads through a strange organic tunnel to Command Center Access.
On the higher level (connected to via an Elevator to the south) is a balcony area, containing many Space Pirate Crates. North on the balcony is a control room protected by glass that can only be accessed via the connecting room Security Station B. This room contains a terminal that can activate a set of blast doors in place over the door connecting to Biostorage Access to south of the room on the ground floor.
When Samus enters the room the first time, she must use a series of Morph Ball tunnels as the entrance is blocked by a purple hatch. The tunnels contain Electric Gates that have varying time windows of deactivation. As Samus does so, a large squadron of Pirate Commandos can be observed entering a Dark Portal at the front of the room. As Samus exits the tunnels and her Morph Ball mode in a sandy alcove, a large set of Blast Doors close, blocking off the door to the main section of the facility. The Space Pirates have been alerted to Samus' presence and begin to attack. Up on the higher level, a Pirate Trooper in a control room hidden behind a set of glass shatters it in order to attack Samus. To reopen the Blast Doors, Samus must enter Security Station B to destroy a Blast Shield around the corner and access the control terminal inside the set of glass. If Samus returns to this room it is guarded by two Pirate Grenadiers, and is the only room in which they are present.
In the Metroid Prime 2: Echoes Bonus Disc demo, the portal is opened by using the cannon, operated by scanning the same computer that open the big doors. The cannon is still present in the final game but inactive.
- Command Center Access (via Morph Ball Door, purple hatch and white hatch)
- Biostorage Access (via Blue Door)
- Security Station B (via Blue Door and Blast Shield)
- Doomed Entry (via one-way Dark Portal)
- Pirate Commandos (Enter Portal upon entering room the first time)
- Pirate Troopers
- "Morphology: Pirate Trooper
Aggressive, well-armed bioform trained for combat and conquest. Sworn enemy of Samus Aran."
- Two Pirate Grenadiers (Later visits)
- "Morphology: Pirate Grenadier
Space Pirate specializing in grenade combat.
Powerful grenade launcher makes this enemy dangerous at range. Minimal close combat ability."
- Missile Expansion
- Inside the tunnel beneath the floor, there is a tangent that leads to the Expansion.
- Dark Portal (inactive)
- "This rift portal is inactive.
The portal field can be energized with dark energy. Walk into an energized portal to transport to Dark Aether."
- Dark Portal (inactive) (demo only)
- "Analysis complete. This portal is inactive.
Portal activation system located on upper level of this room."
- Dark Portal (active)
- "This portal is active.
Walk into the portal to transport to Dark Aether. Extreme caution recommended once transit is complete."
- Space Pirate Crate
- "Object scan complete.
This is a Space Pirate Crate.
Space Pirates, strangely, dislike theft. The only way into their crates is through the use of force."
- Elevator platform
- "Mechanical analysis complete.
This elevator will not function until activated. Scan its control console to bring it online."
- Interface Module
- "Power relays connected.
Elevator unit online.
Step into the hologram to activate the elevator."
- Elevator hologram
- "Elevator platform active."
- Elevator hologram (demo only)
- "Elevator systems online."
- Blast Door control
- "Blast Door control security bypassed.
Door will remain in the open position: security and control systems have been jammed at the source."
- Space Pirate Logs (Phazon Operations)
- "Log 04.468.1
Science teams detected the presence of Phazon in the Dasha system four cycles ago. High Command authorized the deployment of our team shortly thereafter. Our orders are to establish a base on planet Aether and evaluate local Phazon resources. Because this world lies on the periphery of Galactic Federation territory, we are following stealth protocols at the highest level. A cadre of elite Commandos has been dispatched to provide security for our force as well. This operation is now under way."
- Space Pirate Logs (Local Conflict)
- "Log 04.885.3
Intelligence reports on the indigenous population of Aether are in error. This planet is not at peace, nor are the inhabitants docile. Evidence of a class 4 conflict is present here, though hostilities are at a minimal level now. Our territory has suffered several raids by a strange type of shadowy creature. These raids have caused considerable damage, and we have requested more combat troops in response."
- Space Pirate Logs (Great Discoveries)
- "Log 05.008.6
A spatial anomaly has been found within our base. We believe this rift in space-time leads to a parallel dimension of some type, but have been unable to interact with it thus far. A strange artifact was found near the anomaly as well. It may be a weapon or generator of some kind: perhaps it is the key to accessing the anomaly. High Command is eager for reports on the relic. A new weapon for our arsenal is always welcome."
- Space Pirate Logs (Rift Portal)
- "Log 05.442.1
The Rift Portal has been opened. The artifact weapon, dubbed the "Dark Beam" by Science Team, provides energy needed to open the portal, although for a limited time. We've sent expeditions through the portal, and they have returned with incredible news.
The portal leads to a parallel version of Aether. This "Dark Aether" has suffered a global calamity, turning it into a toxic wasteland. It is the homeworld of the shadowy creatures who have been raiding our base for the last cycle. Most importantly, it is the prime location of Phazon in this sector. Extraction plans are being prepared. We will not be denied!"
- Space Pirate Logs (Phazon Raids)
- "Log 06.221.7
Phazon extraction raids are under way on Dark Aether. The toxicity of the atmosphere has taken a toll on our workforce, as have the hostile natives of that world. Science Team is preparing survival gear to protect our work teams, and we have increased our security presence in extraction areas. Fortunately, High Command is sending more troops and supplies. Our troops and resources are spread dangerously thin, and this mission cannot fail."
- "Planet: Aether
Obscure world in the Dasha system.
Planet is unstable due to transdimensional flux. Warfare has devastated a good portion of the world's population. Finally, extreme climate shifts have left most of Aether uninhabitable."
- Dark Aether
- "Planet: Dark Aether
Transdimensional duplicate of Planet Aether.
Can't determine origin of Aether's "dark twin." Contains high levels of Phazon ore.
Native bioforms attack on sight."
- Computer 1
- "Medical Report 07.199.09
Technician 12 relieved after showing symptoms of "Phazon Fever," in where he claimed the Phazon as his own and held us at gunpoint until security arrived."
- Computer 2
- "Security Report 07.201.04
The Marine vessel has been under attack by indigenous predators for several days. Casualties are high: the Marine force is near elimination."
- Computer 3 (GameCube version only)
- "Metroid Handling Protocols, 07.202.02
Metroids are not pets. Metroids are not for target practice. Finally, unauthorized feeding of Metroids is still strictly prohibited."
- Computer 4
- "Phazon Collection Report, 07.202.02
Phazon supply at site 1 is diminishing. Sites 2 and 3 are supply-rated above 90%. Site 4 remains a problem due to high presence of hostile bioforms."
- Computer 5
- "Sentry Report, 07.202.04
I grow weary of standing watch on a wasteland. The accursed Marines are weak and vulnerable. Why do we not attack? They owe us a fate-debt for the attack on our supply ship! Instead of settling accounts, we sit around in this sandpit like a group of timid old spinsters. It is time for action!"
- Computer 6
- "Security Report, 07.202.06
Commando unit 87 has failed to report. Unit was dispatched to recon the swamp, a potential site for a new base. Unit 98 sent to investigate."
- Computer 7
- "Dark Hunter Analysis, 07.202.07
Scans of the "Dark Hunter" have been revealed she grows stronger as she consumes Phazon. Already a class Platinum-AAA threat level, we shudder to think of her power level if she consumes our entire Phazon supply."
- Computer 7 (demo only)
- "Dark Hunter Analysis, 07.202.7
Scans of the "Dark Hunter" have revealed she consumes Phazon to sustain her lifeforce. Judging by her stealing pattern, she requires immense amounts of it to survive."
- Computer 8
- "Metroid Energy Report, 07.202.09
Until we recover more Phazon, we rely on Metroids for power. Command has authorized mass breeding of Metroids for this purpose."
- Computer 9
- "Planetary Stability Report, 07.203.01
Planetary energy is at critical, creating violent climate changes and tectonic shifts. Unless these conditions can be reversed, global destruction is inevitable."
- Computer 10 (Trilogy version only)
- "Metroid Officer Report, 07.203.01
- The order to mass-breed Metroids is insane. We have no space to store them. Perhaps when Command is sharing a bunk with hungry Metroid infants, they will rethink this unwise order."
- Computer 11
- "Casualty Report, 07.203.04
Mining expedition 422 reports 3 dead, 2 injured, 1 missing in action. Captured bioform transferred to Science Team for study 07.203.01."
- Computer 12
- "Dark Aether Transit 424 complete.
Radiation levels within tolerances. Dark Cannon operating at full power: no signs of instability detected. Cooldown cycle under way."
- Computer 13
- "Security analysis complete.
Unable to bypass Space Pirate security: portal control access denied.
Find an alternate method of accessing portal control."
- Computer 14
- "Security Alert, all systems and units.
Datanet has been compromised.
The Hunter has hacked our datanet. All our secrets are now hers. She cannot be allowed to escape.
Terminate her on sight!"
- Computer 15
- "Security Alert.
All units to battle stations.
The Dark Hunter has breached the Metroid production facility. Protect Phazon supply at all costs. Death to the Dark Hunter! Glory to the Space Pirates!"
- Portal activation device (demo only)
- "Mechanical analysis complete.
Device used by Space Pirates to generate the Dark Energy needed to create Portals to Dark Aether.
Control of this system is isolated in a secure command station nearby."
- Portal controls (demo only)
- "Portal control system online.
Walk into portal to transport to Dark Aether. Extreme caution recommended once transit is complete."
- For some reason, the Space Pirates theme does not play in the Trilogy version when the third Pirate Trooper spawns on the upper floor on Samus' first visit. The theme plays on all GameCube versions of the game.
- The Command Center is called the Control Room in one instance in Metroid Prime 2: Echoes: The Official Nintendo Player's Guide.