A recon probe has been discovered, its origin: Gandrayda. The third hunter was sent to scout out the location of the Space Pirate's homeworld, and this final transmission from her reveals that a third Leviathan Seed had impacted the planet and was well on its way to corrupting the planet to turn it completely into pure Phazon. So the Leviathan's ultimate goal is to transform the planets they impact into pure Phazon... Well, they've failed with five planets already, so let's raise that number to six.
Aurora 242 also mentions the Federation's plans for a full scale attack on the Pirate Homeworld, but we'll be sent ahead first to gather more intel. With contact also lost from Gandrayda, there's no doubt she's suffered corruption much like Rundas and Ghor.
Once 242 signs off you might want to fire up the Scan Visor and look out the window into space - Samus' left eye's pupil has almost turned completely blue and the Phazon veins running up her face are more pronounced than before. Use the biohazard scanner as well to learn that her body is now 50% corrupted by Phazon - not looking good at all.
But Samus won't hit full corruption on our watch. Hit the central helm control and bring up the Galaxy Map to see a new location marked up in the top-right corner. Select this Unknown Solar System to reveal the Pirate Homeworld and a lone landing site. For now you're free to backtrack to Bryyo or Norion to scout out any remaining items hidden there (thanks to the Chozo Observatory's handy satellites revealing their locations on your map), but for now we'll move onward.
Select the Command Center landing site and watch as Samus departs Elysian orbit. Arriving near the Pirate Homeworld itself, the planet very much resembles a giant molten rock covered in volcanoes and active magma - a perfect place for the Pirates to call home. As Samus nears the surface you'll spot massive Phazon tentacles sprouting from the surface into the heated red atmosphere - looks like the Pirates don't mind their planet succumbing to Phazon corruption (more on that later).
As Samus nears a massive Pirate facility you'll see a pair of huge shield generators atop the complex, each radiating an energy barrier over the entire region. She'll swoop in low and perform some nifty acrobatics to sneak inside a ventilation shaft - notice the Phazon covering the ground everywhere? Upon touching down at Landing Site Bravo (curiously without opposition) you'll see the Pirate home turf's architecture first hand.
The chamber itself is mammoth, filled with all sorts of machinery, turbines, pipes and a persistent thick red tone. Small automated drones hover overhead performing their duties - scan one for your Logbook. After admiring the Pirate's handiwork, we'll head deeper into the facility.
Scan the blue door at the exit for your Logbook if you haven't already scanned a Space Pirate door back on Bryyo. Step inside and move around the twisting steamy corridor. Watch out for a pair of welcoming Crawltanks loitering near the large dynamo unit, deal with both before moving on.
The following Lift Hub chamber contains a few interesting sights. But first and foremost watch out for a green turret keeping guard, scan the target to reveal it as a Despair-Class Turret (if you're playing the original stand-alone NTSC version of the game, the turret will register as a Remorse-Class Turret - but it will be the Despair turret in the Metroid Prime Trilogy version). This thing packs a nasty punch, so quickly use Missiles or Hypermode to dismantle the automated guard. Take in the scene before you: on your left lies a sealed chamber containing a map station, dead ahead lies an awaiting lift shaft, and on your right lies a sealed door beside a curious purple terminal.
If you try to interface with the terminal beside the sealed map station's chamber, all you're greeted with is a small code and scrambled input buttons. We'll take the open lift for now. But before stepping aboard, look at the wall beside the purple terminal. See the large round red computer display? Scan the object for the first of many Space Pirate lore entries (the objects blend in with the surrounding decor so they can be tricky to spot throughout the facility).
This first entry, Our Mission, details the Pirate's never-ending desire to control Phazon, and their disastrous operations at Tallon IV and Aether. They mention the Federation's recent activities on Aether and the race to secure what little Phazon reserves remain there.
Step aboard the lift and take a look at the floor selection panel. Two upper floors are available from here, but if you select the second-top floor you'll discover a chamber sealed with an enormous mechanical gate (notice the Missile Expansion on the other side?). So let's head up to the top level.
High above you'll discover a long dark corridor leading off in both directions. Taking the right path proves erroneous, all that greets you is an open-air chamber blocked by another mechanical gate. That innocent-looking deluge of rain doesn't help either, as you'll suffer damage if you wander outdoors.
So head down the longer left corridor instead. Further down in the blood-red corner of this region lies an orange door - scan it for your Logbook before stepping through. A massive open-air chamber awaits beyond, watch as the camera sweeps up to reveal the full extent of the view, catching a glimpse of a powerful energy shield high above in the sky. A few Space Pirates wander about as security drones watch from above, but curiously they don't spot you yet.
You'll watch an odd Pirate Trooper dressed in funky orange armour deactivate an energy field on the far side of the rain-swept region before exiting through the door beyond. Aurora 242 then promptly chimes in: Gandrayda's final communication revealed more intel about the layout of the Pirate Homeworld.
Apparently, beyond the door you witnessed the orange-armoured Pirate walk through lies a supply transit station leading directly to the Leviathan Seed. But without protection from the acid rain, (or a method to deactivate the energy shield), there's not much you can do about it for now.
242 gives your Logbook the Acid Rain entry along with your latest objective. Remember just moments ago watching the camera pan over to a double-pair of ventilation fans hidden in an alcove? Looks like that's our best bet for the path ahead. Watch the sky as you move through the Command Courtyard, ensure you stay under cover to avoid nasty damage. As you step towards the alcove, take a close look at one of the bright orange computer displays on the western and eastern walls.
Does the character depicted on the screens look familiar? Something tells me we haven't seen the last of Ridley... Anyway, head around to the ventilation fans to find a dark tunnel leading into the wall - all we need to do is shut the fans down. See the small Grab Ledge nearby? Leap up and climb into the narrow maintenance tunnel. Follow the tunnel along and watch as hapless Pirate Troopers move about above you, totally oblivious to Samus' presence (notice they exit via a number of inaccessible doors around the chamber).
Keep travelling along the tunnels to eventually spot a sealed-off Missile Expansion PH.01 along the way. Move on ahead, then take the left path at the junction to eventually find your way to the Missile's position. Head back to the junction and follow the right path. Hop out the far side and stand up, you're now directly above the fans below.
See the stolen Federation Energy Cell setup to power the fans here? Extract Energy Cell #6 and watch as a nearby vent cover opens wide before the ventilation fans come to a grinding halt. Roll through the vent cover's open tunnel to find yourself handily down at the motionless fans.
Roll on through the now-accessible dark tunnel to ultimately find yourself in the Flux Control chamber, home to a massive generator sending intermittent blasts of energy to the rest of the facility. Look through the generator window - see the Missile Expansion behind it? You'll be picking that one up later.
Move through the narrow twisting confines of the region and be wary of any Crawltanks keeping guard throughout. Beyond the twisting tubes lies a gaping hole in the floor of a chamber. Leap down and move back through the service ducts to a point below the entrance (watch out for more annoying Crawltanks).
Beyond here lies a small chamber home to a pair of service tunnels in the wall. A small cover blocks the left tunnel, scan it to learn that the object can be easily pulled with your Grapple Lasso.
If you follow the open right tunnel you'll find yourself at the base of the tall blue generator, but without the Spider Ball there's no climbing up the region. So instead, grapple the cover to open up the left tunnel. Climb inside and roll through the darkened tunnel to eventually discover the vast Command Station, currently manned by a few Pirate Troopers. But you're confined to the narrow tunnels running under the floor, so don't worry if any of the hostiles finally spot you and open fire.
As you ride down the blue-tinted lift, head right to eventually discover Missile Expansion PH.02 hiding beneath an energy shield. Roll back to the blue lift and head left to eventually discover an orange-tinted lift (see the icky Phazon growth up in the main chamber over on the left?). Ride up the lift and exit the Command Station. Follow the tunnel to eventually find yourself deposited in the cozy Command Vault chamber.
Take a look around, there's plenty to see here. A small Phazite covering blocks your only exit, so there must be a way to breach it. Spin around and look out the spindly viewport here, a massive chamber stretching into the distance houses endless Phazon containment units - just where did the Pirates get all this Phazon if they were desperately trying to fill their reserves at Aether? Don't forget to look down to see just how massive this place really is.
Don't worry about the security drones patrolling the chamber ahead, they won't spot you (but you can shoot them down, along with the Phazon containment units carried along the railings). Hang on a minute, can you hear the item proximity humming sound? Step back from the viewport and look up, see the item upgrade locked inside a small cage? Scan the object to reveal it as the X-Ray Visor!
Step back a bit further, see the five lock pods directly in front of the cage? What a coincidence - simply use the Seeker Missile to hit all five pods at once, sending power into the cage unit to release your prize above the floor. Step forward to claim the X-Ray Visor - now you're able to detect highly concentrated forms of Phazon below any surface.
Hold Minus and point at the lower-left corner of the screen to try out your new toy. You'll be given a light-enhanced view of your surroundings (very similar to the Thermal Visor back on Tallon IV), while anything containing Phazon glows brightly red (including Samus' bones). The Phazon containment units carried along the railings outside the viewport also shine brightly.
Now to get out of here. See the orange control terminal beside the viewport? Switch on your X-Ray Visor before interfacing with it. By doing so, you'll be shown a required sequence of symbols to input, but this time you can easily see the symbols on the buttons surrounding the code. Simply input the correct sequence to realign the conveyer railings (but be aware that as each symbol is entered they all randomly switch places, just to mess with you).
With Phazon containment units now travelling along directly above the sealed Phazite cover behind you, simply wait for one to hover directly above before shooting it down. The resulting explosion easily tears off the cover, granting your exit. Roll into the narrow tunnel and follow it along to deposit Samus into the Defense Access corridor.
See the green door on the eastern side? That's the main entrance to the Command Station. As such, step towards it to find an automated security system engaging, sealing the door in with a huge Phazite wall panel. You can use the X-Ray Visor to see several control locks under the Phazite cover, but currently have no way of striking them. Instead, use the X-Ray Visor to successfully enter the correct code at the nearby terminal and summon a handy lift (don't worry about the energy shield covering the corridor behind you).
Step aboard the lift and exit the chamber at the top. Beyond lies a small observation room filled with computer terminals, overlooking the Command Station below. From here it looks deserted, so scan the central pillar in the chamber to learn that a variety of energy cores power the facility's defense shield from here. No wonder the security is so tight. Before leaving, be sure to scan the round terminal on the wall nearby for the Stowaway lore entry.
Be sure to read this one for some interesting insights. The Space Pirates did indeed manage to secure more Phazon from Aether as the Federation left (I wonder what the Luminoth were doing?). However, we all know that Dark Samus somehow escaped Dark Aether's destruction and escaped into orbit. The Pirates were surely down on their luck, as the accursed Dark Samus managed to sneak aboard their vessel and consume all their recently acquired Phazon (now you know what that scene at the beginning of the game was all about).
Back to full strength and sporting a new appearance, the beast wiped out a third of the Pirate vessel's crew before the lore entry mentions that it began to literally corrupt the minds of the remaining personnel. So despite a lore entry in Metroid Prime 2 mentioning the Pirates pondering the forging of an alliance with Dark Samus, the Pirates were still on hostile terms with the creature? Interesting... Good thing Dark Samus chose the Pirate vessel instead of the Federation one.
Exit the Command Station and ride the lift back down to the Defense Access corridor. Step towards the exit on the western side, but you've got company. Two Pirates sporting the glowing orange armour guard the door, intent on ending your adventure right here.
Scan one to reveal them as Assault Pirate Troopers (you may have already scanned the one that joined a Berserker Knight in battle back on Bryyo, well, before the Knight squashed it flat). These guy's armour is normally vulnerable to Plasma Beam blasts, but don't hesitate to enter Hypermode if they do the same.
Clear both targets and exit the chamber ahead. Beyond you'll discover the Security Air Lock, home to a huge mechanical gate you couldn't pass by earlier. A radio transmission promptly arrives, but it's not Aurora 242... Instead, the barely-audible voice of a GF Marine comes in, claiming he was captured during the Pirate's attack on Norion and has managed to escape captivity here in the heart of Pirate territory.
Revealing he possesses vital information to bypass the acid rain and reach the Seed, you'll receive his current location on your map (which turns out to be in an entirely different section of the base).
Now that's interesting. So now we need go track this fella down before the Pirates find and finish him off. Step further into the Security Air Lock and grab Missile Expansion PH.03 resting within the gate. Stand back and switch on your X-Ray Visor. See the five locking mechanisms inside the gate? Wait for a glowing dot to appear on each and shoot them to release each mechanism.
With all five mechanisms released, the gate will re-energize and a Morph Ball hologram appears before you. Activate the Morph Ball and touch the hologram to rotate the gate around. Step through the exit to find yourself back in the cozy elevator of the Lift Hub region.
Zip down to the ground floor and take out the Despair turret waiting there. Before heading back to your ship, use the X-Ray Visor to successfully power down the nearby energy shield and step inside the alcove to retrieve a map readout of the facility.
This reveals a landing site at the GF Marine's location (along with the Pirate Seed), so we'll head there next. If you take a quick look at your map now you'll see several rooms around the Pirate Command region with large arrows pointing in different directions. You'll eventually discover that the base's major regions are all completely interconnected.