Touch down at Pirate Command and step through to the Lift Hub. Once there, destroy the Despair turret and take a look at the sealed round hatch on the right. Simply attach the Grapple Lasso to the neighbouring purple control terminal and deliver enough energy to restore power to the device, opening the hatch wide.
Right on the other side lies an inactive elevator with Missile Expansion PH.10 visible through a narrow window. But how do we reach it? Step aboard the lift and look at the floor selection panel - it promptly flickers and dies as the elevator creaks and groans. Quickly leap back to the safety of the platform and look above the lift - see the visible (and smoking) cable? Lock on and deliver a single Missile to release the damaged lift and send it plummeting down out of sight. Simply leap across the now-unobstructed elevator shaft as the billowing smoke rises to reach the Missile.
At this point you may have scored 75% of items in the game - if so, the game will inform you of the unlocking of a special ending! Except you'll need to finish the game first to see it...
Anyway, ride the still-functioning elevator up to the second-top floor. Move through the Security Air Lock to the Defense Access chamber. Nothing to stop you know, so step forward to the Command Station's entrance up ahead. Fire up the X-Ray Visor and shoot the lock nodes in the correct order to lower the Phazite blast shield and reveal a green door.
Open it up thanks to the Nova Beam and step inside. You're now inside the main chamber of the Command Station - home to the power generator keeping the planetary defense shield up. A single Assault Shield Trooper and mounted Despair turret greet you immediately, deal with both before looking around.
Down at the base of the chamber you'll discover a large (and very ugly) Phazon growth blocking one exit. Scanning the gross thing reveals that certain Phazon energy can be used to overload and destroy it, but we don't have anything capable of doing that yet.
Also feel free to drain the purple terminal nearby via the Grapple Voltage to open up the energy shield where you discovered a Missile Expansion all those hours ago when travelling under the floor of this room. Scan the central power generator to learn that its energy cores are protected by active shield plates - looks like we'll be climbing up to find the release mechanism.
Watch out for more Despair turrets positioned up the shaft and another Assault Shield Trooper. Once at the top, take a gander at the magnificent view outside the huge observation window. From here you're looking out over the Pirate facility, where huge structures, anti-aircraft turrets, Phazon tentacles and the massive ship-sized planetary defense shield emitter fill your view. You can even see the glowing tip of the Leviathan Seed over on the right.
After taking in the sights have a look at the top of the energy generator. Three rotating shields protect what looks like a Bomb Slot, so all three corresponding energy core sections further down will need to be destroyed to access it. Spin around and face the wall, here lies the control terminal for the core shields. Fire up your X-Ray Visor and interface with the terminal to input the correct code sequence.
With that, all three core shields retract, revealing Phazite panels concealing the tiny energy cores themselves. But that won't matter thanks to our Nova Beam. Unfortunately, releasing the shields also triggered an alarm, summoning never-ending waves of Commando Pirates to your location - definitely not fun on Hypermode difficulty.
Two will assault you high up here at the top of the shaft, but hold off using Hypermode. Instead, fire up the X-Ray Visor and lock onto the nearest one. Just like that Phazon Metroid earlier, your visor zooms in on the Commando's Phazon core. Fire a single shot from the Nova Beam to strike it dead center and knock the target down for good.
A brilliant trick to use against Commando Pirates - pity it only works on them. Be warned however, when the Commandos enter their own Hypermode your X-Ray Visor will fill with static. But that doesn't stop you from sneaking your shots through, so try to lock on and fire quickly before the static arrives. Deal with both hostiles and quickly leap down the shaft.
Start from either the top or bottom - move along and keep your X-Ray Visor on. Three tiny balls bounce around inside each of the three energy cores, try to destroy them quickly as arriving Commando Pirates will likely enter Hypermode and mess with your view. If they do, quickly disengage and enter Hypermode to clear the area. Don't waste any time going after the energy cores, and try to avoid falling off the many platforms (it won't be easy).
This sequence is going to be very fast and frantic, just stick to your objective and only engage the Commandos if they prove too much of a hassle.
With all three cores destroyed, their corresponding energy shields covering the Bomb Slot way up the top power down, granting you easy access. Don't waste any time in climbing back up the shaft - deal with any remaining Commandos along the way. Now you might find yourself scoring another bonus Friend Voucher here by defeating a total of 20 Commando Pirates (anywhere on the Pirate Homeworld) - something very easy to accomplish indeed.
Reach the top and quickly enter Morph Ball mode. Hop in the Bomb Slot and lay a single bomb - this one goes a long way. Watch as the planetary energy shield fails, leaving the facility completely open to aerial assault. The Federation fleet certainly doesn't waste any time as multiple craft descend and tear into the facility, blasting several anti-aircraft turrets apart before sending in troop deployment craft.
Now the fight's really on. The Commandos disappear as you receive a bonus gold credit, so you're free to leave the Command Station. Admiral Dane chimes in with his esteemed congratulations and advises you to meet him personally at the Skyway Access (the chamber where the triple-blast shielded door blocked you in earlier).
Climb down the Command Station and return to the Defense Access. Move through the Security Air Lock and back to the Lift Hub. But before heading topside, you'll definitely want to return to your ship from here and save the game - a very tricky sequence is coming up soon.
Return to the Lift Hub upon saving and travel to the top floor. Step through and outside to the Command Courtyard, where you'll find the area deserted save for a lone Commando Pirate eventually teleporting in. Deal with the target and head north (you may also notice the huge anti-air turret high above now frantically firing at unseen air targets).
Move through the Courtyard Passage and climb over the swarm of Scritters. Step through to the Skyway Access to find the area shaking from booming explosions above and the constant sound of energy weapon fire.