
In the next stage of our full Metroid Prime 2: Echoes walkthrough we’ll be exploring the Pirate Headquarters. It's really a mining facility but we'll be calling it the Pirate Headquarters in our walkthrough. Be prepared to scan a lot of entries in this place, mainly the pirate logs.
On this page: Metroid Prime 2: Echoes: Pirate Headquarters
The Pirate Headquarters

Upon entering the Pirate Headquarters, you’ll notice you won’t be able to proceed through the door. On the ground, there are some damaged grates, blast them with a ball bomb, and you’ll be able to roll down under the grates and head through a slimy hole to progress.
On the other side, you’ll keep rolling under the feet of pirates heading into a dark portal; carefully time your rolls past the pulsing electric barriers in this section as they’ll give you a nasty shock.
Collectible - Missile Expansion Pack
Taking a quick detour right and down in this small tunnel maze will grant you an additional Missile Expansion Pack.
Getting back on track, take a page out of Limp Bizkit’s book and keep rolling, rolling, rolling (what!) left until you drop into a room where a brief cutscene will show a room full of pirates closing an important-looking gate. Yep, we’re going to need to fight these fellas.
Scan Entry - Aether
After defeating the pirates, you’ll see a large orange hologram of the Planet Aether on top of a computer. Scan it for a new logbook entry.
Scan Entry - Dark Aether
Just opposite the previous entry there is another hologram, this time a large red one of Dark Aether, scan it for another logbook entry.
In this room are a lot of logs, all of which need scanning for their lore entry in the logbooks. These appear on the terminals inside this room. Again, important objects will appear as RED on your scan visor prior to scanning them. So flick it on and get to scanning those computers for their lore logs.

Scan Entry - Log #62217
Scan Entry - Log #48853
Scan Entry - Log #44681
Scan Entry - Log #54421
Scan Entry - Log #50086
After you’ve absorbed a lot of lore, there is a control panel that will activate the elevator in the room that will be close to the hologram you scanned to gain the Aether logbook entry. Head up the elevator and make your way across the rafters in the room, keeping an eye out for the odd pirates, of course.

Keep walking, and you’ll come across a pirate shooting at you through the glass of a control room. After dealing with them, head on through the door nearby, and you’ll witness Dark Samus crashing onto the scene.
Scan Entry - Log #70136
After Dark Samus floats away, peek through the security gate with your scan visor until you see a console - scanning it will give you a new logbook entry for Log #70136.

After you’ve done that, follow the tunnel right and use a missile to blast through the red blast door to gain access to the control room. Scanning the main computer will open the large gate in the main room; head back in there, and make your way through that door.
Scan Entry - Humility Class Turret
Inside, you’ll find a corridor full of lasers and turrets, just lovely. Remember to scan at least one of the turrets to gain the Humility Class Turret logbook entry. I wonder if they’ve been given that namesake to teach you some humility. Thread the needle past the laser grid and head into a new room behind a red blast door.
Scan Entry - Tallon Metroid
Inside a pirate will roam around this room riding a skiff. There will be an elevator accessible via its control panel, so you can keep up with the pirate and eliminate it. After defeating them, you’ll find a familiar face behind a cage all Metroid fans know. Scan the Tallon Metroid for its logbook entry.
Scan Entry - Log #63622
Heading up towards the exit of this room, just before you aim to leave, turn around and scan the console in front of the Metroid cage to obtain the Log #63622 lore logbook entry. Because we haven’t scanned enough logs, have we? Anyway, head through the exit, and you’ll find a bomb slot. Use it to turn the room’s walls around and proceed onward until you reach a large aircraft hangar.
Scan Entry - Pirate Aerotrooper

Up in the sky! It’s a bird! It’s a plane! Nope, it’s just a Pirate Aerotrooper. A flying variant of your run-of-the-mill Pirate Trooper. Quickly scan it to gain its logbook entry, then shoot it back down to Earth, or in this case, Aether.

Beating the Pirate Aerotroopers will gain you access to the main control panel in the room; activating it will cause some pillars to rise from the floor. Using the small control panels in the hangar, two on each side of each main console per pillar. These will allow you to change the elevation of these pillars, one raising and the other lowering accordingly, with the goal being to make stairs jump across to reach the exit.
Collectible - Energy Tank

While making stairs that aim towards the exit is the goal. If you aim them the opposite way and jump up them, your curiosity will be rewarded with another Energy Tank. Return to the control panels and make it so the pillars are aiming upwards towards the exit. It’s time to move on.
Next up, bomb jump into a tunnel behind the door, and you’ll roll into a Morph Ball puzzle. There’s not a lot to say about this section. Destroy what’s blocking your way with ball bombs while timing your jumps and rolls carefully to avoid the obstacles.
After the puzzle, shoot the red blast door with a Missle and proceed onward.
Scan Entry - Log #67135
Behind the door will be a room with a much-appreciated save point and also Log #67135 on the console behind it. Scan the console to gain the logbook entry, have a rest, and prepare to move on.
]You’ll enter into a room with a pair of turrets blocking a seemingly out-of-reach door, but you’re not licked yet. Make short work of the turrets with your beam cannon, and scan the glass just left of the large door - it’s breakable! Fire a missile and walk onward through a corridor. You’ll see a large room through a window. We need to get in there, so head left and drop down into the room.
Scan Entry - Dark Samus 1
In the room, we’ll watch a cutscene of Dark Samus getting up to no good firing energy at a large crystal. Let’s interrupt her impersonating Emperor Palpatine with a good old-fashioned standoff. As the fight begins, quickly scan Dark Samus for their first logbook entry.
