The Space Pirates have stolen some Luminoth technology and you're going to need it to get any further.
Mining Station A
Go to the platform in the shape of a child Luminoth on the ledge at the far end. Space Jump onto it, then Space jump again to a tunnel on the left. Follow it around to a bridge over the river of sand and get a scan of the Amber hologram at the end. Then scan the control panel on the left to open the gate in front of the sandfall behind the platform. At the same time, the sandfall stops and a ledge appears allowing you to reach a door where the sandfall was.
Central Station Access
Up in the distance you can see some Space Pirates playing with some canisters of Phazon. You can defeat them normally or, for style points, fire a missile at the Phazon while explodes wiping out the Pirates in one shot.
Central Mining Station
This is a large area and Pirates attack as you enter. You get a glimpse of a Pirate Skiff delivering reinforcements, but it's difficult to get a scan of it before it disappears; it will be much easier later so we'll list it then. Meanwhile, when you've cleared the Pirate ground forces, two of the remaining ones will take control of the turrets on the ledge on the far side. Do get a scan of one of these since it seems it's the only chance. Then, while staying out of range of one (there is plenty of cover), fire missiles at the other, and when that's gone use missiles to clear the remaining one.
Finally, go through the doorway under the far ledge and on to the next room. You will be able to get to the top of the ledge eventually, but not now.
Command Center Access
The passage seems to be blocked at the end, but use the Scan Visor on the floor to reveal two places where floor is made of Talloric. Bomb one or both of them, drop into a hole, bomb the crates under the floor to reveal a tunnel, and roll into the next room.
You're still under the floor and though the room is filled with Pirates, they seems to be too busy to notice you down there. As you go farther into the room many of them disappear into a portal, but there are still a few left.
There are electric barriers under the floor that switch on and off, but it's fairly easy to time your way past them. Start by taking the right side path when you come to it and grab the Missile Expansion at the end. Go back and follow the main path as it winds around to the end. You come out in a corner and when you do, one of the Pirates closes a gate in front of one of the exits. Other Pirates attack so, staying in the cover of the corner, fire missiles at them until they are gone.
There are plenty of scans to get here; get the two planet holograms and the Pirate computer consoles on ground level. Now scan the control panel next to the left and step into the hologram to reach the second level. Another Pirate appears, and a second Pirate hiding in a control booth attacks as well, so fire missiles at them until they are history as well.
Go through the door to the left of the control booth.
Security Station B
The mysterious figure from Hive Chamber B appears again, but then disappears down the passage where you can't follow. So circle to the right and blast open the Missile door. It looks like your destination is in the very next room, but you're going to have to go around the long way to get there.
Command Center (cont.)
Scan the computer terminal to open the gate that the Pirate closed when you first entered the room. Then backtrack, through the Security Station, into the main part of the room and go through the door that's now visible.
Scan and fire missiles at the turrets to clear them. You can avoid being hit by dodging from side to side while locked on. Weave your way through the lasers and blast open the Missile door at the end.
There are more Pirates here and you catch another glimpse of the skiff, but there's still another chance to scan it. There are Metroids trapped in containment cylinders here but they can't get at you for the moment.
Scan the panel next to the lift and ride up to the second level. More Pirates attack so fire more Missiles to clear them. Follow the ledge to a large tank with Metroids inside, and get a scan of one of them. There is another Pirate log entry to scan on the other side of the tank.
Security Station A
Clear the turret, then use the Bomb Slot to rotate the gate.
Pirate Aerotroopers, updated versions of the Flying Pirates from Metroid Prime, attack as you enter. Shoot them down with Missiles, but be sure to get out of the way when they do their final kamikaze move.
There are three square platforms in the middle of the room and ledges with computer panels to the left and right. Go to the left ledge and scan the device with the hologram to raise the three platforms to the ceiling. You need to solve a little puzzle to get them in the right configuration to get to the exit, but while you're at it you can get an expansion too.
Go to the other ledge and look for the alpha control console, it's on the right as you're facing the platforms. Scan the hexagon to the left of the display panel to lower one section of the the platform in front. Scan it two more times to lower two more sections and create a platform three sections high.
Now go to the next console, which controls the delta platform, and scan the hexagon to the left of the display panel twice to lower create a platform two sections high. (It's not clear where Space Pirates would have learned the Greek alphabet, but most of the time beta comes after alpha and before gamma. The game says delta so we'll just have to go with it.) Finally move to the gamma console and scan the hexagon to the left of the display panel once to create a platform one section high.
You've now created a kind of stairway so you can space jump from gamma to delta to alpha, and finally to a ledge to grab an Energy Tank.
Go back to the control consoles and this time the idea to make the stair go the other way. So go to console alpha, scan the hexagon to the right of the display panel twice to raise two of the sections. Skip delta and go to alpha, then scan the hexagon to the left of the display panel twice to lower two of the sections. Space jump from alpha to delta to gamma and then to the exit.
Ventilation Area B
Switch to Morph Ball and drop a bomb to hop into the tunnel. There is a kind of maze you have to follow because the direct route along the bottom is blocked in two places by energy beams. Where a side path splits off above the main one, drop a bomb to reach it and drop another to destroy the first beam. Drop a bomb to go up another level, and yet another to hop over a spinning fan. You don't have to worry about getting hit by the fan, but you do have to time your jump to avoid hitting the laser beams that go on and off above it.
The rest of the maze is very similar, and eventually you reach the top of the second energy beam. Drop a bomb to destroy it, clearing the path below so you don't have to go through the obstacles the next time through.
Save Station C
Scan the console and it's a good idea to save here because a battle is coming up. Note that this room is called Save Station B in the Wii version; there is no Save Station B in the GameCube version.
Head down the sand slope and take out the two turrets on either side of the far end. Then fire a Missile to break through the Brinstone section of wall to the left.
The door you come in through locks behind you, and the only way to go is down into the lower level of the room. When you do, the mysterious figure is seen absorbing Phazon from a large supply. You look at each other for a bit and it's obvious that she's a copy of you in the Phazon Suit from Metroid Prime. But though she's seems a bit confused, she definitely not friendly and a battle begins.
When the battle is over, Dark Samus explodes into a cloud of blue sparks, but it shouldn't be much of a spoiler to learn that she'll be back. Get a scan of the Phazon in the walls, then take the lift in the far corner.
Scan the console and pick up the Dark Beam, your reward for winning the battle. Use this to open black doors and activate light colored crystals.
The new weapon uses ammo, and while you start with 50 shots, you don't get refills in the normal way. So don't go around fighting any battles with it yet. If you're completely out you can get refills, but only way to get back to 50 at the moment is by going back to the ship or finding an ammo station. There should be plenty for opening doors, but if you run out you can still open a door by charging the Dark Beam.
Use the Dark beam to get back to the Main Reactor, then use it again on the white crystal to open the gate to the right, and use it a third time to open another Black door.
Security Station B (cont.)
Use the Dark beam to open the gates, scanning the consoles on the way.
Command Center (cont.)
A new type of Pirate has arrived here while you were gone so get a quick scan. From here you can start on getting the next upgrade, but first we'll cover the expansions you can get now.
Expansions (Agon Wastes)
Retrace you steps to the Biostorage Station. The Metroids will have broken free of their cages by now, you you'll need to learn how to battle them. If they manage to attach themselves to you then switch to Morph Ball and drop bombs to shake them loose. Otherwise fire missiles at them unless they're Phazon shield is glowing. The Dark beam is affective against them but you need to conserve your ammo for it a while longer.
Take the lift to the upper ledge and go through the Black door there.
Yes, more Office Space jokes, then grab the Missile Expansion.
Central Mining Station
Backtrack to the Command Center, then through the Black door to Command Center Access and on to the Central Mining Station. The Pirates are gone but they left a skiff just parked there for you to get a scan.
Continue to Agon Temple and follow the path around the edge left to a Black door.
Switch to Morph Ball for another maze. There are Pillbugs all over, so drop bombs to stun and destroy them if they start to get annoying. Quickly roll over the first stone block, otherwise it will disappear and you'll fall to the bottom.
Just to the left of this is a path at a higher level, but to reach it you need to do a double jump. Learning this maneuver was a must in Metroid Prime, and it's useful here as well but not used as often.
In case you haven't already mastered it in the first game, the idea is to do a jump from the top of another jump. To do that, you need to drop two bombs at ground level about a second apart. When the first bomb lifts you into the air, drop another bomb at the top. If you time it correctly, the second bomb will lift you back into the air as you land, and then the third bomb will lift you again to bring you twice as high as a normal jump. It takes a while to learn the particular dotted rhythm needed to carry this off, but mastering this double jump will earn rewards later in the game.
When you get to the upper path, do a single jump to the next higher path, roll over another disappearing block and over to a stack of disappearing blocks. You need to roll into a tunnel about half way down these, so keep pushing left, but stop as soon as you're in the tunnel.
Roll over another disappearing block and onto a pair where again you have to keep pushing left to get to the next passage. Go up two levels and over to another stack of blocks. The passage to the left is there as before, but you can't see it this time. Do the same thing though and remember to stop right away to keep from rolling off the end of the path.
The way you want to go from here is up through a hidden path to a level above. (The path is really only partially hidden, you can see it if you look carefully.) Go up yet one more level on the left, then drop down two more blocks pushing left and you should land on an Energy Tank. If you miss a turn or drop through a block too many then go back to the start and try again; it may seem like a lot of trouble but remember that those energy tanks are going to be very handy in a tough boss battle.
The way out of this room is blocked for now so just head back; just keep rolling right and jumping up when you need to. Go back to the Portal Terminal, activate the portal and go through.
Expansions (Dark Agon Wastes)
There are two new scan you can get now. Shoot a light Crystal with the Dark beam to nullify it, then get a scan. Do the same thing with a Light Beacon. The game makes it sound like the only thing that will restore a nullified crystal or beacon is light energy, but a couple of Power Beam shots do the trick as well.
Follow the path as before to the Dueling Range. There is a Black door you couldn't open before, so go through now.
Ing Cache 4
Roll into the tunnel under the ledge at the start for a Missile Expansion.
There is another Black door here you can now open.
Save Station 1
It's just a Save Station but since you might as well fill it in on the map as you're passing by.
Get back to the light side and go back to the Command Center for your next excursion to Dark Aether.