After the Restricted Laboratory is destroyed, Adam orders you to return to your ship and leave the station.
Sector 1 (SRX)
After riding the elevator up from where the Restricted Laboratory was, Space Jump to the top left corner of this area, then stand on the top of the pillar and shoot a charged Diffusion Missile at the wall. This will freeze the Rippers below and will reveal an Energy Tank in the wall. Enter the tunnel and take the Energy Tank, then fall down below the Rippers. Kill the Gerutas. One of them might drop a red X. From there, make your way up to the door in the upper left of the room and go through it.
Don't touch the green liquid. It will drain your energy. Go to the right, shooting the Amoebas that attack. At the right side of the room, go through the door.
Shoot the floor near the middle, then fall down the hole. Go to the left and use two Power Bombs to kill the Gravitt inside of the enclosed area, but move away from where the bomb exploded to allow the free-floating X to transform into a Geruta. Kill the Geruta, and let the X become a Golden Space Pirate. It's back is the only vulnerable spot, so approach it to make it jump over you, then quickly shoot a Missile at its back. Three Missiles will kill it. After that, collect all of the X that it dropped. It may drop a red X. Then go to the right side of the room and go through the hatch that is now unlocked. Take the Power Bomb tank in this room, then go back to the previous room and Space Jump up through the hole in the ceiling.
You can go through the door on the right to reach a Save Room. Outside of the Save Room, Space Jump up to a ladder. Climb to the top and roll through the tunnel. Up above, go to the right wall and drop a bomb there to reveal a ladder. Climb to the top, kill or avoid the Space Pirate, and go through the door on the left.
In this room, go to the left and drop a bomb next to the barrier in the middle of the room. Then kill two of the Genesises by shooting your beam at the floor, but don't collect the free-floating X. The X will transform into a Golden Space Pirate. (If this doesn't happen, kill Genesises one by one until it does.) Get close to the Space Pirate to make it jump over you, then shoot a Missile at its back before it can turn around. After it dies, its X will turn into another Golden Space Pirate. Kill it the same way. The hatch on the left will unlock. Go through it.
Go to the top of the room and go through the door there to find a Save Room. Outside of the Save Room, go down to the bottom of the room and go through the door on the left.
Freeze the Rippers and go to the left side of the room, where there is a Living Door. Kill it, take the red X that it drops, and go through the door. At the bottom, approach Ridley.
Use charged shots or Missiles on Ridley. Charged shots are more effective because the Wave Beam will cause it to do repeated damage as it goes through Ridley's body. Hold L throughout the battle to aim up at Ridley. Avoid the fireballs. If Ridley grabs you, shoot Missiles up at it until it lets go.
Eventually, Ridley will start using its tail to attack. It will swing its tail at you, and will sometimes move back and forth while stabbing downward with it. Keep attacking it until it turns into a Core-X. Destroy it, then take the Core-X to regain your Screw Attack ability. With the Screw Attack, you can damage enemies and break through Screw Attack blocks and other types of blocks (but not Boost Blocks, Bomb Blocks, or Pit Blocks) whenever you Space Jump.
Now that you have the Screw Attack, you can access all Sectors of the station, allowing you to collect any upgrades that you might have missed. Don't use any Navigation Rooms until you are done exploring all of the Sectors. Adam will close off access to the Sectors the next time you use a Navigation Room.
From the room where you fought Ridley, Space Jump to the top and go through the door. Screw Attack through the Rippers to kill them, and go through the door on the right. Go to the top of this room if you want to use the Save Room up above, then go down to the upper right door of this room and go through it.
Use a normal bomb to destroy the barrier to the right, then go through the door on the right. Screw Attack the Space Pirate to kill it instantly, then bomb the floor to the right to reveal a ladder. Climb down it, then roll through the narrow passage to the left and get on the ladder below. Shoot a Diffusion Missile against the wall to open a tunnel to the door to the right. Roll through the tunnel and go through the door.
Shoot through the gate to hit the red light and open the gate, then go through the door on the right. Screw Attack through the thin floor in the middle, then go down and Screw Attack the Space Pirate to kill it. Roll through the gap above the wall on the right, then go to the bottom of this room and go through the door.
Screw Attack against the wall on the right to open a small hole. Roll through it, then Screw Attack to the right to break through the walls. When you see a gate to the right, shoot through the wall to hit the red light, then Screw Attack against the wall to open a hole if you did not do so already. Roll through it and go through the door on the right.
Screw Attack up through this room, killing Space Pirates if you want to replenish energy and weapons, then Screw Attack the striped platform at the top to go through it. Go through the door on the right. Go to the right and go through the door on the right, then Screw Attack upward through this room, and go through the door at the top. Shoot the red light to open the gate, and go through the door on the left. In the room with water and Scizors, go to the left and roll through the tunnel, and go through the door on the left. Walk to the left to fall through the Pit Blocks. Go through the door on the left and keep going to the left to reach a Save Room. In the Save Room, go to the far left of the room, then go to the right while shooting. After you break through the wall, crouch as soon as you enter the next room. Do a Space Jump (don't Shinespark yet) while falling down into the water. At the bottom, walk up against the wall on the right and jump straight up to do a Shinespark through some Boost Blocks in the ceiling. Press left to grab the ledge before you fall, then shoot the left wall to reveal a Power Bomb Tank. Take it, then return to the Save Room.
Speed Boost from the left side of the Save Room again, but this time, crouch in the room where you fought the Living Door before the Charge Core-X. Space Jump to the door that used to be a Living Door, shoot it open, jump up and press left to Shinespark through the door. You will hit a ramp and Speed Boost to the left. Crouch before the ledge, then walk up against the left wall and Shine Spark straight up. Go to the right and take the Energy Tank, then fall back down into the room where you fought the Charge Core-X. Go through the upper right door.
In this room, go through the upper right door. The next room is where you cleared one of the atmospheric stabilizers. Go to the bottom right of the room and go through the door there. In the small room, shoot open the gate and go through the door on the right.
In this room, you can Screw Attack through the striped platforms. You can go through the upper right door to reach a Save Room. Outside of the Save Room, go through the upper left door. In this room, go upward and go through the first door on the left. Go through it, then keep going to the left until you reach a room filled with lava. Space Jump to the upper left corner of the room and take the Missile Tank. Then fall down into the lava, which will not damage you anymore because the Gravity Suit protects you from it, and go to the bottom of the area. Go to the right and roll into a ball, and roll to the right through a hidden passage to find another Missile Tank.
Go to the bottom left corner of this room and go through the green door in the bottom left corner. Space Jump up out of the lava and go to the top of the room. Go through the blue door at the top. You are now in the first room of this Sector. Go to the upper right corner of this room and go through the green hatch at the upper right. Screw Attack through the ceiling to get a Power Bomb Tank.
If you want to collect all of the upgrades in the station, don't go into the Navigation Room yet. If you enter any Navigation Room and use the Navigation Computer, Adam will close off all of the Sectors, preventing you from collecting any other upgrades that you might have missed. However, after you beat the game, you can reload the save file and the Sectors will be open again.