Having defeated Arachnus, Samus must investigate the disturbance in the SRX section of the station, which resembles SR388.
Reach the Main Elevators
After visiting the Navigation Room, go to the left. Don't go into the door immediately to the left, because there is a sub-zero containment room, and you will be damaged by the cold. Go up the tall room. There is a tunnel here that you can roll through to get a Missile Tank.
Go back to the tall room and go to the top, then go through the door.
Jump across the gap and roll into a ball to go through the damaged wall. Go through the door, and go left through another door. Take the elevator down. After a brief cut scene, the elevator reaches the bottom, and you hear another power outage.
There is a flashing number 1 on the wall to tell you which direction to go to reach the Sector 1 elevator. Go through the left door to take the elevator down to Sector 1.
Sector 1 (SRX)
Go right to enter the Navigation Room and talk to Adam, who tells you that the Main Elevator has been severely damaged by a non-human "unknown agent".
The atmospheric stabilizers of Sector 1 have been infested with X. Your goal is to clear all 5 atmospheric stabilizers.
Exit right to reach the Save Room, followed by the Recharge Room. In the next room, go to the bottom of the room, killing a Zombie in your way, and go through the bottom right door. In there, some free-floating X will transform into Amoeba, which will drain your energy if they touch you. Kill them quickly to prevent them from becoming larger Amoeba, or just run through them and let yourself get hurt. Use three Missiles on the living barrier in your way, and go through the door.
On the other side of the wall you see an atmospheric stabilizer infested with X. It emits free-floating X, so collect them if needed.
From the entrance, jump up against the metal railing to grab it, then jump up to the ledge on the right. Go to the right until you can jump down. At the bottom, go to the left to find the atmospheric stabilizer. You have to shoot three missiles at the X infestation. There are pieces of metal above and below the X, and if your missle hits the metal, the missile will bounce off. Be sure to wait for the opening to be centered before shooting.
Go to the right and the flashing door will open. Go through it.
If you kill the Hornoads in here, their Xs will become Halzyns that float from side to side. The Halzyns will try to fall on you if you walk under them. The Halzyns metallic wings can't be damaged by your normal beam, so you either have to make the Halzyn drop to the floor and then shoot upward between its wings to damage it, or you can use missiles, which can damage their wings.
To get the Energy Tank in this room, crouch down to shoot at the rock blocking the pipe that the Tank is in. Roll into a ball to go through the pipe and get the Tank.
Go through the door on the right to exit the room.
The next room is a tall metallic room. Ignore the platforms below. Just go through the door on the right.
Shoot through the rock wall in front of you, and go to the right, past the Hornoads, until you can jump up onto the ledge above and to the left. Go to the left, kill the Hornoad, and shoot the ceiling near the left wall. Jump up through the hole that you created. Kill the Hornoad here, then go to the right and kill the Hornoad across the small rock bridge. The bridge is made of Pit Blocks, so jump over it. Then shoot missiles upward at the atmospheric stabilizer to kill the X infestation.
Walk onto the bridge to the right and you will fall through the Pit Blocks to the area below. Go to the bottom left corner of the room and go through the door.
Go downward in this tall metallic room to find a door on the left. Go through it. There are Moto in this room. You have to jump over them and hit their backs to hurt them, or you can shoot their faces with missiles. Go to the left and go through the door there.
You are in another tall metallic room. Ignore the platforms below, and jump across to the door on the left. Go through.
Jump and press up to grab the rungs in the ceiling. Go to the left to find a Missile Tank. Take it, then go to the right and go through the door to reach the tall metallic room.
Make your way downward, killing the Space Pirates with missiles. One of them may drop a red X. Go to the bottom of the tall room and go through the door there. This room has some water with a Scizor in it. Go to the right and go through the door there.
Jump onto the small platform to the right, then grab the rungs above and go to the platform on the right. There are Hornoads below if you need X. Stand on the bottom right platform and jump onto the ladder to the right. Climb up as far as you can go and shoot Missiles to the left to hit the X in the stabilizer. Afterward, drop down below, killing any more Hornoads that might have appeared, and go through the door on the right. There is a Moto in this room. Go through the door on the right, then in the next room, go through the door on the right.
Grab onto the metallic ledges sticking out of the walls. Hold left or right while holding onto one and then jump to reach the next one. Grab the bars above and go to the right, shooting the X in the stabilizer with Missiles. Afterward, go to the upper left corner of the room and go through the door there to get a Missile Tank, then leave that room and go to the lower right corner of the room. Go through the door there.
Go up this tall room, killing Space Pirates as you go along. Go through the door at the top.
Shoot the flashing light to open the gate, then go through the left door.
There is water in this room, which will slow you down. If you kill the Scizors, they will regenerate elsewhere. Grab onto the rungs above, and go to the left side of the room. While hanging from the rungs, shoot the left wall three times to make a tunnel. Jump up to the tunnel to hold onto the edge, then press up to roll into it. Go to the left and go through the door on the other side of the tunnel.
Walk forward to fall through some pit blocks. Roll through the tunnel below, and go through the door on the left.
There are Hornoads in this room that will keep regenerating, so you can use them to heal up and replenish your weapons. Go through the door to the left to save. Go back through the Hornoad room and return to the yellow room.
Climb the ladder to find a Living Door. If it shoots a yellow membrane, press the jump button to let go of the ladder to avoid it. After you kill the Living Door, go through the door.
Go to the lower left corner of the room. Shoot the orb that the statue is holding. After a moment, it will turn into a Core-X.
This Core-X floats directly toward you and will sometimes open an eye. When you shoot the eye with a missile, it will shoot a beam at you, so keep shooting the eye while avoiding the beams that come out. Be warned that if you don't shoot it for a while, it will charge itself up and shoot a beam at you.
After it dies, collect the Core-X to regain your Charge Beam ability. Hold the shoot button to charge up the beam. The charge beam is stronger than missiles. You can do additional damage by hitting enemies at close range with the charge beam. If you hold the button to fully charge up the beam, and keep holding the button, you can spin jump into enemies to damage them while fully charged.
Sector 1 (SRX) Part 2
Go through the door at the upper right of this room. Go onto the platform on the right and shoot upward at the block in the ceiling. Go up through the hole that opens, then grab onto the rungs on the ceiling, and shoot a missile and two beams at the wall to the left to open a hole. Roll through that tunnel to reach a new area.
There is a Missile Tank in the bottom right corner of the room. Kill or avoid the Scizors to get the Missile Tank. Then go back to the previous room and go through the door on the right.
Go to the right, then go downward. You will see the atmospheric stabilizer, but it is blocked by metal. Go to the bottom left of the room, then go onto the ledge on the right. Shoot through the wall on the right, then shoot missiles through the hole to kill the X in the stabilizer.
Exit through the bottom right door, shoot the flashing light to open this gate, and continue to the next room. Climb up and use the door to the right to reach a Save Room. There is a Missile Tank hidden nearby, but it is a little bit difficult to get with your current abilities. To get the Missile Tank, shoot the cracked wall to the right of the floating save platform. Jump, and while still in the air, quickly press down twice to roll into a ball, then quickly press right to land in the tunnel before you hit the floor. Roll to the right to reach the next room. To go up this tall room with your current abilities, you need to use the wall jump technique. To wall jump, you have to jump against a wall, then press the jump button while pressing the button in the direction away from the wall. For example, if you jump up against a wall on the right, press left and jump at the same time. If done correctly, you will kick off of the wall and jump higher.
At the top of the tall room, there is a Missile Tank. After you get it, go back to the bottom of the room and roll through the tunnel to reach the save room. Then go through the door on the left.
In this room, go through the door on the left. Then go up the platforms in the next room and go through the door at the upper left of the room. Continue going to the left until you reach the first room of the area, and go through the upper left door there to reach the recharge room. Keep going to the left to reach the Navigation room. Adam informs you that the X have infiltrated Sector 2 (TRO), and orders you to investigate.