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 shaft. There is a tunnel here that you can roll through to get a Missile Tank.
Go back to the shaft 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 lets out free-floating X, so collect them if you want. Just follow the path to reach the stabilizer. When you get there, stand on the ledge and shoot three Missiles through the unblocked portion of the stabilizer to destroy the X and return the stabilizer to normal working order.
Exit right through the flashing door that will now open.
If you kill the Hornoads in here, their Xs will become Halzyns that float from side to side. Run under one then run away to make it fall to the ground, then while it goes back up, run under it and shoot it a few times to kill it.
To get the Energy Tank in here, 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. Get back out and exit right.
Don't go down below. Instead go through the door straight ahead.
Shoot through the rock wall in front of you, and go to the right until you can jump up onto the ledge above. Head left, kill the Hornoad, and shoot the ceiling by the left wall to break through. Get up there, shoot the Hornoad across the bridge to the right, then jump over the bridge (it's made of Pit Blocks) to get to the stabilizer. Shoot it with some Missiles to clear it out.
Walk onto the bridge to the right and you'll fall through the Pit Blocks to the area below. Exit this area the way you came in.
Drop down to the door to the left and go through. There are Moto in here. You have to jump over them and hit their backs to hurt them. Exit left, then jump over the shaft and exit left again. Cling to the rungs above (jump up and press up) and go left until you reach a Missile Tank. Grab it, then go back the way you came.
Drop down to the lower level and go through the door.
Go across to the save room. Shoot the cracked wall to the right of the floating save platform. You can skip this until later when you have an ability that will help, but if you want an extra missile upgrade now, you should give it a try. After shooting open the wall, jump against the wall and roll into a morph ball, then press right while falling to enter the hole. In the room beyond, use the wall jump technique to go up to the top of the shaft. To do this, jump against the right wall, then press the jump button and the control pad in the direction away from the wall. If you time it correctly, you will jump off of the wall and go higher. Do a bunch of wall jumps to reach the top of the room, where there is a missile upgrade. Then go back out of the save room.
Go back the way you came until you reach a shaft where yellow Xs turn into purple Space Pirates. Descend the shaft carefully, shooting the Space Pirates with Missiles to get them out of your way, or just avoid them. They will shoot beams at you and jump across the shaft at you. Go through the right-hand exit at the bottom of the shaft. Jump over the Scizor and exit right.
Jump onto the small platform to the right, then grab the rungs above and make your way to the platform on the right. Drop down below, killing any Hornoads there, then get 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. Once it's clear, drop down below, killing any more Hornoads that might have appeared, and exit right. Kill the Moto in your way and exit right twice.
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 head right, shooting the X in the stabilizer with Missiles as usual. Once it's clear, go a little to the lfet and drop below, hopefully landing on a small platform out of the way of the Hornoads.
Make your way to the top-left door that you passed but couldn't go through earlier to get a Missile Tank. Go back out. Drop to the bottom floor here and exit right.
There are Zebesian Space Pirates on the walls of this shaft. Avoid or kill them. One of them turns into a red free-floating X, which replenishes a lot of your energy and weapons. Make your way to the door at the top. Go through.
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 Scizor in here, they'll just regenerate. Grab onto the rungs above, and make your way to the left side of the room. Shoot the left wall three times to make a tunnel, then drop down and pull into it and roll through. Go through the door at the other end.
Just walk forward to drop through the floor. Roll through the tunnel below, and go through the first door you see.
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 back to the last room.
Climb the ladder and kill the Living Door protecting the door. It can be difficult to avoid the yellow membrane it shoots out. If you are holding the ladder, you may want to simply press the jump button to start falling if the eye shoots out a membrane. Once the eye is gone, go through the door.
Shoot the orb that the statue is holding, then approach it and it will turn into a Core-X.
This Core-X is different from the last one you fought. This one will open an eye. When you shoot the eye, it will shoot out a beam that you have to jump over, or it will hurt you. Jump over the Core-X when it flies toward you, wait for its eye to open, shoot it with a Missile, and jump right away so you don't get hit by the beam. If you don't attack quickly, it will shoot a beam.
When you beat it, absorb the Core-X to regain your Charge Beam ability. Hold the shoot button to charge up the beam.
Sector 1 (SRX) Part 2
Jump up to the top right door and go through. Shoot the wall above you and jump through the hole you just opened. Above, grab onto the rungs on the ceiling, and shoot Missiles at the wall to the left to open a hole. Pull up into the passage and roll into the secret room.
Kill the Scizors and get the Missile Tank in the water, then return to the last room and go through the door ahead.
Get past the Hornoads ahead, drop below where you can see the X-infested stabilizer, and when you are on the ground, go left and roll through the narrow passage to the left. Jump up and shoot the wall behind where the stabilizer is, then shoot Missiles through the hole to kill the X in the stabilizer. That was the last one.
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 in here. If you didn't see the explanation earlier on this page for how to get it, here it is again:
Shoot the cracked wall to the right of the floating save platform. You can skip this until later when you have an ability that will help, but if you want an extra missile upgrade now, you should give it a try. After shooting open the wall, jump against the wall and roll into a morph ball, then press right while falling to enter the hole. In the room beyond, use the wall jump technique to go up to the top of the shaft. To do this, jump against the right wall, then press the jump button and the control pad in the direction away from the wall. If you time it correctly, you will jump off of the wall and go higher. Do a bunch of wall jumps to reach the top of the room, where there is a missile upgrade.
Leave the save room and exit through the door straight ahead. Go to the top of the shaft and exit left, and just follow the path to the left until you reach the Recharge, Save and Navigation rooms. Adam informs you that the X have infiltrated Sector 2 (TRO), and orders you to go and investigate.