Sector 1 (SRX) - First Visit
Once you get off the elevators, head left into the first room and go down. You'll enter Sector 1 (SRX). Talk to Adam in the Navigation Room and he'll show you the area's map. Adam then reports that the atmospheric stabilizers are malfunctioning - it's probably the X's doing. Head right into the Save Station and save.
Atmospheric Stabilizers
From the Save Station, head right. Run through the recharge room and into the next big room. Run to the bottom right hand door and go through. Destroy the flying enemies in the hallway, then get rid of the green thing with a few missiles. In the next area, jump up to the top ledge using the metal protrusion on your left. Run across and jump down to where the vent is. Shoot a few missiles atthe right time to destroy the green thing that is effecting it, then leave through the door on your right.
In the next corridor, shoot the enemies down, then shoot the bottom of the tiny ledge. Turn into a ball and roll through the chute for an energy tank. Exit into the next area and jump across the gap. Enter the room and shoot the wall to proceed. Go all the way to the right, then jump to the left and shoot the floor out from under the enemy there. An opening should appear. When you see the bridge-like ground, jump over it or you'll fall through. Destroy the thing hampering the stabilizer in this room and exit the way you came.
Jump down one level and go through the door. There are three enemies that charge at you in here; you can kill them by shooting at them from behind or just jump over them. Either way, leave through the door on the far left and then jump across to the next door. Open it and jump to the ladder on the ceiling - more like monkey bars now - and go across the lava. When you reach the small island, push 
to jump down so you can get the missile expansion. Head back now and jump down the whole room, dodging the space pirates on the sides of the walls. At the bottom, go through the door and kill the crab in the water, then move on. Jump to the floating island in this room, then use the monkey bars to get across. If you fall just use the ladders on the sides to get back up. Once you're on the ledge in the middle of the room, jump down a litle to your right and land on another floating platform. If you miss, be careful because there are enemies below you. Either way, climb up the ladder on the right side wall and fix the vent with a few missiles - just hold the left button to aim away from the ladder.
Exit through the side door. There is another one of those charging things in here; a quick missile should kill it, then move on. Continue until you reach another room with a broken vent. Use the metal ledges to jump up to the top of the room, then grab hold of the monkey bars and climb over to see the broken vent. Give it a few missiles, then climb back to the door you passed a moment ago climbing up. Inside is a missile tank - just beware the crab.
Exit the room through the door on the bottom right and use the platforms and ladders to jump to the top of the room. To kill the space pirates, shoot a missile at them. Shooting without holding any buttons makes Samus shoot up. Once at the top, go through the door and shoot the flashing light to raise the gate. In the next room, hop up to the monkey bars and kill the crabs. Head to the end of the room. Kill the crab on the wall, then shoot the wall itself, revealing a hole big enough for a morph ball to go through. Exit the room.
To the Second Boss
Jump onto the blocks blocking the hole; they'll crumble. Head to the door on your immediate left, kill the enemies and keep going to find a save room. Head back the way you came until you get to the yellow room. Climb the ladder and jump to the platform. Get ready to jump to the side for the energy blasts! When the eyes shows a pupil, shoot it with a missile like the last time. Three shots will do it. Enter the room and head to the far side. There will be a Chozo statue holding a ball. Shoot the ball to initiate the boss fight. For information regarding the fight, check the bosses section.
The Last Stabilizer
After you gain the charge beam ability, which greatly increases your firepower, jump on the platforms to the upper door and exit. This room looks like a dead-end, but look at the ceiling: there is a little bit that isn't connected to the rest. Shoot it out and jump on up. Grab hold of the monkey bars before going through the door, and shoot at the blank wall three times, then jump and grab onto the hole and roll in. Kill all the crabs then jump down into the water to find a missile expansion.
Leave the secret room and go right, into the next room, which contains the last broken atmospheric stabilizer. Kill the enemies in your path and jump down, then kill those enemies too. Roll into a ball and go through the gap, then jump up and shoot at the wall using your beam. A part of it will be destroyed. Get right up to the hole and shot missiles through it in order to fix the last vent. Once this is done, exit through the right hand door and shoot the light to release the gate. Jump up and save if you want to.
From the save room, jump across the gap and go through the left side door. Jump to the top of the room and then go through the left hand door. Kill the enemies in this familiar room and go through the room with a stabilizer in it right afterwards. In the next hallway, there are those irritating floating enemies that combine very quickly; take them out then move on.
Proceed to the next large room. Jump up to the door to the Recharge Room and go in. Recharge if you need to, and save if you want. Then talk to Adam. He says that Sector Two (TRO) has been breached by the X, so exit to the left and ride the elevator up. On the way up, Samus remembers what the real, human Adam was like.
To Sector Two (TRO) - Visit One
Back at the Main Deck, open the door on the right and run across to the door on the far side. Use the elevator and then link up to Adam. He explains that the X mimicking you is mimicking you when you're at full power. The map of (TRO) looks small, but it has a lot of secret paths. Adam says to find the secrity room and get the Bomb data, and shows you where the data room is - but it's locked. Head into the Save Station and save before looking for the Security Room.