After killing the X infestations in the atmospheric stabilizers of SRX, Samus is ordered to investigate abnormalities in TRO.
Sector 2 (TRO)
After receiving Adam's orders in SRX, go to the left and go up the elevator. After a monologue, go to the right until you reach the Sector 2 elevator. Go down.
In the Navigation room, Adam tells you that there is an X parasite mimicking you. Adam names it SA-X and tells you to run if you encounter it, because it is mimicking you at full power.
Adam says to download Bomb data from the TRO Data Room, but you will need to find the Security Room to unlock Level 1 hatches first. The Security Room is not marked on the map.
Find the TRO Security Room
Go to the right, through the Save and Recharge rooms. In the large room, go downward, but ignore the first door for now. Keep going downward, and when a small rectangular platform blocks the way, shoot it to destroy it. Go down below, and ignore this door as well. Make your way to the door in the upper right corner, and go through.
Go to the right and exit through the door on the right. Go upward through this room, ignoring the blue hatch along the way, and go through the door at the top. This is the Security Room. Go down to the bottom and connect to the Security Console to unlock Level 1 hatches.
Get Bomb Data
After unlocking blue hatches, exit via the blue hatch on the right, then go to the bottom of this tall room and go through the bottom left door. Go to the left to return to the large room. Go to the bottom left and go through the door there.
This hallway has some crawling Zeros on the floor and ceiling. Go to the left and go through the door there. There is a platform above the door, but there is a Reo there, so try to kill it before you jump up onto that platform. From this platform, go to the upper left and go through the door there to reach the data room. Stand in front of the glowing machine to get bombs.
Find a Way Out
To use Bombs, roll into a ball and press B. Bombs can't hurt you even if you are right next to them. Bombs are useful because if there are hidden special blocks anywhere, a bomb will reveal what it is. You will encounter blocks that can only be destroyed by special means, and placing a bomb next to one will reveal its nature (or will destroy it, if it's a bomb block).
Exit the Data Room. You will hear an explosion and will hear the footsteps of the SA-X. If you go down below (you don't need to at this point) you discover that the door that you used to enter this room earlier has been destroyed by the SA-X. At the top right of the room, there are some blocks on a ledge that look slightly different. These can be bombed, so morph into a ball, bomb them, and roll through the path you open. Get the Missile Tank, then go back through the little tunnel.
Go to the bottom left of the room and bomb the corner there, then fall down below, into a narrow tunnel. Roll to the right and fall into the corridor below. Go through the door on the right to find a Save room, then go back to the corridor and go through the door on the left.
In this room, you can get a missile upgrade. Jump to the top area and wall jump to reach the upper right area, then crouch on the raised platform shoot the wall to the left to break open a hole. Grab onto the ledge that you opened, then roll through. Bomb the floor a couple of squares to the left of the block that sticks up. This will activate a rising platform. Use it to reach the missile upgrade up above. Then go back to the last room.
Morph into a ball and roll into the narrow crawlspace in this room. To go past the block in your way, plant a bomb in that corner and it will shoot you upward (if you are in morph ball mode) so you can go over the block. Down below, bomb the block in your way, and fall below where you land on a block above some Zeros. Go toward the left of the room where there is a conspicuous-looking block. Bomb it and drop below to another block that you can bomb.
To safely get rid of the Zeros in this tunnel, wait for them to move to the right, away from where you are about to drop down. Once you've bombed the block and dropped down, kneel and shoot your beam at the Zeros to kill them, then roll into a ball and go to the right.
There are two blocks here that can be bombed. Bomb the one on the right. When you drop down below, kill the Zero, then go to the left and fall into the pit, then jump and grab the ledge on the left and press up to roll into it. Bomb the block at the end and fall below, and bomb the last block below you to land next to the exit door. Go through.
Drop down below and go through the door. Go to the right and bomb the thin floor to drop below. When you shoot the Dessgeega, it will shoot out spines, so jump to avoid them. Go to the left and drop down, then stand on the thin floor to fall below. The blue Zero here will release a red X when you kill it, but you have to hit it many times to kill it.
There is a hidden Missile Tank nearby. Bomb the bottom right corner of this small area that had the blue Zero. A tunnel will appear. Roll through it and you'll fall below, where a Zero is crawling. Roll left to get the Missile Tank, then shoot the ceiling here and jump up into the tunnel above. Roll to the left, then jump up to the small block, bomb it, then go to the right and go through the door there.
Jump up onto the tall platform on the right and roll through the narrow part at the top. Kill the Puyos, then bomb the floor one space to the left of the platform to the right to cause an elevator to come out of the floor. Get on top of it and use it to get past the platform to the right. Exit through the door on the right.
If you want to go to a Save Room, go through the door on the right. Go to the right side of this room by either rolling through the tunnel at the bottom or by shooting the walled area and killing the Puyos in the middle. Bomb the blocks above you if you went through the tunnel, and go through the door on the right to reach the Save Room. Then go back the way you came until you reach the tall room.
Climb up the tall room, ignoring the first and second doors you pass. When you see a tall wall on the right with a door behind it, jump onto that tall wall and go through the door on the right. Kill the Dessgeega carefully, avoiding the spines it shoots out, and continue through the door to the right. Go right once again to find another Save Room.
From the Save Room, go through the door on the right. This room has Owtches slithering along the walls. Go through the door on the right, take the Energy Tank, then shoot the lower part of the floor and go through the hole. Kill the Living Door and go through the door that it was blocking. Jump over the wall ahead and drop below to discover a Core-X that turns into a one-eyed creature called Zazabi.
Zazabi will jump to the left and right. Run under it when it jumps. Sometimes it will just jump over you. Other times, when it's at the peak of its jump, it will open the mouth at its base and slowly float downward. This is your cue to shoot a bunch of Missiles into its mouth. When it gets too close, run to one side of it so it doesn't eat you. If it does eat you, morph into a ball and bomb it repeatedly to make it spit you out. Once you've shot it enough times in the mouth (it shrinks as you damage it more, and so does its mouth) it will turn back into a Core-X. Kill it as usual, waiting for it to stop flashing before shooting it each time. Collect the Core-X when you beat it, and you get the Hi-Jump and Jumpball abilities.
Sector 2 (TRO) Part 2
Now you will be able to jump high enough to get out of the pit. Go left and jump and climb up to the door you came in, and exit.
Jump up through a hole above you and go through the door on the left. Keep going left to reach the Save Room, then go through the door on the left there. The Zeros are turning into cocoons. Go through the door on the left, and go to the left side of this room to find that the door has been damaged. Morph into a ball and bomb the cracked floor to the right of the door, then go onto the pit block below the blocks that you bombed. You will fall into another room.
You will hear footsteps. The SA-X is in the room. Do not fight it. Just stay where you are and don't shoot the floor until SA-X has left the room and you can't hear its footsteps. When SA-X is gone, go to the right and shoot the floor, then go down below and go through the door on the left.
SA-X is gone for now. Jump onto the platform on the left that has the cocoon on it, then go upward and go through the door on the left. In this room, jump up and grab the rungs on the ceiling, then go to the left side of the room and get the Missile Tank there.
Fall into the water. If you kill the Skultera fish and don't collect the X quickly enough, the X will fuse with another Skultera to transform it into a Skultera-X, which can only be damaged with missiles or charge beam. Drop a bomb at the base of the tree on the left to make an elevator come up. Use the elevator to jump over the platform on the left. Go through the door there.
Drop a bomb between the tree and the flower to make another elevator come up. Get on top of it and roll into a ball, then use your Jumpball ability to jump over to the left. Try to place a bomb just when you're next to the block in the wall to destroy it. Once it's gone, roll through the narrow space and get the Missile Tank. Then exit this room.
Stand on the raised block and bomb it to make another elevator rise up. Use it to go over the wall on the right. Go to the right and climb the ladder, then go through the door on the right.
Go to the very top of this tall room, jumping on cocoons to reach the top. At the top, roll into the tunnel, bomb the block in the way, then go to the left and use jumpball to drop a bomb in front of the block up above. Roll through the opening, then go through the door on the right. Kill the Reo in this room and go through the door on the right.
Kill the Dessgeega, then jump and grab the ledge up above, then press right and jump to the ledge on the right. Don't go up yet. Instead, roll into the tunnel on the right and bomb the wall on the right. Keep going to the right to find a Missile Tank. Take it, then jump up into the tunnel in the upper left, roll to the end and bomb the block at the end. Then go to the left and roll through the tunnel there to return to the first room of TRO. Bomb the block in the way, then go upward to find a blue hatch. Go through and kill the Owtches slithering on the walls, then roll into a ball and go to the right wall. Jump up as a ball and drop a bomb at the peak of your jump, then roll through, bombing a second block in your way, and go to the right to get a Missile Tank. Go back the way you came to return to the first room of TRO.
Drop down to the floor and go to the bottom left corner of the room, shoot the blocks above you, and jump up above. Go through the next door that you find, and jump over the obstacles in this room to get a Missile Tank. Then go back to the big room.
Go up and through the top left door, recharge in the Recharge Room, save in the Save Room, and uplink in the Navigation Room to get your briefing from Adam. Releasing the lock on the Level 1 hatches allowed the SA-X to enter Sector 4 (AQA) with several thousand X. Exit left, go up the elevator, then go down the elevator to Sector 4.