Exit left and use the elevator up. On the way up, Samus has some thoughts about her new CO's namesake, Adam Malkovich. Exit right and continue past the main elevator through the door to the elevator down to Sector 2. Go down.
In the Navigation room, Adam will reveal the identity of the "unknown agent" that has been sabotaging the station: an X mimicking Samus, which Adam names the SA-X. It most likely came from the capsules containing the infected parts of Samus's Power Suit. When it used a Power Bomb to escape the Quarantine Bay, it breached the capsules containing the X specimens that have now infiltrated and multiplied within the station.
The SA-X is at full power, so you can't face it yet, and Adam advises you to run if you see it. You are still vulnerable to cold from the Metroid vaccine, so you can be frozen by the SA-X's Ice Beam.
Adam says HQ has sent down Bomb data to the TRO Data Room. However, the Data Room is behind a Level 1 hatch, and Samus must find the Security Room (not marked on the map per safety protocols) and unlock Level 1 hatches to reach it.
Sector 2 (TRO)
Exit right through the Save and Recharge rooms. In the big room, head down but ignore the first door you see, because you can't get anything in there yet. Down below in the big room there is a block in the floor. Shoot it to clear it away, and drop down. Ignore the door to the left and continue right and up, and ignore the blue door on the way and exit through the top-right door.
Get the Zeros out of your way and exit right. Head up the next room, ignore the blue hatch, and exit through the door above. Fall down below and connect to the Security Console. The blue hatch behind you (and all the rest in the station) will now be open. Exit via the blue hatch, head for the door at the bottom and go through, and pass through this corridor to the big room. Ignore the blue hatch below, and find the door at the bottom left and go through.
Pass through this corridor to a room with more Zeros, and flying Reos. The path straight ahead is a dead end (for now), so jump up above to reach a blue hatch to the Data Room. Inside, stand in the pod and you will download Bomb data. To use Bombs, roll into a ball and press B. 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'll 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 back out has been destroyed by the SA-X. At the top right of the room, there are some blocks on a ledge that look slightly out of place. 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.
Head to the bottom left of the room, and bomb the corner, and fall down below to a narrow tunnel. Roll to the right and fall into the corridor below. First exit right to the Save Room and save your game. Then exit back to the corridor and exit left.
In this room, you can get a missile upgrade. Jump to the top area and wall jump against the right wall, then shoot the wall to the left to break open a hole. Wall jump again to grab onto the ledge that you opened, then roll through with morph ball. Bomb the floor 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 straight ahead. To get over 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 clear the block. Fall below, bomb the block in your way, and fall below where you land on a block above some Zeros. Get rid of those, then 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 collect the X if you can.
Now there are two blocks that can be bombed. Bomb the right one. When you drop down below, head left and fall below, then get up and pull yourself up into the tunnel to the left. Bomb the block at the end and fall below, and bomb the last block below you to land by the door out. Go through.
Drop down below and go through the door. Get rid of the Zeros and Reo, then bomb the thin floor to drop below. When you shoot the Dessgeega, it will shoot out spines, so jump. Head left and drop down, then stand on the thin floor to fall below. The blue Zeros here will release a red X when you kill it (it takes many hits) so grab it to replenish a large amount of energy and Missiles.
There is a hidden Missile Tank nearby; bomb the bottom right corner of this little room that had the blue Zero and a tunnel will appear. Roll through it and you'll fall below (be careful of the Zeros), kill the Zeros, and roll left for the Missile Tank. Aim above you to shoot the ceiling and pull back up into the tunnel. Get up and bomb the block to the right, and exit through the hatch.
Jump up onto the platform and roll through the narrow part at the top. Kill the Puyo, 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.
Before heading up, go through the door straight ahead. You can shoot the wall ahead to get onto the platform with the Puyo, or you can avoid them all by rolling underneath. Get to the far right of the room, bomb the blocks above you if you went through the tunnel, and go through the door for the Save Room. Then head back to the shaft you came from.
Climb up the shaft, ignoring the first and second doors you pass. Jump up onto the platform to get down to the third door, and go through. Kill the Dessgeega carefully, avoiding the spines it shoots out, and continue through the door to the right. Go right once again for another Save Room.
From this room continue right, get rid of any Owtches in your way, and exit right once more. Grab the Energy Tank, then shoot the lower part of the floor to fall below. 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 each time, 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 the hole above you and exit left, continuing left to the Save Room. Continue left and you'll find that the Zeros have become cocoons. Keep going left and you discover that damage has been done to this room and you can't get through the door. Morph into a ball and bomb the cracked floor to the right of the door to fall below.
Now you hear footsteps. The SA-X is in the room. You do NOT want to fight it, so stay where you are and don't shoot the floor anywhere below you (the floor to the right will be destroyed if you shoot it, and you'll fall below, the SA-X will freeze you, then kill you with Missiles). Wait for it to exit the room, then head right, shoot the floor, and go through the door to the left.
The SA-X is fortunately no longer around. You'll see some cocoons with Keyhunters moving around inside. Those will open up later. Jump on the platform with the cocoon, then jump up to the left and go through the door to the left. Now you can jump high enough to reach those rungs in the ceiling, so grab on and pull yourself to the left side of the room where a Missile Tank awaits.
Get in the water. If you kill a Skultera and don't collect the X quickly enough, the X will fuse with another Skultera and it will become a Skultera-X that can only be damaged by Missiles, so be quick. Plant a bomb by the tree on the left to make an elevator rise up, jump onto it, and jump over the platform to the left and go to the next room. Place 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, pull up through the narrow space and get the Missile Tank. Then exit this room.
Get on the block and bomb it to make another elevator rise up. Use it to get back over to the right side of the wall. Head right and climb the ladder to get to the room with the cocoons.
Make your way to the very top of this shaft (you can stand on the cocoons). The door on the way is blocked by a cocoon, so ignore it and continue up. Get in the tunnel at the top, bomb the block in the way, continue left and jump as a ball to bomb the block. Climb through and go to the next room. Kill the Reo and continue on.
Kill the Dessgeega and grab onto the ledge, then press right and jump over to the next ledge. Don't jump to the left just yet. Instead, pull up into a ball and bomb the wall to the right to open the way to a small room. Get the Missile Tank, then jump up and hang from the ledge to the left, pull up and roll through, bombing the block in your way to get to the ledge where you were a moment ago. Roll through the tunnel to the left to get to a new room, bomb the block in your way, and get out of the tunnel.
Go straight up and go through the blue hatch. Kill the Owtches in here, then roll into a ball against the right wall, jump and plant a bomb at the peak of your jump to break a block. Roll through, get the Missile Tank, then go back to the big room.
Drop down to the floor, then head left, shoot the blocks above you, and head up to the second door in the left wall. Go through. If you kill one of the Reos in here, its X will fuse with the first Kago on the floor, making it grow taller (you will still be able to jump over it). Jump over the second Kago and grab the 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.