After you deal with the Nightmare, Adam tells you to get rid of the Rogue Security Robot in Sector 6.
Find the Robot
Uplink in the Sector 6 Navigation Room for your briefing. The Security Robot appears to now be much stronger. Adam then conveys some unsettling news: the SA-X is tracking you, so after destroying the Security Robot you must leave NOC immediately.
Exit right through the Save and Recharge Rooms. Keep going right until you reach a shaft, then make your way down it, past the door on the right, and through the first door on the left. At the far wall, drop a Power Bomb and go through to the red hatch beyond where the blocks were. Get the Eeleyes and Puyo out of the way and exit through the door below. Walk ahead to fall through some Pit Blocks, and go through the door below.
Head left and go through the door at the end. Drop down and through the door here to a Save Room. Once you've saved, head back out and bomb the floor to the left to fall below. Go through the door here. Approach the gate at the end, and the computer will warn you that you can't enter without authorization. (It'll keep saying that for a while, so you might as well get used to it.) Head back and you'll hear an explosion. Continue your way back and the Security Robot will attack.
The Security Robot has electrified the water, so stay out of it. At the start, use a Power Bomb to reveal rungs in the ceiling, and grab hold. Hang from the extreme left side of the rungs. When the Robot shoots Missiles at you, just destroy them with your beam before they can knock you off of the rungs. The Security Robot will run towards the left, will bump into the raised floor, will be bumped back, and will sit there for a few moments. At this time, hold L and shoot a bunch of Missiles at it while it's stunned. You shouldn't have to move from the far left of the rungs for the entire battle. Once you've hit the Robot enough times, it turns into a Wave Core-X. It has an eye, so once you shoot it with a Missile, jump to avoid the Wave Beam it shoots out. Once you've destroyed it, collect the Core-X to recover your Wave Beam ability, which can pass through walls and other obstacles.
Sector 6 (NOC)
Exit through the door to the right. Go to the far right, where there is a Missile Tank that looks inaccessible. Now that you have the Wave Beam, it will pass through the gate and hit the flashing light and open it. Shoot the light and get the Missile Tank beyond.
Go back to the last room, continue on until you reach the gate that the computer warned you you couldn't go through. With the Wave Beam, you can now open it, so do so. Roll through the tunnel, and you find yourself in the "Restricted Zone".
Roll left to fall through some Pit Blocks. Through the door is a Save Room, so save and exit left. Keep heading left, through a tunnel through which you can see the stars, and you reach a Restricted Laboratory, with Metroids in the background! Continue through the Restricted Laboratory, witnessing captive Metroids in various stages of development, until you hear a hatch opening, glass breaking, an alarm, and gunfire (which is confusing, because there are no weapons in the game that sound like that). Return to the first room of the Laboratory.
Oh no! The SA-X is here! It has released the Metroids, and is trying to kill them, but the Metroids attack it. A one-minute timer begins, and you have to escape before the Restricted Laboratory detaches from the station.
Space Jump up the shaft, trying your best to avoid the floating Metroids, which will drain your energy and knock you down from your Space Jump if you touch one. Once you've made it out, a cutscene will show the lab detaching from the station and self-destructing. Is the SA-X gone..?
Exit right and you find a Navigation Room. Uplink. Adam scolds you for ignoring orders. He explains the Federation's secret Metroid breeding program. He then reveals that the SA-X you encountered in the Restricted Lab was not the only one; there are no less than 10 in the station, and one is on its way here. Adam orders you to escape the station before the SA-X destroys you.