After defeating Serris in AQA, Adam tells you to go to sector 3.
Go to Sector 3
In the Navigation Room Adam will tell you that the X haven't entered Sector 3 yet. The Data Room is sealed by a Level 2 hatch, so you must find the Security Room (not marked on the map) and release the lock, possibly allowing the SA-X and X parasites in. There are ultra-heated areas in this sector that must be avoided, as your suit can't handle extreme temperatures yet.
Exit right to the Save and Recharge rooms, then exit right to Sector 3 proper. If you encounter an ultra-heated area, you've gone the wrong way, because there are no such areas on the path to the Data Room.
In the big room, follow the path down until you reach a door. DON'T go through, as it is ultra-heated in there. Instead, shoot the floor in front of that door to break it open, and fall below, down below the platform you landed on. Shoot to the right and continue shooting as you make your way right, but don't go through the door to the right. Instead, make a running start towards the left and you'll Speed Boost through some blocks in the next room.
You'll land on a sort of bump; bomb to the left of it to break a hole below. Fall down below and shoot the ceiling near the upper right corner to reveal a Missile Tank. Collect it, then shoot the cracked blocks to get back up.
Go to the far right, make a running start towards the left, and once you reach the bump near the green hatch, jump to break some blocks above the door. Roll into a ball and jump up into the niche, and bomb towards the left to the next room.
Roll left to fall through the Pit Block, stand on the pod to release the lock on the Level 2 hatches. The green hatch behind you will unlock, so go through it.
The X have now invaded this sector (rather quickly), so kill the Side-Hoppers with missiles, and use your beam on the other enemies. Go to the far left and make a running start right. Once you reach the far right bump, jump and you'll break through the blocks that you broke through to get in here in the first place. Exit this room.
Keep shooting as you head right to break through the walls, and exit right.
Jump onto the ledge above and use Missiles on the Fune to kill it. Walk to where it was and you'll fall below on the other side of the gate. Shoot the light to open it, then run to the door on the left and make a running start towards the right to Speed Boost. In the next room you'll break some blocks in the floor. Walk left and you'll fall through a Pit Block. Go through the door here.
Make your way to the bottom of this shaft. Open the green hatch on the right and go through. Get rid of the Owtches. There's a Missile Tank hidden in the top edge of the platform, right in the center. Plant a bomb to reveal it, then return to the shaft.
Climb to the very top of this shaft, moving quickly up the ladders to stay clear of the Funes. At the top, head through the left door (the one on the right is damaged). As a ball, jump a little bit up the left wall and bomb it, the two blocks in the wall can be destroyed. Roll into the top tunnel and all the way left for a Missile Tank. Then roll all the way left and plant a bomb to break the blocks above you. Jump up into the upper tunnel, roll to the end, and bomb the blocks here out of the way. Jump up into the higher tunnel. Once again, roll all the way right and plant a bomb to break more blocks. Now you can access the corridor above. Jump out and exit through the door on the right.
Get rid of the Side-Hoppers and Nova, and exit right. Continue right and go through the green hatch to access the Data Room. Stand in the pod to get the Super Missile data, and you'll hear an explosion. Exit back to the room that had the Side-Hoppers and Nova and you will see a hole in the floor to the left. Drop down and exit through the door to a Save Room. A Recharge Room is to the right so you may want to recharge before you save. Save your game, then exit right through the Recharge Room. Kill the Side-Hoppers (only one Super Missile is necessary) and destroy the purple barrier with three Super Missiles to get the Missile Tank.
Return to the room where the hole was opened in the floor, jump up and head left. The door has been destroyed, and suddenly you'll hear some mechanical noise and some dirt will fall from above. Exit right and you'll be attacked by a rogue Security Robot.
Get up on the rungs above, and stay there for the duration of the battle, getting back up if you get knocked down. If the robot stops and crouches, it's about to shoot out a grenade. Pull yourself out of the way so as not to get hit by the grenade, and get at a distance from it because it will create two flame walls moving in both directions. Shoot Super Missiles into the center of the robot's body to damage it. When it starts flashing and crawls to the right, you've beaten it. It will launch itself through the ceiling to the right.
Sector 3 (PYR)
Use the debris that fell when the robot jumped through the ceiling to climb up above. Kill the monsters in here. From the left, make a running start to the right. When you reach the little piece of floor sticking up just before the hole, kneel down. Then, press A so you float up while glowing, and hit left-up to jump diagonally to reach a Missile Tank (not as hard as it sounds).
Go back down to the corridor below and shoot the door open but don't go through. Make a running start from the right, then crouch before the door and press the jump button, then press left to Shine Spark to the left. In the next room, you will break through some Boost Blocks. Bomb the little pit at the bottom-left corner of this small room until you reach an Energy Tank. Bomb your way out of this enclosed space.
If you weren't able to do all that, you ended up in an area with a Side-Hopper when you entered this room. You can either try some wall jumps to get back to the last room, or just kill the Side-Hopper and jump as a ball along the left wall to plant a bomb at the block to blow it open. Roll through the gap. To the left you'll see a structure hanging from the ceiling. Plant a bomb directly below it and an elevator will come up. As a ball, bounce from the top of it and try to bomb the space above you to reveal an Energy Tank. Once you get it, bomb your way back out of the enclosed space.
Head left, bomb the blocks above, and roll through the gap to the first room of Sector 3. Exit through the top left door to the Recharge, Save, and Navigation rooms. Uplink to get your briefing from Adam.
Adam says to destroy the Security Robot if you encounter it again. With the Level 2 locks open, Sectors 5 and 6 can now be accessed, and have probably been infiltrated by the X. Sector 5 (ARC) is sub-zero, so you can't enter it safely. All the Data Rooms you've used thus far have been destroyed by the X. You must use the Data Room in the night habitat, Sector 6 (NOC).
Exit left from the Navigation room and take the elevator up. As you head up, a suspicious conversation will transpire between Adam and an unknown man (probably from the Galactic Federation), who asks Adam if Samus "suspects anything", and asks Adam to monitor her closely.
Make your way to the elevator on the Main Deck down to Sector 6.