After defeating Serris in AQA, Adam tells you to go to sector 3.
Go to Sector 3
In the PYR Navigation Room, Adam tells you to find the Security Room and unlock Level 2 hatches, even though this may allow SA-X to enter the area with more X parasites. There are ultra-heated areas in this sector that must be avoided, because your suit can't handle extreme temperatures yet.
Go to the right to go through the Save and Recharge rooms, then go right to reach the first room of PYR. If you Speed Boost into this room, you will break through some Boost Blocks and fall through some Pit Blocks to reach the lower right door in the first room of PYR (don't go through).
If you did not Speed Boost, you can either go back to the Navigation Room and do so, or just follow the path in the large room until you see a ladder down below, go down that ladder and go toward the left, don't go through the door but shoot the floor in front of it and go down through the hole, then go to the lowest level and shoot the walls to the right to reach the lower right door (don't go through).
Stand near the lower right door of the first room of PYR, then run left while shooting your beam to break through the blocks and open the lower left door of the room. This will allow you to Speed Boost through some blocks in the next room. You will land on a bump in the floor. Drop a bomb a couple of squares to the left of this bump to open a hole in the floor.
Go down the hole, bombing any more blocks in the way, then shoot the ceiling near the upper right corner to reveal a Missile Tank. Collect it, then shoot the upper left ceiling to go up to the upper area again.
Wait for the cracked blocks to reappear, then go to the far right, and run to the left. When you run over another bump, jump to break some Boost Blocks above the green hatch on the left. Roll into a ball and jump into the small niche in the upper left corner, then drop a bomb and roll to the left to enter the Security Room. Stand in front of the console to unlock green hatches. Leave this room via the green door.
With the hatches unlocked, X parasites will quickly invade the area. Use charged shots or missiles to kill the Side-Hoppers in this room. Your regular beam is effective on the other enemies here. After you kill them, go to the far left of the room and run to the right, then jump when you run over the bump on the right. You will break through the Boost Blocks. Go through the door on the right.
Shoot your beam as you go to the right, and you will reach the lower right door. Go through.
Jump up above, but beware of the Fune in the wall. It will extend toward you, so keep your distance. Use charged shots or missiles on the Fune to kill it, then walk to where it was and you will fall through some Pit Blocks. Before you go through the door, shoot the red light to open the gate, then go to the far left side of the room and run to the right. In the next room, you will break through some Boost Blocks in the floor. Walk to the left to fall through a Pit Block. Go through the door here.
Go down to the bottom of this shaft, being careful of the Fune in the walls and flaming Novas on the way down. At the bottom, go through the green door on the right.
Kill the Owtches slithering on the center platform, then get on top of the platform and drop a bomb in the middle to reveal a Missile Tank. Take it, then go back to the last room.
Now make your way up to the top of this shaft, and go through the door on the left.
Go to the left wall of this room, roll into a ball, and drop a bomb next to the block in the middle. Jump up into that tunnel, then go all the way to the left to get a Missile Tank. Drop a bomb to the left of where the tank was, then jump up into the upper right tunnel. Roll all the way to the right and drop a bomb, then jump up into the upper tunnel, roll to the right, and drop a bomb. Go up to the upper area, and go through the door on the right.
Go to the right, avoiding or killing the Side-Hoppers and Novas, then go through the door on the right. Keep going to the right until you reach a green door. Go through it to reach the Data Room. Stand in front of the machine to receive Super Missiles. These replace your regular missiles. You will hear an explosion after you receive the data.
Go to the left until you find a hole in the floor. Go down that hole and go through the door on the right. You will find a Save Room, then go through the door on the right to find a Recharge Room. Then go through the door on the right, kill the Side-Hoppers and use missiles on the purple barrier to get the Missile Tank.
Go back the way you came. When you go up through the hole in the floor, go to the left until you reach a dead end. Suddenly you will hear some mechanical movement and some small debris will fall from above.
Go to the right until you are attacked by the B.O.X Security Robot.
B.O.X Security Robot
Jump up and grab the rungs in the ceiling, and stay there throughout the battle. Shoot Super Missiles downward at the center of the robot's body to damage it. If the robot stops and crouches, it will soon shoot out a grenade. If the grenade hits you, you will fall off of the ceiling rungs, so don't stay above the robot when it stops. When the grenade stops rolling, get directly above it. The grenade will create two walls of flame moving in opposite directions from where the grenade was, but if it explodes when you are directly above it, the flame walls won't hit you. When the robot starts flashing and crawling to the right, the battle is over. The robot will launch itself through the ceiling to the right.
Sector 3 (PYR), part 2
Go to the right side of the room and jump onto the debris to make your way to the hole in the ceiling. Go up through the hole to reach the next room.
Kill the monsters in this room, then go to the far left of the room and run to the right. When you are almost at the hole in the floor, crouch down, then press the jump button to float up, and before you start moving, press left-up to do a diagonal Shinespark. You will reach a Missile Tank.
Go back down to the area that you Shinesparked from, then go to the far left and shoot open the door, but don't go through it yet. Instead, go to the far right of the room and run to the left, then crouch before you go through the door, then press jump to float up, and before you start moving, press left to do a Shinespark to the left. You will break through some Boost Blocks in the next room. Get into the small pit on the left side of this area and drop a bomb there, then shoot downward to reveal a hidden Energy Tank. Drop another bomb to go down to the lower area.
If you were unable to Shinespark as described above, you can just go to the left until you reach a room where you can go downward to find a Side-Hopper, then jump as a ball against the left wall to drop a bomb next to the block, roll through that opening, then go to the left until you see some blocks hanging from the ceiling. Drop a bomb directly below the center of these blocks and an elevator will raise you up to them. Jump and bomb this area to reveal an Energy Tank, then use bombs to escape from the enclosed area.
From there, go to the left and bomb the three blocks at the end of a tunnel. Jump up into that tunnel and go to the left to reach the first room of PYR. Go to the upper left door and go through it to reach the Recharge, Save, and Navigation rooms. Use the Navigation computer. Adam will tell you to go to Sector 6 (NOC) to use the Data Room there.
Go left until you reach the elevator, then go up and you will see a cut scene. Afterward, go to the Sector 6 elevator and go down.